2024-07-02T14:46:24,401 Created temporary directory: /tmp/pip-build-tracker-ft_geqt3 2024-07-02T14:46:24,402 Initialized build tracking at /tmp/pip-build-tracker-ft_geqt3 2024-07-02T14:46:24,403 Created build tracker: /tmp/pip-build-tracker-ft_geqt3 2024-07-02T14:46:24,403 Entered build tracker: /tmp/pip-build-tracker-ft_geqt3 2024-07-02T14:46:24,404 Created temporary directory: /tmp/pip-wheel-kh5elng8 2024-07-02T14:46:24,407 Created temporary directory: /tmp/pip-ephem-wheel-cache-gw4j272b 2024-07-02T14:46:24,430 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-02T14:46:24,433 2 location(s) to search for versions of moleculekit: 2024-07-02T14:46:24,433 * https://pypi.org/simple/moleculekit/ 2024-07-02T14:46:24,433 * https://www.piwheels.org/simple/moleculekit/ 2024-07-02T14:46:24,434 Fetching project page and analyzing links: https://pypi.org/simple/moleculekit/ 2024-07-02T14:46:24,435 Getting page https://pypi.org/simple/moleculekit/ 2024-07-02T14:46:24,436 Found index url https://pypi.org/simple/ 2024-07-02T14:46:24,673 Fetched page https://pypi.org/simple/moleculekit/ as application/vnd.pypi.simple.v1+json 2024-07-02T14:46:24,715 Skipping link: No binaries permitted for moleculekit: https://files.pythonhosted.org/packages/91/e6/25b6853357dfef8a4026325e420d8213d34c17c078a2f13b60cbb6213ea3/moleculekit-0.1.4-py3-none-any.whl (from https://pypi.org/simple/moleculekit/) 2024-07-02T14:46:24,716 Found link https://files.pythonhosted.org/packages/13/0f/a200e8e7632d3a521cfc7c15fa4d0270802efce40f98ac5a5cae58385b7e/moleculekit-0.1.4.tar.gz (from https://pypi.org/simple/moleculekit/), version: 0.1.4 2024-07-02T14:46:24,716 Skipping link: No binaries permitted for moleculekit: https://files.pythonhosted.org/packages/9f/a5/eac32fcb2e9ff0d30298aa4cec8e152c95d675c4dd1a1a5d7676986d4d75/moleculekit-0.1.5-py3-none-any.whl (from https://pypi.org/simple/moleculekit/) 2024-07-02T14:46:24,717 Found link 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2024-07-02T14:46:24,904 Found link https://files.pythonhosted.org/packages/d4/0f/1b1f0d41c3ff855afca374140213f1c43b3a9659eebc4460899fead843ff/moleculekit-1.8.34.tar.gz (from https://pypi.org/simple/moleculekit/) (requires-python:>=3.8), version: 1.8.34 2024-07-02T14:46:24,905 Found link https://files.pythonhosted.org/packages/26/6b/1104888679e9faf8b0e4e9b15586ea7532e171fe127c06e067c9ad563238/moleculekit-1.8.35.tar.gz (from https://pypi.org/simple/moleculekit/) (requires-python:>=3.8), version: 1.8.35 2024-07-02T14:46:24,906 Found link https://files.pythonhosted.org/packages/cf/5e/035ee54b5606e7489eed8e94571ca014339f5a6959902eff9f40bf4e0d7f/moleculekit-1.8.36.tar.gz (from https://pypi.org/simple/moleculekit/) (requires-python:>=3.8), version: 1.8.36 2024-07-02T14:46:24,906 Fetching project page and analyzing links: https://www.piwheels.org/simple/moleculekit/ 2024-07-02T14:46:24,907 Getting page https://www.piwheels.org/simple/moleculekit/ 2024-07-02T14:46:24,908 Found index url 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https://www.piwheels.org/simple/moleculekit/moleculekit-0.1.4-py3-none-any.whl#sha256=5784491ff294e145a00311f8239aaa0b92c12605db0508ee3e10469b80d4cadd (from https://www.piwheels.org/simple/moleculekit/) 2024-07-02T14:46:25,398 Skipping link: not a file: https://www.piwheels.org/simple/moleculekit/ 2024-07-02T14:46:25,399 Skipping link: not a file: https://pypi.org/simple/moleculekit/ 2024-07-02T14:46:25,442 Given no hashes to check 1 links for project 'moleculekit': discarding no candidates 2024-07-02T14:46:25,462 Collecting moleculekit==1.8.36 2024-07-02T14:46:25,465 Created temporary directory: /tmp/pip-unpack-9nhpxv94 2024-07-02T14:46:25,848 Downloading moleculekit-1.8.36.tar.gz (6.8 MB) 2024-07-02T14:46:29,263 Added moleculekit==1.8.36 from https://files.pythonhosted.org/packages/cf/5e/035ee54b5606e7489eed8e94571ca014339f5a6959902eff9f40bf4e0d7f/moleculekit-1.8.36.tar.gz to build tracker '/tmp/pip-build-tracker-ft_geqt3' 2024-07-02T14:46:29,271 Created temporary directory: /tmp/pip-build-env-i6d6y4aa 2024-07-02T14:46:29,275 Installing build dependencies: started 2024-07-02T14:46:29,277 Running command pip subprocess to install build dependencies 2024-07-02T14:46:30,405 Using pip 24.0 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-07-02T14:46:30,908 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-02T14:46:32,379 Collecting setuptools 2024-07-02T14:46:32,394 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.2.0-py3-none-any.whl (930 kB) 2024-07-02T14:46:33,063 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) 2024-07-02T14:46:33,067 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) 2024-07-02T14:46:33,070 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) 2024-07-02T14:46:33,073 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) 2024-07-02T14:46:33,077 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) 2024-07-02T14:46:33,368 Collecting numpy>=1.18.5 2024-07-02T14:46:33,385 Using cached https://www.piwheels.org/simple/numpy/numpy-2.0.0-cp311-cp311-linux_armv7l.whl (5.9 MB) 2024-07-02T14:46:34,836 Collecting Cython>=0.29.21 2024-07-02T14:46:34,854 Using cached https://www.piwheels.org/simple/cython/Cython-3.0.10-cp311-cp311-linux_armv7l.whl (11.8 MB) 2024-07-02T14:46:35,249 Collecting toml 2024-07-02T14:46:35,264 Using cached https://www.piwheels.org/simple/toml/toml-0.10.2-py2.py3-none-any.whl (16 kB) 2024-07-02T14:46:35,360 Collecting versioneer==0.28 (from versioneer[toml]==0.28) 2024-07-02T14:46:35,377 Using cached https://www.piwheels.org/simple/versioneer/versioneer-0.28-py3-none-any.whl (45 kB) 2024-07-02T14:46:38,001 Installing collected packages: versioneer, toml, setuptools, numpy, Cython 2024-07-02T14:46:38,032 Creating /tmp/pip-build-env-i6d6y4aa/overlay/local/bin 2024-07-02T14:46:38,034 changing mode of /tmp/pip-build-env-i6d6y4aa/overlay/local/bin/versioneer to 755 2024-07-02T14:46:48,982 changing mode of /tmp/pip-build-env-i6d6y4aa/overlay/local/bin/f2py to 755 2024-07-02T14:46:48,984 changing mode of /tmp/pip-build-env-i6d6y4aa/overlay/local/bin/numpy-config to 755 2024-07-02T14:46:52,567 changing mode of /tmp/pip-build-env-i6d6y4aa/overlay/local/bin/cygdb to 755 2024-07-02T14:46:52,569 changing mode of /tmp/pip-build-env-i6d6y4aa/overlay/local/bin/cython to 755 2024-07-02T14:46:52,571 changing mode of /tmp/pip-build-env-i6d6y4aa/overlay/local/bin/cythonize to 755 2024-07-02T14:46:52,616 Successfully installed Cython-3.0.10 numpy-2.0.0 setuptools-70.2.0 toml-0.10.2 versioneer-0.28 2024-07-02T14:46:52,925 [notice] A new release of pip is available: 24.0 -> 24.1.1 2024-07-02T14:46:52,925 [notice] To update, run: python3 -m pip install --upgrade pip 2024-07-02T14:46:53,374 Installing build dependencies: finished with status 'done' 2024-07-02T14:46:53,378 Getting requirements to build wheel: started 2024-07-02T14:46:53,379 Running command Getting requirements to build wheel 2024-07-02T14:47:29,515 warning: moleculekit/wrapping/wrapping.pyx:47:4: Unreachable code 2024-07-02T14:47:38,111 Compiling moleculekit/interactions/hbonds/hbonds.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,111 Compiling moleculekit/interactions/pipi/pipi.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,112 Compiling moleculekit/interactions/cationpi/cationpi.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,113 Compiling moleculekit/interactions/sigmahole/sigmahole.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,113 Compiling moleculekit/wrapping/wrapping.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,113 Compiling moleculekit/bondguesser_utils/bondguesser_utils.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,114 Compiling moleculekit/atomselect_utils/atomselect_utils.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,114 Compiling moleculekit/distance_utils/distance_utils.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,115 Compiling moleculekit/occupancy_utils/occupancy_utils.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,115 Compiling moleculekit/cython_utils/cython_utils.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,116 Compiling moleculekit/fileformats/xtc/xtc.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-07-02T14:47:38,117 Compiling moleculekit/fileformats/xtc/trr.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-07-02T14:47:38,117 Compiling moleculekit/fileformats/dcd/dcd.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-07-02T14:47:38,118 Compiling moleculekit/fileformats/binpos/binpos.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-07-02T14:47:38,118 Compiling moleculekit/tmalign/tmalign_util.pyx because it depends on /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-02T14:47:38,119 [ 1/15] Cythonizing moleculekit/atomselect_utils/atomselect_utils.pyx 2024-07-02T14:47:38,119 [ 2/15] Cythonizing moleculekit/bondguesser_utils/bondguesser_utils.pyx 2024-07-02T14:47:38,120 [ 3/15] Cythonizing moleculekit/cython_utils/cython_utils.pyx 2024-07-02T14:47:38,121 [ 4/15] Cythonizing moleculekit/distance_utils/distance_utils.pyx 2024-07-02T14:47:38,121 [ 5/15] Cythonizing moleculekit/fileformats/dcd/dcd.pyx 2024-07-02T14:47:38,122 [ 6/15] Cythonizing moleculekit/interactions/cationpi/cationpi.pyx 2024-07-02T14:47:38,122 [ 7/15] Cythonizing moleculekit/interactions/hbonds/hbonds.pyx 2024-07-02T14:47:38,123 [ 8/15] Cythonizing moleculekit/interactions/pipi/pipi.pyx 2024-07-02T14:47:38,123 [ 9/15] Cythonizing moleculekit/interactions/sigmahole/sigmahole.pyx 2024-07-02T14:47:38,123 [10/15] Cythonizing moleculekit/occupancy_utils/occupancy_utils.pyx 2024-07-02T14:47:38,124 [11/15] Cythonizing moleculekit/tmalign/tmalign_util.pyx 2024-07-02T14:47:38,125 [12/15] Cythonizing moleculekit/wrapping/wrapping.pyx 2024-07-02T14:47:38,125 [13/15] Cythonizing moleculekit/fileformats/binpos/binpos.pyx 2024-07-02T14:47:38,125 [14/15] Cythonizing moleculekit/fileformats/xtc/trr.pyx 2024-07-02T14:47:38,126 [15/15] Cythonizing moleculekit/fileformats/xtc/xtc.pyx 2024-07-02T14:47:38,408 running egg_info 2024-07-02T14:47:38,414 writing moleculekit.egg-info/PKG-INFO 2024-07-02T14:47:38,418 writing dependency_links to moleculekit.egg-info/dependency_links.txt 2024-07-02T14:47:38,420 writing requirements to moleculekit.egg-info/requires.txt 2024-07-02T14:47:38,421 writing top-level names to moleculekit.egg-info/top_level.txt 2024-07-02T14:47:38,450 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:38,450 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:38,451 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:38,451 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:38,452 dependency 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won't be automatically included in the manifest: the path must be relative 2024-07-02T14:47:42,984 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,985 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,985 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,985 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,986 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,986 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,987 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,987 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,988 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:42,989 reading manifest file '/tmp/pip-modern-metadata-qpz4de8i/moleculekit.egg-info/SOURCES.txt' 2024-07-02T14:47:42,989 reading manifest template 'MANIFEST.in' 2024-07-02T14:47:43,222 no previously-included directories found matching 'moleculekit/test-data' 2024-07-02T14:47:43,223 no previously-included directories found matching 'moleculekit/tests' 2024-07-02T14:47:43,223 no previously-included directories found matching 'package' 2024-07-02T14:47:43,224 adding license file 'LICENSE' 2024-07-02T14:47:43,236 writing manifest file '/tmp/pip-modern-metadata-qpz4de8i/moleculekit.egg-info/SOURCES.txt' 2024-07-02T14:47:43,243 creating '/tmp/pip-modern-metadata-qpz4de8i/moleculekit-1.8.36.dist-info' 2024-07-02T14:47:43,462 Preparing metadata (pyproject.toml): finished with status 'done' 2024-07-02T14:47:43,467 Source in /tmp/pip-wheel-kh5elng8/moleculekit_1b1b9c76407d4250a75fb06c1753e5cf has version 1.8.36, which satisfies requirement moleculekit==1.8.36 from https://files.pythonhosted.org/packages/cf/5e/035ee54b5606e7489eed8e94571ca014339f5a6959902eff9f40bf4e0d7f/moleculekit-1.8.36.tar.gz 2024-07-02T14:47:43,468 Removed moleculekit==1.8.36 from https://files.pythonhosted.org/packages/cf/5e/035ee54b5606e7489eed8e94571ca014339f5a6959902eff9f40bf4e0d7f/moleculekit-1.8.36.tar.gz from build tracker '/tmp/pip-build-tracker-ft_geqt3' 2024-07-02T14:47:43,473 Created temporary directory: /tmp/pip-unpack-wk7uwj3m 2024-07-02T14:47:43,474 Created temporary directory: /tmp/pip-unpack-xvanm8va 2024-07-02T14:47:43,482 Building wheels for collected packages: moleculekit 2024-07-02T14:47:43,486 Created temporary directory: /tmp/pip-wheel-4lop_2xt 2024-07-02T14:47:43,486 Destination directory: /tmp/pip-wheel-4lop_2xt 2024-07-02T14:47:43,488 Building wheel for moleculekit (pyproject.toml): started 2024-07-02T14:47:43,490 Running command Building wheel for moleculekit (pyproject.toml) 2024-07-02T14:47:45,694 running bdist_wheel 2024-07-02T14:47:45,708 running build 2024-07-02T14:47:45,708 running build_py 2024-07-02T14:47:45,715 creating build 2024-07-02T14:47:45,715 creating build/lib.linux-armv7l-cpython-311 2024-07-02T14:47:45,716 creating build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,717 copying moleculekit/util.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,720 copying moleculekit/bondguesser.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,722 copying moleculekit/align.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,725 copying moleculekit/home.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,727 copying moleculekit/vmdgraphics.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,729 copying moleculekit/config.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,730 copying moleculekit/writers.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,733 copying moleculekit/version.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,735 copying moleculekit/molecule.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,739 copying moleculekit/vmdviewer.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,741 copying moleculekit/rcsb.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,743 copying moleculekit/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,744 copying moleculekit/viewer.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,747 copying moleculekit/periodictable.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,749 copying moleculekit/rdkitintegration.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,751 copying moleculekit/readers.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,755 copying moleculekit/distance.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,758 copying moleculekit/dihedral.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,759 copying moleculekit/pymolgraphics.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,761 copying moleculekit/opm.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,763 copying moleculekit/_version.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:45,765 creating build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-02T14:47:45,766 copying moleculekit/smallmol/util.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-02T14:47:45,768 copying moleculekit/smallmol/smallmollib.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-02T14:47:45,771 copying moleculekit/smallmol/smallmol.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-02T14:47:45,774 copying moleculekit/smallmol/test_smallmol.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-02T14:47:45,776 copying moleculekit/smallmol/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-02T14:47:45,778 copying moleculekit/smallmol/smallmolcdp.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-02T14:47:45,780 copying moleculekit/smallmol/test_smallmollib.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-02T14:47:45,782 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-02T14:47:45,783 copying moleculekit/fileformats/utils.py -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-02T14:47:45,785 copying moleculekit/fileformats/netcdf.py -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-02T14:47:45,792 copying moleculekit/fileformats/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-02T14:47:45,794 creating build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,795 copying moleculekit/tools/docking.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,798 copying moleculekit/tools/preparation_customres.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,800 copying moleculekit/tools/voxeldescriptors.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,803 copying moleculekit/tools/sequencestructuralalignment.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,805 copying moleculekit/tools/preparation.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,809 copying moleculekit/tools/modelling.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,811 copying moleculekit/tools/hhblitsprofile.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,813 copying moleculekit/tools/moleculechecks.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,814 copying moleculekit/tools/autosegment.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,817 copying moleculekit/tools/crystalpacking.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,819 copying moleculekit/tools/detect.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,822 copying moleculekit/tools/atomtyper.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,824 copying moleculekit/tools/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,826 copying moleculekit/tools/graphalignment.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-02T14:47:45,829 creating build/lib.linux-armv7l-cpython-311/moleculekit/pdbx 2024-07-02T14:47:45,830 copying moleculekit/pdbx/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx 2024-07-02T14:47:45,832 creating build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-02T14:47:45,833 copying moleculekit/atomselect/atomselect.py -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-02T14:47:45,836 copying moleculekit/atomselect/languageparser.py -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-02T14:47:45,838 copying moleculekit/atomselect/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-02T14:47:45,840 copying moleculekit/atomselect/analyze.py -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-02T14:47:45,842 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions 2024-07-02T14:47:45,843 copying moleculekit/interactions/interactions.py -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions 2024-07-02T14:47:45,846 copying moleculekit/interactions/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions 2024-07-02T14:47:45,848 creating build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,849 copying moleculekit/projections/util.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,851 copying moleculekit/projections/metricshell.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,853 copying moleculekit/projections/metricsasa.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,856 copying moleculekit/projections/metricrmsd.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,858 copying moleculekit/projections/projection.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,859 copying moleculekit/projections/metricsecondarystructure.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,862 copying moleculekit/projections/metricsphericalcoordinate.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,864 copying moleculekit/projections/metricgyration.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,866 copying moleculekit/projections/metricfluctuation.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,869 copying moleculekit/projections/metriccoordinate.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,871 copying moleculekit/projections/metricdistance.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,874 copying moleculekit/projections/metricdihedral.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,877 copying moleculekit/projections/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,878 copying moleculekit/projections/metrictmscore.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,881 copying moleculekit/projections/metricplumed2.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-02T14:47:45,884 creating build/lib.linux-armv7l-cpython-311/moleculekit/ply 2024-07-02T14:47:45,885 copying moleculekit/ply/yacc.py -> build/lib.linux-armv7l-cpython-311/moleculekit/ply 2024-07-02T14:47:45,889 copying moleculekit/ply/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/ply 2024-07-02T14:47:45,890 copying moleculekit/ply/lex.py -> build/lib.linux-armv7l-cpython-311/moleculekit/ply 2024-07-02T14:47:45,894 creating build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-02T14:47:45,895 copying moleculekit/smallmol/tools/restrainedembed.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-02T14:47:45,897 copying moleculekit/smallmol/tools/test_tools.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-02T14:47:45,899 copying moleculekit/smallmol/tools/clustering.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-02T14:47:45,901 copying moleculekit/smallmol/tools/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-02T14:47:45,903 creating build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools 2024-07-02T14:47:45,904 copying moleculekit/tools/obabel_tools/obabel_cli.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools 2024-07-02T14:47:45,906 copying moleculekit/tools/obabel_tools/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools 2024-07-02T14:47:45,909 creating build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer 2024-07-02T14:47:45,910 copying moleculekit/pdbx/writer/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer 2024-07-02T14:47:45,911 copying moleculekit/pdbx/writer/PdbxWriter.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer 2024-07-02T14:47:45,914 creating build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-02T14:47:45,915 copying moleculekit/pdbx/tests/PdbxWriterTests.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-02T14:47:45,917 copying moleculekit/pdbx/tests/PdbxReaderTests.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-02T14:47:45,919 copying moleculekit/pdbx/tests/PdbxReadWriteTests.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-02T14:47:45,921 copying moleculekit/pdbx/tests/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-02T14:47:45,922 creating build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-02T14:47:45,923 copying moleculekit/pdbx/reader/PdbxParser.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-02T14:47:45,926 copying moleculekit/pdbx/reader/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-02T14:47:45,928 copying moleculekit/pdbx/reader/PdbxContainers.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-02T14:47:45,931 copying moleculekit/pdbx/reader/PdbxReader.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-02T14:47:45,933 running egg_info 2024-07-02T14:47:45,938 writing moleculekit.egg-info/PKG-INFO 2024-07-02T14:47:45,941 writing dependency_links to moleculekit.egg-info/dependency_links.txt 2024-07-02T14:47:45,942 writing requirements to moleculekit.egg-info/requires.txt 2024-07-02T14:47:45,943 writing top-level names to moleculekit.egg-info/top_level.txt 2024-07-02T14:47:45,960 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,961 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,961 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,962 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,962 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,963 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,964 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,964 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,965 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,965 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,966 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,967 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,967 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,968 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,968 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,969 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,969 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,970 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,970 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,971 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,972 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,972 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,973 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,973 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,974 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,974 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,975 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,976 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,977 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,977 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,978 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,978 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,978 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,979 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,979 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,980 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,980 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,981 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,981 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,982 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,983 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,983 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,984 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,984 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,985 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,985 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,986 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,987 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,987 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,987 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,988 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,988 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,989 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,989 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,989 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,990 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,991 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,991 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,992 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,992 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,993 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,994 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,994 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,995 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,995 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,996 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,997 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,997 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,998 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,998 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,998 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,999 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:45,999 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:46,000 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:46,001 dependency /tmp/pip-build-env-i6d6y4aa/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 2024-07-02T14:47:46,001 reading manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-07-02T14:47:46,002 reading manifest template 'MANIFEST.in' 2024-07-02T14:47:46,241 no previously-included directories found matching 'moleculekit/test-data' 2024-07-02T14:47:46,242 no previously-included directories found matching 'moleculekit/tests' 2024-07-02T14:47:46,244 no previously-included directories found matching 'package' 2024-07-02T14:47:46,244 adding license file 'LICENSE' 2024-07-02T14:47:46,260 writing manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-07-02T14:47:46,269 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.atomselect_utils' is absent from the `packages` configuration. 2024-07-02T14:47:46,269 !! 2024-07-02T14:47:46,270 ******************************************************************************** 2024-07-02T14:47:46,271 ############################ 2024-07-02T14:47:46,272 # Package would be ignored # 2024-07-02T14:47:46,272 ############################ 2024-07-02T14:47:46,273 Python recognizes 'moleculekit.atomselect_utils' as an importable package[^1], 2024-07-02T14:47:46,274 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,275 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,276 package, please make sure that 'moleculekit.atomselect_utils' is explicitly added 2024-07-02T14:47:46,277 to the `packages` configuration field. 2024-07-02T14:47:46,278 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,278 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,278 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,279 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,280 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,281 If you don't want 'moleculekit.atomselect_utils' to be distributed and are 2024-07-02T14:47:46,281 already explicitly excluding 'moleculekit.atomselect_utils' via 2024-07-02T14:47:46,281 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,282 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,282 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,283 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,284 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,285 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,285 even if it does not contain any `.py` files. 2024-07-02T14:47:46,286 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,286 directory, all directories are treated like packages. 2024-07-02T14:47:46,286 ******************************************************************************** 2024-07-02T14:47:46,288 !! 2024-07-02T14:47:46,288 check.warn(importable) 2024-07-02T14:47:46,289 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.bondguesser_utils' is absent from the `packages` configuration. 2024-07-02T14:47:46,289 !! 2024-07-02T14:47:46,291 ******************************************************************************** 2024-07-02T14:47:46,291 ############################ 2024-07-02T14:47:46,292 # Package would be ignored # 2024-07-02T14:47:46,293 ############################ 2024-07-02T14:47:46,293 Python recognizes 'moleculekit.bondguesser_utils' as an importable package[^1], 2024-07-02T14:47:46,294 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,295 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,295 package, please make sure that 'moleculekit.bondguesser_utils' is explicitly added 2024-07-02T14:47:46,296 to the `packages` configuration field. 2024-07-02T14:47:46,297 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,297 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,298 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,299 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,299 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,300 If you don't want 'moleculekit.bondguesser_utils' to be distributed and are 2024-07-02T14:47:46,301 already explicitly excluding 'moleculekit.bondguesser_utils' via 2024-07-02T14:47:46,301 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,302 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,303 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,304 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,305 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,306 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,306 even if it does not contain any `.py` files. 2024-07-02T14:47:46,307 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,307 directory, all directories are treated like packages. 2024-07-02T14:47:46,307 ******************************************************************************** 2024-07-02T14:47:46,308 !! 2024-07-02T14:47:46,308 check.warn(importable) 2024-07-02T14:47:46,309 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.cython_utils' is absent from the `packages` configuration. 2024-07-02T14:47:46,309 !! 2024-07-02T14:47:46,310 ******************************************************************************** 2024-07-02T14:47:46,310 ############################ 2024-07-02T14:47:46,311 # Package would be ignored # 2024-07-02T14:47:46,311 ############################ 2024-07-02T14:47:46,311 Python recognizes 'moleculekit.cython_utils' as an importable package[^1], 2024-07-02T14:47:46,312 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,313 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,313 package, please make sure that 'moleculekit.cython_utils' is explicitly added 2024-07-02T14:47:46,313 to the `packages` configuration field. 2024-07-02T14:47:46,314 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,315 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,315 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,316 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,317 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,319 If you don't want 'moleculekit.cython_utils' to be distributed and are 2024-07-02T14:47:46,319 already explicitly excluding 'moleculekit.cython_utils' via 2024-07-02T14:47:46,320 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,320 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,321 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,322 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,323 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,324 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,325 even if it does not contain any `.py` files. 2024-07-02T14:47:46,325 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,326 directory, all directories are treated like packages. 2024-07-02T14:47:46,326 ******************************************************************************** 2024-07-02T14:47:46,327 !! 2024-07-02T14:47:46,328 check.warn(importable) 2024-07-02T14:47:46,328 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.distance_utils' is absent from the `packages` configuration. 2024-07-02T14:47:46,329 !! 2024-07-02T14:47:46,330 ******************************************************************************** 2024-07-02T14:47:46,330 ############################ 2024-07-02T14:47:46,331 # Package would be ignored # 2024-07-02T14:47:46,331 ############################ 2024-07-02T14:47:46,332 Python recognizes 'moleculekit.distance_utils' as an importable package[^1], 2024-07-02T14:47:46,332 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,333 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,333 package, please make sure that 'moleculekit.distance_utils' is explicitly added 2024-07-02T14:47:46,333 to the `packages` configuration field. 2024-07-02T14:47:46,334 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,335 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,335 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,336 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,336 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,337 If you don't want 'moleculekit.distance_utils' to be distributed and are 2024-07-02T14:47:46,337 already explicitly excluding 'moleculekit.distance_utils' via 2024-07-02T14:47:46,338 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,338 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,339 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,339 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,341 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,342 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,343 even if it does not contain any `.py` files. 2024-07-02T14:47:46,343 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,344 directory, all directories are treated like packages. 2024-07-02T14:47:46,344 ******************************************************************************** 2024-07-02T14:47:46,345 !! 2024-07-02T14:47:46,346 check.warn(importable) 2024-07-02T14:47:46,346 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.binpos' is absent from the `packages` configuration. 2024-07-02T14:47:46,347 !! 2024-07-02T14:47:46,348 ******************************************************************************** 2024-07-02T14:47:46,349 ############################ 2024-07-02T14:47:46,349 # Package would be ignored # 2024-07-02T14:47:46,350 ############################ 2024-07-02T14:47:46,350 Python recognizes 'moleculekit.fileformats.binpos' as an importable package[^1], 2024-07-02T14:47:46,350 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,351 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,352 package, please make sure that 'moleculekit.fileformats.binpos' is explicitly added 2024-07-02T14:47:46,352 to the `packages` configuration field. 2024-07-02T14:47:46,353 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,354 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,354 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,355 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,357 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,358 If you don't want 'moleculekit.fileformats.binpos' to be distributed and are 2024-07-02T14:47:46,358 already explicitly excluding 'moleculekit.fileformats.binpos' via 2024-07-02T14:47:46,359 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,359 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,359 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,360 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,361 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,362 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,362 even if it does not contain any `.py` files. 2024-07-02T14:47:46,363 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,363 directory, all directories are treated like packages. 2024-07-02T14:47:46,364 ******************************************************************************** 2024-07-02T14:47:46,365 !! 2024-07-02T14:47:46,365 check.warn(importable) 2024-07-02T14:47:46,366 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.binpos.include' is absent from the `packages` configuration. 2024-07-02T14:47:46,366 !! 2024-07-02T14:47:46,367 ******************************************************************************** 2024-07-02T14:47:46,367 ############################ 2024-07-02T14:47:46,368 # Package would be ignored # 2024-07-02T14:47:46,369 ############################ 2024-07-02T14:47:46,369 Python recognizes 'moleculekit.fileformats.binpos.include' as an importable package[^1], 2024-07-02T14:47:46,370 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,371 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,372 package, please make sure that 'moleculekit.fileformats.binpos.include' is explicitly added 2024-07-02T14:47:46,372 to the `packages` configuration field. 2024-07-02T14:47:46,374 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,374 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,375 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,376 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,377 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,378 If you don't want 'moleculekit.fileformats.binpos.include' to be distributed and are 2024-07-02T14:47:46,379 already explicitly excluding 'moleculekit.fileformats.binpos.include' via 2024-07-02T14:47:46,379 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,380 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,380 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,381 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,382 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,384 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,384 even if it does not contain any `.py` files. 2024-07-02T14:47:46,385 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,385 directory, all directories are treated like packages. 2024-07-02T14:47:46,386 ******************************************************************************** 2024-07-02T14:47:46,387 !! 2024-07-02T14:47:46,387 check.warn(importable) 2024-07-02T14:47:46,388 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.binpos.src' is absent from the `packages` configuration. 2024-07-02T14:47:46,388 !! 2024-07-02T14:47:46,389 ******************************************************************************** 2024-07-02T14:47:46,389 ############################ 2024-07-02T14:47:46,390 # Package would be ignored # 2024-07-02T14:47:46,390 ############################ 2024-07-02T14:47:46,396 Python recognizes 'moleculekit.fileformats.binpos.src' as an importable package[^1], 2024-07-02T14:47:46,396 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,397 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,397 package, please make sure that 'moleculekit.fileformats.binpos.src' is explicitly added 2024-07-02T14:47:46,398 to the `packages` configuration field. 2024-07-02T14:47:46,398 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,399 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,399 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,400 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,401 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,402 If you don't want 'moleculekit.fileformats.binpos.src' to be distributed and are 2024-07-02T14:47:46,402 already explicitly excluding 'moleculekit.fileformats.binpos.src' via 2024-07-02T14:47:46,403 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,403 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,404 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,405 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,406 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,408 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,408 even if it does not contain any `.py` files. 2024-07-02T14:47:46,409 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,409 directory, all directories are treated like packages. 2024-07-02T14:47:46,410 ******************************************************************************** 2024-07-02T14:47:46,411 !! 2024-07-02T14:47:46,411 check.warn(importable) 2024-07-02T14:47:46,412 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.dcd' is absent from the `packages` configuration. 2024-07-02T14:47:46,412 !! 2024-07-02T14:47:46,413 ******************************************************************************** 2024-07-02T14:47:46,414 ############################ 2024-07-02T14:47:46,414 # Package would be ignored # 2024-07-02T14:47:46,415 ############################ 2024-07-02T14:47:46,415 Python recognizes 'moleculekit.fileformats.dcd' as an importable package[^1], 2024-07-02T14:47:46,416 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,417 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,417 package, please make sure that 'moleculekit.fileformats.dcd' is explicitly added 2024-07-02T14:47:46,418 to the `packages` configuration field. 2024-07-02T14:47:46,419 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,419 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,420 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,420 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,421 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,422 If you don't want 'moleculekit.fileformats.dcd' to be distributed and are 2024-07-02T14:47:46,422 already explicitly excluding 'moleculekit.fileformats.dcd' via 2024-07-02T14:47:46,422 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,423 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,423 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,424 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,425 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,426 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,426 even if it does not contain any `.py` files. 2024-07-02T14:47:46,426 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,427 directory, all directories are treated like packages. 2024-07-02T14:47:46,427 ******************************************************************************** 2024-07-02T14:47:46,428 !! 2024-07-02T14:47:46,429 check.warn(importable) 2024-07-02T14:47:46,429 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.dcd.include' is absent from the `packages` configuration. 2024-07-02T14:47:46,430 !! 2024-07-02T14:47:46,431 ******************************************************************************** 2024-07-02T14:47:46,432 ############################ 2024-07-02T14:47:46,432 # Package would be ignored # 2024-07-02T14:47:46,433 ############################ 2024-07-02T14:47:46,433 Python recognizes 'moleculekit.fileformats.dcd.include' as an importable package[^1], 2024-07-02T14:47:46,434 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,435 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,435 package, please make sure that 'moleculekit.fileformats.dcd.include' is explicitly added 2024-07-02T14:47:46,436 to the `packages` configuration field. 2024-07-02T14:47:46,437 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,437 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,438 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,439 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,440 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,441 If you don't want 'moleculekit.fileformats.dcd.include' to be distributed and are 2024-07-02T14:47:46,441 already explicitly excluding 'moleculekit.fileformats.dcd.include' via 2024-07-02T14:47:46,442 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,442 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,443 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,445 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,446 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,447 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,447 even if it does not contain any `.py` files. 2024-07-02T14:47:46,447 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,448 directory, all directories are treated like packages. 2024-07-02T14:47:46,448 ******************************************************************************** 2024-07-02T14:47:46,449 !! 2024-07-02T14:47:46,449 check.warn(importable) 2024-07-02T14:47:46,450 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.dcd.src' is absent from the `packages` configuration. 2024-07-02T14:47:46,450 !! 2024-07-02T14:47:46,451 ******************************************************************************** 2024-07-02T14:47:46,451 ############################ 2024-07-02T14:47:46,452 # Package would be ignored # 2024-07-02T14:47:46,452 ############################ 2024-07-02T14:47:46,453 Python recognizes 'moleculekit.fileformats.dcd.src' as an importable package[^1], 2024-07-02T14:47:46,453 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,454 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,454 package, please make sure that 'moleculekit.fileformats.dcd.src' is explicitly added 2024-07-02T14:47:46,455 to the `packages` configuration field. 2024-07-02T14:47:46,456 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,456 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,457 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,458 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,459 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,460 If you don't want 'moleculekit.fileformats.dcd.src' to be distributed and are 2024-07-02T14:47:46,461 already explicitly excluding 'moleculekit.fileformats.dcd.src' via 2024-07-02T14:47:46,461 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,462 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,462 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,463 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,464 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,466 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,467 even if it does not contain any `.py` files. 2024-07-02T14:47:46,467 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,468 directory, all directories are treated like packages. 2024-07-02T14:47:46,468 ******************************************************************************** 2024-07-02T14:47:46,469 !! 2024-07-02T14:47:46,470 check.warn(importable) 2024-07-02T14:47:46,470 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.xtc' is absent from the `packages` configuration. 2024-07-02T14:47:46,471 !! 2024-07-02T14:47:46,472 ******************************************************************************** 2024-07-02T14:47:46,473 ############################ 2024-07-02T14:47:46,474 # Package would be ignored # 2024-07-02T14:47:46,474 ############################ 2024-07-02T14:47:46,475 Python recognizes 'moleculekit.fileformats.xtc' as an importable package[^1], 2024-07-02T14:47:46,475 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,476 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,477 package, please make sure that 'moleculekit.fileformats.xtc' is explicitly added 2024-07-02T14:47:46,477 to the `packages` configuration field. 2024-07-02T14:47:46,492 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,495 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,495 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,496 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,497 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,499 If you don't want 'moleculekit.fileformats.xtc' to be distributed and are 2024-07-02T14:47:46,499 already explicitly excluding 'moleculekit.fileformats.xtc' via 2024-07-02T14:47:46,499 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,500 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,500 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,501 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,502 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,504 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,504 even if it does not contain any `.py` files. 2024-07-02T14:47:46,505 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,505 directory, all directories are treated like packages. 2024-07-02T14:47:46,506 ******************************************************************************** 2024-07-02T14:47:46,507 !! 2024-07-02T14:47:46,507 check.warn(importable) 2024-07-02T14:47:46,509 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.xtc.include' is absent from the `packages` configuration. 2024-07-02T14:47:46,510 !! 2024-07-02T14:47:46,516 ******************************************************************************** 2024-07-02T14:47:46,522 ############################ 2024-07-02T14:47:46,522 # Package would be ignored # 2024-07-02T14:47:46,523 ############################ 2024-07-02T14:47:46,524 Python recognizes 'moleculekit.fileformats.xtc.include' as an importable package[^1], 2024-07-02T14:47:46,524 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,526 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,526 package, please make sure that 'moleculekit.fileformats.xtc.include' is explicitly added 2024-07-02T14:47:46,527 to the `packages` configuration field. 2024-07-02T14:47:46,528 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,528 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,529 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,530 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,531 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,532 If you don't want 'moleculekit.fileformats.xtc.include' to be distributed and are 2024-07-02T14:47:46,533 already explicitly excluding 'moleculekit.fileformats.xtc.include' via 2024-07-02T14:47:46,533 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,535 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,542 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,547 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,547 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,549 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,549 even if it does not contain any `.py` files. 2024-07-02T14:47:46,550 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,550 directory, all directories are treated like packages. 2024-07-02T14:47:46,551 ******************************************************************************** 2024-07-02T14:47:46,551 !! 2024-07-02T14:47:46,552 check.warn(importable) 2024-07-02T14:47:46,552 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.xtc.src' is absent from the `packages` configuration. 2024-07-02T14:47:46,553 !! 2024-07-02T14:47:46,554 ******************************************************************************** 2024-07-02T14:47:46,554 ############################ 2024-07-02T14:47:46,555 # Package would be ignored # 2024-07-02T14:47:46,555 ############################ 2024-07-02T14:47:46,556 Python recognizes 'moleculekit.fileformats.xtc.src' as an importable package[^1], 2024-07-02T14:47:46,556 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,557 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,558 package, please make sure that 'moleculekit.fileformats.xtc.src' is explicitly added 2024-07-02T14:47:46,558 to the `packages` configuration field. 2024-07-02T14:47:46,559 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,560 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,560 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,562 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,563 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,564 If you don't want 'moleculekit.fileformats.xtc.src' to be distributed and are 2024-07-02T14:47:46,564 already explicitly excluding 'moleculekit.fileformats.xtc.src' via 2024-07-02T14:47:46,565 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,565 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,566 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,567 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,569 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,570 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,571 even if it does not contain any `.py` files. 2024-07-02T14:47:46,572 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,572 directory, all directories are treated like packages. 2024-07-02T14:47:46,573 ******************************************************************************** 2024-07-02T14:47:46,574 !! 2024-07-02T14:47:46,574 check.warn(importable) 2024-07-02T14:47:46,575 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.cationpi' is absent from the `packages` configuration. 2024-07-02T14:47:46,575 !! 2024-07-02T14:47:46,577 ******************************************************************************** 2024-07-02T14:47:46,577 ############################ 2024-07-02T14:47:46,578 # Package would be ignored # 2024-07-02T14:47:46,578 ############################ 2024-07-02T14:47:46,579 Python recognizes 'moleculekit.interactions.cationpi' as an importable package[^1], 2024-07-02T14:47:46,579 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,587 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,588 package, please make sure that 'moleculekit.interactions.cationpi' is explicitly added 2024-07-02T14:47:46,589 to the `packages` configuration field. 2024-07-02T14:47:46,589 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,590 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,591 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,592 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,593 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,594 If you don't want 'moleculekit.interactions.cationpi' to be distributed and are 2024-07-02T14:47:46,594 already explicitly excluding 'moleculekit.interactions.cationpi' via 2024-07-02T14:47:46,595 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,595 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,596 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,597 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,598 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,601 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,607 even if it does not contain any `.py` files. 2024-07-02T14:47:46,611 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,612 directory, all directories are treated like packages. 2024-07-02T14:47:46,613 ******************************************************************************** 2024-07-02T14:47:46,614 !! 2024-07-02T14:47:46,614 check.warn(importable) 2024-07-02T14:47:46,615 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.hbonds' is absent from the `packages` configuration. 2024-07-02T14:47:46,616 !! 2024-07-02T14:47:46,617 ******************************************************************************** 2024-07-02T14:47:46,618 ############################ 2024-07-02T14:47:46,618 # Package would be ignored # 2024-07-02T14:47:46,619 ############################ 2024-07-02T14:47:46,619 Python recognizes 'moleculekit.interactions.hbonds' as an importable package[^1], 2024-07-02T14:47:46,620 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,621 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,621 package, please make sure that 'moleculekit.interactions.hbonds' is explicitly added 2024-07-02T14:47:46,622 to the `packages` configuration field. 2024-07-02T14:47:46,623 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,624 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,624 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,625 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,626 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,627 If you don't want 'moleculekit.interactions.hbonds' to be distributed and are 2024-07-02T14:47:46,627 already explicitly excluding 'moleculekit.interactions.hbonds' via 2024-07-02T14:47:46,628 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,628 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,628 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,629 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,630 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,631 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,632 even if it does not contain any `.py` files. 2024-07-02T14:47:46,632 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,633 directory, all directories are treated like packages. 2024-07-02T14:47:46,633 ******************************************************************************** 2024-07-02T14:47:46,634 !! 2024-07-02T14:47:46,635 check.warn(importable) 2024-07-02T14:47:46,636 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.pipi' is absent from the `packages` configuration. 2024-07-02T14:47:46,636 !! 2024-07-02T14:47:46,637 ******************************************************************************** 2024-07-02T14:47:46,638 ############################ 2024-07-02T14:47:46,639 # Package would be ignored # 2024-07-02T14:47:46,639 ############################ 2024-07-02T14:47:46,640 Python recognizes 'moleculekit.interactions.pipi' as an importable package[^1], 2024-07-02T14:47:46,640 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,642 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,642 package, please make sure that 'moleculekit.interactions.pipi' is explicitly added 2024-07-02T14:47:46,643 to the `packages` configuration field. 2024-07-02T14:47:46,644 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,645 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,645 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,646 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,647 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,648 If you don't want 'moleculekit.interactions.pipi' to be distributed and are 2024-07-02T14:47:46,649 already explicitly excluding 'moleculekit.interactions.pipi' via 2024-07-02T14:47:46,650 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,650 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,651 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,653 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,653 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,655 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,655 even if it does not contain any `.py` files. 2024-07-02T14:47:46,656 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,656 directory, all directories are treated like packages. 2024-07-02T14:47:46,657 ******************************************************************************** 2024-07-02T14:47:46,657 !! 2024-07-02T14:47:46,658 check.warn(importable) 2024-07-02T14:47:46,658 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.sigmahole' is absent from the `packages` configuration. 2024-07-02T14:47:46,659 !! 2024-07-02T14:47:46,660 ******************************************************************************** 2024-07-02T14:47:46,661 ############################ 2024-07-02T14:47:46,662 # Package would be ignored # 2024-07-02T14:47:46,662 ############################ 2024-07-02T14:47:46,663 Python recognizes 'moleculekit.interactions.sigmahole' as an importable package[^1], 2024-07-02T14:47:46,663 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,664 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,664 package, please make sure that 'moleculekit.interactions.sigmahole' is explicitly added 2024-07-02T14:47:46,665 to the `packages` configuration field. 2024-07-02T14:47:46,666 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,667 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,667 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,668 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,669 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,671 If you don't want 'moleculekit.interactions.sigmahole' to be distributed and are 2024-07-02T14:47:46,671 already explicitly excluding 'moleculekit.interactions.sigmahole' via 2024-07-02T14:47:46,672 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,672 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,673 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,674 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,676 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,677 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,678 even if it does not contain any `.py` files. 2024-07-02T14:47:46,678 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,679 directory, all directories are treated like packages. 2024-07-02T14:47:46,679 ******************************************************************************** 2024-07-02T14:47:46,681 !! 2024-07-02T14:47:46,681 check.warn(importable) 2024-07-02T14:47:46,682 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.occupancy_utils' is absent from the `packages` configuration. 2024-07-02T14:47:46,682 !! 2024-07-02T14:47:46,684 ******************************************************************************** 2024-07-02T14:47:46,684 ############################ 2024-07-02T14:47:46,685 # Package would be ignored # 2024-07-02T14:47:46,686 ############################ 2024-07-02T14:47:46,686 Python recognizes 'moleculekit.occupancy_utils' as an importable package[^1], 2024-07-02T14:47:46,687 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,688 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,688 package, please make sure that 'moleculekit.occupancy_utils' is explicitly added 2024-07-02T14:47:46,688 to the `packages` configuration field. 2024-07-02T14:47:46,689 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,705 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,716 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,749 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,780 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,822 If you don't want 'moleculekit.occupancy_utils' to be distributed and are 2024-07-02T14:47:46,823 already explicitly excluding 'moleculekit.occupancy_utils' via 2024-07-02T14:47:46,823 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,824 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,824 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,825 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,826 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,828 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,828 even if it does not contain any `.py` files. 2024-07-02T14:47:46,829 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,830 directory, all directories are treated like packages. 2024-07-02T14:47:46,830 ******************************************************************************** 2024-07-02T14:47:46,831 !! 2024-07-02T14:47:46,832 check.warn(importable) 2024-07-02T14:47:46,833 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.share' is absent from the `packages` configuration. 2024-07-02T14:47:46,833 !! 2024-07-02T14:47:46,835 ******************************************************************************** 2024-07-02T14:47:46,835 ############################ 2024-07-02T14:47:46,835 # Package would be ignored # 2024-07-02T14:47:46,836 ############################ 2024-07-02T14:47:46,837 Python recognizes 'moleculekit.share' as an importable package[^1], 2024-07-02T14:47:46,838 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,839 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,839 package, please make sure that 'moleculekit.share' is explicitly added 2024-07-02T14:47:46,840 to the `packages` configuration field. 2024-07-02T14:47:46,841 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,841 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,842 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,843 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,845 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,846 If you don't want 'moleculekit.share' to be distributed and are 2024-07-02T14:47:46,847 already explicitly excluding 'moleculekit.share' via 2024-07-02T14:47:46,848 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,849 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,849 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,850 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,851 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,853 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,854 even if it does not contain any `.py` files. 2024-07-02T14:47:46,854 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,855 directory, all directories are treated like packages. 2024-07-02T14:47:46,855 ******************************************************************************** 2024-07-02T14:47:46,856 !! 2024-07-02T14:47:46,857 check.warn(importable) 2024-07-02T14:47:46,857 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.share.atomselect' is absent from the `packages` configuration. 2024-07-02T14:47:46,857 !! 2024-07-02T14:47:46,858 ******************************************************************************** 2024-07-02T14:47:46,859 ############################ 2024-07-02T14:47:46,859 # Package would be ignored # 2024-07-02T14:47:46,860 ############################ 2024-07-02T14:47:46,860 Python recognizes 'moleculekit.share.atomselect' as an importable package[^1], 2024-07-02T14:47:46,861 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,862 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,862 package, please make sure that 'moleculekit.share.atomselect' is explicitly added 2024-07-02T14:47:46,863 to the `packages` configuration field. 2024-07-02T14:47:46,864 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,864 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,865 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,866 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,867 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,868 If you don't want 'moleculekit.share.atomselect' to be distributed and are 2024-07-02T14:47:46,868 already explicitly excluding 'moleculekit.share.atomselect' via 2024-07-02T14:47:46,869 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,869 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,870 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,871 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,872 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,873 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,874 even if it does not contain any `.py` files. 2024-07-02T14:47:46,874 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,875 directory, all directories are treated like packages. 2024-07-02T14:47:46,875 ******************************************************************************** 2024-07-02T14:47:46,877 !! 2024-07-02T14:47:46,877 check.warn(importable) 2024-07-02T14:47:46,878 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.share.pdb2pqr.residues' is absent from the `packages` configuration. 2024-07-02T14:47:46,878 !! 2024-07-02T14:47:46,879 ******************************************************************************** 2024-07-02T14:47:46,879 ############################ 2024-07-02T14:47:46,880 # Package would be ignored # 2024-07-02T14:47:46,880 ############################ 2024-07-02T14:47:46,880 Python recognizes 'moleculekit.share.pdb2pqr.residues' as an importable package[^1], 2024-07-02T14:47:46,881 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,882 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,882 package, please make sure that 'moleculekit.share.pdb2pqr.residues' is explicitly added 2024-07-02T14:47:46,882 to the `packages` configuration field. 2024-07-02T14:47:46,883 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,884 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,884 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,885 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,886 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,887 If you don't want 'moleculekit.share.pdb2pqr.residues' to be distributed and are 2024-07-02T14:47:46,888 already explicitly excluding 'moleculekit.share.pdb2pqr.residues' via 2024-07-02T14:47:46,888 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,889 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,889 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,890 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,891 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,893 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,893 even if it does not contain any `.py` files. 2024-07-02T14:47:46,894 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,894 directory, all directories are treated like packages. 2024-07-02T14:47:46,895 ******************************************************************************** 2024-07-02T14:47:46,896 !! 2024-07-02T14:47:46,896 check.warn(importable) 2024-07-02T14:47:46,897 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign' is absent from the `packages` configuration. 2024-07-02T14:47:46,897 !! 2024-07-02T14:47:46,898 ******************************************************************************** 2024-07-02T14:47:46,899 ############################ 2024-07-02T14:47:46,899 # Package would be ignored # 2024-07-02T14:47:46,900 ############################ 2024-07-02T14:47:46,900 Python recognizes 'moleculekit.tmalign' as an importable package[^1], 2024-07-02T14:47:46,901 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,902 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,902 package, please make sure that 'moleculekit.tmalign' is explicitly added 2024-07-02T14:47:46,903 to the `packages` configuration field. 2024-07-02T14:47:46,904 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,904 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,905 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,906 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,907 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,907 If you don't want 'moleculekit.tmalign' to be distributed and are 2024-07-02T14:47:46,908 already explicitly excluding 'moleculekit.tmalign' via 2024-07-02T14:47:46,908 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,909 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,909 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,910 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,911 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,912 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,913 even if it does not contain any `.py` files. 2024-07-02T14:47:46,913 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,913 directory, all directories are treated like packages. 2024-07-02T14:47:46,914 ******************************************************************************** 2024-07-02T14:47:46,915 !! 2024-07-02T14:47:46,916 check.warn(importable) 2024-07-02T14:47:46,916 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign.include' is absent from the `packages` configuration. 2024-07-02T14:47:46,917 !! 2024-07-02T14:47:46,917 ******************************************************************************** 2024-07-02T14:47:46,918 ############################ 2024-07-02T14:47:46,918 # Package would be ignored # 2024-07-02T14:47:46,919 ############################ 2024-07-02T14:47:46,919 Python recognizes 'moleculekit.tmalign.include' as an importable package[^1], 2024-07-02T14:47:46,920 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,921 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,921 package, please make sure that 'moleculekit.tmalign.include' is explicitly added 2024-07-02T14:47:46,922 to the `packages` configuration field. 2024-07-02T14:47:46,923 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,923 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,924 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,925 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,926 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,927 If you don't want 'moleculekit.tmalign.include' to be distributed and are 2024-07-02T14:47:46,928 already explicitly excluding 'moleculekit.tmalign.include' via 2024-07-02T14:47:46,928 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,929 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,929 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,930 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,931 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,933 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,934 even if it does not contain any `.py` files. 2024-07-02T14:47:46,934 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,934 directory, all directories are treated like packages. 2024-07-02T14:47:46,935 ******************************************************************************** 2024-07-02T14:47:46,936 !! 2024-07-02T14:47:46,936 check.warn(importable) 2024-07-02T14:47:46,937 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign.src' is absent from the `packages` configuration. 2024-07-02T14:47:46,937 !! 2024-07-02T14:47:46,938 ******************************************************************************** 2024-07-02T14:47:46,938 ############################ 2024-07-02T14:47:46,939 # Package would be ignored # 2024-07-02T14:47:46,939 ############################ 2024-07-02T14:47:46,939 Python recognizes 'moleculekit.tmalign.src' as an importable package[^1], 2024-07-02T14:47:46,940 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,942 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,942 package, please make sure that 'moleculekit.tmalign.src' is explicitly added 2024-07-02T14:47:46,943 to the `packages` configuration field. 2024-07-02T14:47:46,944 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,945 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,945 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,947 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,948 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,949 If you don't want 'moleculekit.tmalign.src' to be distributed and are 2024-07-02T14:47:46,949 already explicitly excluding 'moleculekit.tmalign.src' via 2024-07-02T14:47:46,950 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,951 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,952 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,953 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,955 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,957 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,957 even if it does not contain any `.py` files. 2024-07-02T14:47:46,958 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,958 directory, all directories are treated like packages. 2024-07-02T14:47:46,959 ******************************************************************************** 2024-07-02T14:47:46,961 !! 2024-07-02T14:47:46,961 check.warn(importable) 2024-07-02T14:47:46,962 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.wrapping' is absent from the `packages` configuration. 2024-07-02T14:47:46,963 !! 2024-07-02T14:47:46,964 ******************************************************************************** 2024-07-02T14:47:46,965 ############################ 2024-07-02T14:47:46,965 # Package would be ignored # 2024-07-02T14:47:46,966 ############################ 2024-07-02T14:47:46,967 Python recognizes 'moleculekit.wrapping' as an importable package[^1], 2024-07-02T14:47:46,967 but it is absent from setuptools' `packages` configuration. 2024-07-02T14:47:46,970 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-02T14:47:46,971 package, please make sure that 'moleculekit.wrapping' is explicitly added 2024-07-02T14:47:46,971 to the `packages` configuration field. 2024-07-02T14:47:46,973 Alternatively, you can also rely on setuptools' discovery methods 2024-07-02T14:47:46,973 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-02T14:47:46,974 instead of `find_packages(...)`/`find:`). 2024-07-02T14:47:46,975 You can read more about "package discovery" on setuptools documentation page: 2024-07-02T14:47:46,977 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-02T14:47:46,978 If you don't want 'moleculekit.wrapping' to be distributed and are 2024-07-02T14:47:46,978 already explicitly excluding 'moleculekit.wrapping' via 2024-07-02T14:47:46,979 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-02T14:47:46,979 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-02T14:47:46,980 combination with a more fine grained `package-data` configuration. 2024-07-02T14:47:46,982 You can read more about "package data files" on setuptools documentation page: 2024-07-02T14:47:46,983 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-02T14:47:46,985 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-02T14:47:46,986 even if it does not contain any `.py` files. 2024-07-02T14:47:46,986 On the other hand, currently there is no concept of package data 2024-07-02T14:47:46,987 directory, all directories are treated like packages. 2024-07-02T14:47:46,987 ******************************************************************************** 2024-07-02T14:47:46,989 !! 2024-07-02T14:47:46,989 check.warn(importable) 2024-07-02T14:47:46,990 copying moleculekit/logging.ini -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:46,990 copying moleculekit/vmd_wrapper -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:46,991 creating build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils 2024-07-02T14:47:46,992 copying moleculekit/atomselect_utils/atomselect_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils 2024-07-02T14:47:46,993 copying moleculekit/atomselect_utils/atomselect_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils 2024-07-02T14:47:46,993 creating build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils 2024-07-02T14:47:46,994 copying moleculekit/bondguesser_utils/bondguesser_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils 2024-07-02T14:47:46,995 copying moleculekit/bondguesser_utils/bondguesser_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils 2024-07-02T14:47:46,995 creating build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils 2024-07-02T14:47:46,996 copying moleculekit/cython_utils/cython_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils 2024-07-02T14:47:46,997 copying moleculekit/cython_utils/cython_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils 2024-07-02T14:47:46,997 creating build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils 2024-07-02T14:47:46,998 copying moleculekit/distance_utils/distance_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils 2024-07-02T14:47:46,998 copying moleculekit/distance_utils/distance_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils 2024-07-02T14:47:46,999 creating build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils 2024-07-02T14:47:47,000 copying moleculekit/occupancy_utils/occupancy_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils 2024-07-02T14:47:47,001 copying moleculekit/occupancy_utils/occupancy_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils 2024-07-02T14:47:47,001 creating build/lib.linux-armv7l-cpython-311/moleculekit/share 2024-07-02T14:47:47,002 copying moleculekit/share/ALA.cif -> build/lib.linux-armv7l-cpython-311/moleculekit/share 2024-07-02T14:47:47,002 copying moleculekit/share/backbone.cif -> build/lib.linux-armv7l-cpython-311/moleculekit/share 2024-07-02T14:47:47,003 copying moleculekit/share/opm_sequences.json -> build/lib.linux-armv7l-cpython-311/moleculekit/share 2024-07-02T14:47:47,003 creating build/lib.linux-armv7l-cpython-311/moleculekit/share/atomselect 2024-07-02T14:47:47,004 copying moleculekit/share/atomselect/atomselect.json -> build/lib.linux-armv7l-cpython-311/moleculekit/share/atomselect 2024-07-02T14:47:47,004 creating build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr 2024-07-02T14:47:47,005 creating build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,006 copying moleculekit/share/pdb2pqr/residues/.gitkeep -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,006 copying moleculekit/share/pdb2pqr/residues/004.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,007 copying moleculekit/share/pdb2pqr/residues/004.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,007 copying moleculekit/share/pdb2pqr/residues/03Y.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,008 copying moleculekit/share/pdb2pqr/residues/03Y.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,008 copying moleculekit/share/pdb2pqr/residues/0A1.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,009 copying moleculekit/share/pdb2pqr/residues/0A1.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,009 copying moleculekit/share/pdb2pqr/residues/0AF.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,010 copying moleculekit/share/pdb2pqr/residues/0AF.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,010 copying moleculekit/share/pdb2pqr/residues/0BN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,011 copying moleculekit/share/pdb2pqr/residues/0BN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,011 copying moleculekit/share/pdb2pqr/residues/1MH.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,012 copying moleculekit/share/pdb2pqr/residues/1MH.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,012 copying moleculekit/share/pdb2pqr/residues/2AS.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,013 copying moleculekit/share/pdb2pqr/residues/2AS.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,013 copying moleculekit/share/pdb2pqr/residues/2GX.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,014 copying moleculekit/share/pdb2pqr/residues/2GX.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,014 copying moleculekit/share/pdb2pqr/residues/2ML.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,015 copying moleculekit/share/pdb2pqr/residues/2ML.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,016 copying moleculekit/share/pdb2pqr/residues/2MR.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,016 copying moleculekit/share/pdb2pqr/residues/2MR.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,017 copying moleculekit/share/pdb2pqr/residues/4IN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,017 copying moleculekit/share/pdb2pqr/residues/4IN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,018 copying moleculekit/share/pdb2pqr/residues/4PH.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,018 copying moleculekit/share/pdb2pqr/residues/4PH.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,019 copying moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,019 copying moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,019 copying moleculekit/share/pdb2pqr/residues/5JP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,020 copying moleculekit/share/pdb2pqr/residues/5JP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,020 copying moleculekit/share/pdb2pqr/residues/AA4.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,021 copying moleculekit/share/pdb2pqr/residues/AA4.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,021 copying moleculekit/share/pdb2pqr/residues/ABA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,022 copying moleculekit/share/pdb2pqr/residues/ABA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,022 copying moleculekit/share/pdb2pqr/residues/AHP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,023 copying moleculekit/share/pdb2pqr/residues/AHP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,024 copying moleculekit/share/pdb2pqr/residues/ALC.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,024 copying moleculekit/share/pdb2pqr/residues/ALC.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,025 copying moleculekit/share/pdb2pqr/residues/ALN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,025 copying moleculekit/share/pdb2pqr/residues/ALN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,026 copying moleculekit/share/pdb2pqr/residues/ALY.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,026 copying moleculekit/share/pdb2pqr/residues/ALY.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,027 copying moleculekit/share/pdb2pqr/residues/APD.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,027 copying moleculekit/share/pdb2pqr/residues/APD.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,028 copying moleculekit/share/pdb2pqr/residues/BB8.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,028 copying moleculekit/share/pdb2pqr/residues/BB8.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,029 copying moleculekit/share/pdb2pqr/residues/BCS.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,029 copying moleculekit/share/pdb2pqr/residues/BCS.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,030 copying moleculekit/share/pdb2pqr/residues/BTK.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,031 copying moleculekit/share/pdb2pqr/residues/BTK.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,031 copying moleculekit/share/pdb2pqr/residues/CCS.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,032 copying moleculekit/share/pdb2pqr/residues/CCS.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,032 copying moleculekit/share/pdb2pqr/residues/CGU.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,033 copying moleculekit/share/pdb2pqr/residues/CGU.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,033 copying moleculekit/share/pdb2pqr/residues/CSA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,034 copying moleculekit/share/pdb2pqr/residues/CSA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,034 copying moleculekit/share/pdb2pqr/residues/CSO.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,035 copying moleculekit/share/pdb2pqr/residues/CSO.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,035 copying moleculekit/share/pdb2pqr/residues/CSP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,036 copying moleculekit/share/pdb2pqr/residues/CSP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,036 copying moleculekit/share/pdb2pqr/residues/CSS.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,037 copying moleculekit/share/pdb2pqr/residues/CSS.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,037 copying moleculekit/share/pdb2pqr/residues/D4P.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,038 copying moleculekit/share/pdb2pqr/residues/D4P.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,038 copying moleculekit/share/pdb2pqr/residues/DA2.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,039 copying moleculekit/share/pdb2pqr/residues/DA2.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,039 copying moleculekit/share/pdb2pqr/residues/DAB.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,040 copying moleculekit/share/pdb2pqr/residues/DAB.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,040 copying moleculekit/share/pdb2pqr/residues/DAH.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,041 copying moleculekit/share/pdb2pqr/residues/DAH.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,041 copying moleculekit/share/pdb2pqr/residues/DPP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,042 copying moleculekit/share/pdb2pqr/residues/DPP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,042 copying moleculekit/share/pdb2pqr/residues/ESC.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,043 copying moleculekit/share/pdb2pqr/residues/ESC.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,044 copying moleculekit/share/pdb2pqr/residues/FGL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,044 copying moleculekit/share/pdb2pqr/residues/FGL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,045 copying moleculekit/share/pdb2pqr/residues/GHG.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,045 copying moleculekit/share/pdb2pqr/residues/GHG.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,046 copying moleculekit/share/pdb2pqr/residues/GME.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,046 copying moleculekit/share/pdb2pqr/residues/GME.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,047 copying moleculekit/share/pdb2pqr/residues/GNC.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,047 copying moleculekit/share/pdb2pqr/residues/GNC.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,048 copying moleculekit/share/pdb2pqr/residues/HHK.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,048 copying moleculekit/share/pdb2pqr/residues/HHK.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,049 copying moleculekit/share/pdb2pqr/residues/HLU.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,050 copying moleculekit/share/pdb2pqr/residues/HLU.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,052 copying moleculekit/share/pdb2pqr/residues/HLX.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,054 copying moleculekit/share/pdb2pqr/residues/HLX.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,056 copying moleculekit/share/pdb2pqr/residues/HOX.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,058 copying moleculekit/share/pdb2pqr/residues/HOX.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,060 copying moleculekit/share/pdb2pqr/residues/HPE.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,062 copying moleculekit/share/pdb2pqr/residues/HPE.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,064 copying moleculekit/share/pdb2pqr/residues/HQA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,066 copying moleculekit/share/pdb2pqr/residues/HQA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,068 copying moleculekit/share/pdb2pqr/residues/HTR.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,070 copying moleculekit/share/pdb2pqr/residues/HTR.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,072 copying moleculekit/share/pdb2pqr/residues/HYP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,074 copying moleculekit/share/pdb2pqr/residues/HYP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,077 copying moleculekit/share/pdb2pqr/residues/I2M.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,079 copying moleculekit/share/pdb2pqr/residues/I2M.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,081 copying moleculekit/share/pdb2pqr/residues/IGL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,083 copying moleculekit/share/pdb2pqr/residues/IGL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,085 copying moleculekit/share/pdb2pqr/residues/IIL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,087 copying moleculekit/share/pdb2pqr/residues/IIL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,089 copying moleculekit/share/pdb2pqr/residues/IML.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,091 copying moleculekit/share/pdb2pqr/residues/IML.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,093 copying moleculekit/share/pdb2pqr/residues/KYN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,095 copying moleculekit/share/pdb2pqr/residues/KYN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,097 copying moleculekit/share/pdb2pqr/residues/LME.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,099 copying moleculekit/share/pdb2pqr/residues/LME.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,101 copying moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,103 copying moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,105 copying moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,107 copying moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,109 copying moleculekit/share/pdb2pqr/residues/M3L.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,111 copying moleculekit/share/pdb2pqr/residues/M3L.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,113 copying moleculekit/share/pdb2pqr/residues/ME0.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,115 copying moleculekit/share/pdb2pqr/residues/ME0.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,117 copying moleculekit/share/pdb2pqr/residues/MEA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,119 copying moleculekit/share/pdb2pqr/residues/MEA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,121 copying moleculekit/share/pdb2pqr/residues/MEN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,123 copying moleculekit/share/pdb2pqr/residues/MEN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,125 copying moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,127 copying moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,129 copying moleculekit/share/pdb2pqr/residues/MLE.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,131 copying moleculekit/share/pdb2pqr/residues/MLE.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,133 copying moleculekit/share/pdb2pqr/residues/MLY.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,136 copying moleculekit/share/pdb2pqr/residues/MLY.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,138 copying moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,140 copying moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,142 copying moleculekit/share/pdb2pqr/residues/MME.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,145 copying moleculekit/share/pdb2pqr/residues/MME.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,147 copying moleculekit/share/pdb2pqr/residues/MMO.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,149 copying moleculekit/share/pdb2pqr/residues/MMO.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,151 copying moleculekit/share/pdb2pqr/residues/MVA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,152 copying moleculekit/share/pdb2pqr/residues/MVA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,154 copying moleculekit/share/pdb2pqr/residues/NAL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,156 copying moleculekit/share/pdb2pqr/residues/NAL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,158 copying moleculekit/share/pdb2pqr/residues/NCY.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,160 copying moleculekit/share/pdb2pqr/residues/NCY.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,162 copying moleculekit/share/pdb2pqr/residues/NLE.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,164 copying moleculekit/share/pdb2pqr/residues/NLE.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,166 copying moleculekit/share/pdb2pqr/residues/NVA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,169 copying moleculekit/share/pdb2pqr/residues/NVA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,171 copying moleculekit/share/pdb2pqr/residues/NZC.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,173 copying moleculekit/share/pdb2pqr/residues/NZC.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,176 copying moleculekit/share/pdb2pqr/residues/OCY.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,178 copying moleculekit/share/pdb2pqr/residues/OCY.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,180 copying moleculekit/share/pdb2pqr/residues/OMX.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,182 copying moleculekit/share/pdb2pqr/residues/OMX.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,184 copying moleculekit/share/pdb2pqr/residues/ONL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,186 copying moleculekit/share/pdb2pqr/residues/ONL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,188 copying moleculekit/share/pdb2pqr/residues/ORM.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,190 copying moleculekit/share/pdb2pqr/residues/ORM.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,192 copying moleculekit/share/pdb2pqr/residues/P1L.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,194 copying moleculekit/share/pdb2pqr/residues/P1L.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,197 copying moleculekit/share/pdb2pqr/residues/PCA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,199 copying moleculekit/share/pdb2pqr/residues/PCA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,201 copying moleculekit/share/pdb2pqr/residues/PRK.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,203 copying moleculekit/share/pdb2pqr/residues/PRK.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,205 copying moleculekit/share/pdb2pqr/residues/PTR.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,207 copying moleculekit/share/pdb2pqr/residues/PTR.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,209 copying moleculekit/share/pdb2pqr/residues/SEP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,211 copying moleculekit/share/pdb2pqr/residues/SEP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,213 copying moleculekit/share/pdb2pqr/residues/TPO.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,215 copying moleculekit/share/pdb2pqr/residues/TPO.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,217 copying moleculekit/share/pdb2pqr/residues/TRO.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,219 copying moleculekit/share/pdb2pqr/residues/TRO.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,221 copying moleculekit/share/pdb2pqr/residues/TY2.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,223 copying moleculekit/share/pdb2pqr/residues/TY2.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,225 copying moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,227 copying moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,229 copying moleculekit/share/pdb2pqr/residues/YCM.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,231 copying moleculekit/share/pdb2pqr/residues/YCM.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,233 copying moleculekit/share/pdb2pqr/residues/YNM.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,235 copying moleculekit/share/pdb2pqr/residues/YNM.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-02T14:47:47,238 creating build/lib.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-02T14:47:47,239 copying moleculekit/tmalign/tmalign_util.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-02T14:47:47,267 copying moleculekit/tmalign/tmalign_util.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-02T14:47:47,270 copying moleculekit/tmalign/tmalignlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-02T14:47:47,271 creating build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/include 2024-07-02T14:47:47,272 copying moleculekit/tmalign/include/TMAlign.h -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/include 2024-07-02T14:47:47,275 creating build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/src 2024-07-02T14:47:47,275 copying moleculekit/tmalign/src/TMAlign.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/src 2024-07-02T14:47:47,281 creating build/lib.linux-armv7l-cpython-311/moleculekit/wrapping 2024-07-02T14:47:47,282 copying moleculekit/wrapping/wrapping.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/wrapping 2024-07-02T14:47:47,309 copying moleculekit/wrapping/wrapping.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/wrapping 2024-07-02T14:47:47,311 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-02T14:47:47,312 copying moleculekit/fileformats/binpos/binpos.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-02T14:47:47,327 copying moleculekit/fileformats/binpos/binpos.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-02T14:47:47,330 copying moleculekit/fileformats/binpos/binposlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-02T14:47:47,331 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include 2024-07-02T14:47:47,332 copying moleculekit/fileformats/binpos/include/binposplugin.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include 2024-07-02T14:47:47,334 copying moleculekit/fileformats/binpos/include/largefiles.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include 2024-07-02T14:47:47,336 copying moleculekit/fileformats/binpos/include/molfile_plugin.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include 2024-07-02T14:47:47,339 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src 2024-07-02T14:47:47,339 copying moleculekit/fileformats/binpos/src/binposplugin.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src 2024-07-02T14:47:47,342 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-02T14:47:47,343 copying moleculekit/fileformats/dcd/dcd.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-02T14:47:47,358 copying moleculekit/fileformats/dcd/dcd.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-02T14:47:47,360 copying moleculekit/fileformats/dcd/dcdlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-02T14:47:47,362 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-02T14:47:47,363 copying moleculekit/fileformats/dcd/include/dcdplugin.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-02T14:47:47,365 copying moleculekit/fileformats/dcd/include/endianswap.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-02T14:47:47,368 copying moleculekit/fileformats/dcd/include/fastio.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-02T14:47:47,370 copying moleculekit/fileformats/dcd/include/largefiles.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-02T14:47:47,372 copying moleculekit/fileformats/dcd/include/molfile_plugin.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-02T14:47:47,375 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src 2024-07-02T14:47:47,376 copying moleculekit/fileformats/dcd/src/dcdplugin.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src 2024-07-02T14:47:47,380 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:47:47,381 copying moleculekit/fileformats/xtc/trr.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:47:47,402 copying moleculekit/fileformats/xtc/trr.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:47:47,405 copying moleculekit/fileformats/xtc/trrlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:47:47,407 copying moleculekit/fileformats/xtc/xdrlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:47:47,408 copying moleculekit/fileformats/xtc/xtc.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:47:47,427 copying moleculekit/fileformats/xtc/xtc.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:47:47,429 copying moleculekit/fileformats/xtc/xtclib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:47:47,431 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-02T14:47:47,432 copying moleculekit/fileformats/xtc/include/trr_header.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-02T14:47:47,434 copying moleculekit/fileformats/xtc/include/xdr_seek.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-02T14:47:47,435 copying moleculekit/fileformats/xtc/include/xdrfile.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-02T14:47:47,438 copying moleculekit/fileformats/xtc/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-02T14:47:47,440 copying moleculekit/fileformats/xtc/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-02T14:47:47,442 copying moleculekit/fileformats/xtc/include/xtc.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-02T14:47:47,444 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-02T14:47:47,444 copying moleculekit/fileformats/xtc/src/xdr_seek.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-02T14:47:47,446 copying moleculekit/fileformats/xtc/src/xdrfile.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-02T14:47:47,449 copying moleculekit/fileformats/xtc/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-02T14:47:47,452 copying moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-02T14:47:47,454 copying moleculekit/fileformats/xtc/src/xtc.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-02T14:47:47,457 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi 2024-07-02T14:47:47,458 copying moleculekit/interactions/cationpi/cationpi.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi 2024-07-02T14:47:47,478 copying moleculekit/interactions/cationpi/cationpi.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi 2024-07-02T14:47:47,481 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds 2024-07-02T14:47:47,482 copying moleculekit/interactions/hbonds/hbonds.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds 2024-07-02T14:47:47,502 copying moleculekit/interactions/hbonds/hbonds.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds 2024-07-02T14:47:47,504 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi 2024-07-02T14:47:47,505 copying moleculekit/interactions/pipi/pipi.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi 2024-07-02T14:47:47,527 copying moleculekit/interactions/pipi/pipi.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi 2024-07-02T14:47:47,529 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole 2024-07-02T14:47:47,530 copying moleculekit/interactions/sigmahole/sigmahole.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole 2024-07-02T14:47:47,550 copying moleculekit/interactions/sigmahole/sigmahole.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole 2024-07-02T14:47:47,561 UPDATING build/lib.linux-armv7l-cpython-311/moleculekit/_version.py 2024-07-02T14:47:47,561 set build/lib.linux-armv7l-cpython-311/moleculekit/_version.py to '1.8.36' 2024-07-02T14:47:47,562 running build_ext 2024-07-02T14:47:47,571 building 'moleculekit.interactions.hbonds' extension 2024-07-02T14:47:47,572 creating build/temp.linux-armv7l-cpython-311 2024-07-02T14:47:47,573 creating build/temp.linux-armv7l-cpython-311/moleculekit 2024-07-02T14:47:47,574 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions 2024-07-02T14:47:47,574 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions/hbonds 2024-07-02T14:47:47,576 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/interactions/hbonds/hbonds.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/interactions/hbonds/hbonds.o -O3 2024-07-02T14:47:47,907 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:47:47,908 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:47:47,909 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:47:47,909 from moleculekit/interactions/hbonds/hbonds.cpp:1265: 2024-07-02T14:47:47,910 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:47:47,910 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:47:47,910 | ^~~~~~~ 2024-07-02T14:47:48,774 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:47:48,774 from moleculekit/interactions/hbonds/hbonds.cpp:1269: 2024-07-02T14:47:48,775 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:47:48,776 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:47:48,777 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:47:48,777 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:48:15,255 In function ‘PyObject* __pyx_pf_11moleculekit_12interactions_6hbonds_calculate(PyObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, float, float, bool, bool)’, 2024-07-02T14:48:15,256 inlined from ‘PyObject* __pyx_pw_11moleculekit_12interactions_6hbonds_1calculate(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at moleculekit/interactions/hbonds/hbonds.cpp:20443:68: 2024-07-02T14:48:15,256 moleculekit/interactions/hbonds/hbonds.cpp:21469:52: warning: ‘__pyx_v_d_idx_h’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:48:15,257 21469 | (__pyx_v_results[__pyx_v_f]).push_back(__pyx_v_d_idx_h); 2024-07-02T14:48:15,258 | ^~~~~~~~~~~~~~~ 2024-07-02T14:48:15,259 moleculekit/interactions/hbonds/hbonds.cpp: In function ‘PyObject* __pyx_pw_11moleculekit_12interactions_6hbonds_1calculate(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’: 2024-07-02T14:48:15,259 moleculekit/interactions/hbonds/hbonds.cpp:20486:57: note: ‘__pyx_v_d_idx_h’ was declared here 2024-07-02T14:48:15,260 20486 | __pyx_t_11moleculekit_12interactions_6hbonds_UINT32_t __pyx_v_d_idx_h; 2024-07-02T14:48:15,261 | ^~~~~~~~~~~~~~~ 2024-07-02T14:48:18,886 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/interactions/hbonds/hbonds.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:48:19,182 building 'moleculekit.interactions.pipi' extension 2024-07-02T14:48:19,183 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions/pipi 2024-07-02T14:48:19,184 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/interactions/pipi/pipi.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/interactions/pipi/pipi.o -O3 2024-07-02T14:48:19,533 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:48:19,533 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:48:19,534 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:48:19,534 from moleculekit/interactions/pipi/pipi.cpp:1265: 2024-07-02T14:48:19,535 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:48:19,535 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:48:19,536 | ^~~~~~~ 2024-07-02T14:48:20,394 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:48:20,394 from moleculekit/interactions/pipi/pipi.cpp:1269: 2024-07-02T14:48:20,395 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:48:20,396 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:48:20,397 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:48:20,397 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:48:52,432 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/interactions/pipi/pipi.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:48:52,732 building 'moleculekit.interactions.cationpi' extension 2024-07-02T14:48:52,733 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions/cationpi 2024-07-02T14:48:52,734 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/interactions/cationpi/cationpi.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/interactions/cationpi/cationpi.o -O3 2024-07-02T14:48:53,085 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:48:53,086 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:48:53,087 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:48:53,087 from moleculekit/interactions/cationpi/cationpi.cpp:1265: 2024-07-02T14:48:53,088 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:48:53,088 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:48:53,089 | ^~~~~~~ 2024-07-02T14:48:53,950 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:48:53,950 from moleculekit/interactions/cationpi/cationpi.cpp:1269: 2024-07-02T14:48:53,951 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:48:53,951 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:48:53,952 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:48:53,952 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:49:25,302 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/interactions/cationpi/cationpi.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:49:25,623 building 'moleculekit.interactions.sigmahole' extension 2024-07-02T14:49:25,624 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole 2024-07-02T14:49:25,624 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/interactions/sigmahole/sigmahole.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole/sigmahole.o -O3 2024-07-02T14:49:25,928 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:49:25,929 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:49:25,929 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:49:25,930 from moleculekit/interactions/sigmahole/sigmahole.cpp:1265: 2024-07-02T14:49:25,931 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:49:25,931 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:49:25,932 | ^~~~~~~ 2024-07-02T14:49:26,792 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:49:26,795 from moleculekit/interactions/sigmahole/sigmahole.cpp:1269: 2024-07-02T14:49:26,796 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:49:26,841 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:49:26,848 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:49:26,849 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:49:58,407 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole/sigmahole.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:49:58,711 building 'moleculekit.wrapping' extension 2024-07-02T14:49:58,713 creating build/temp.linux-armv7l-cpython-311/moleculekit/wrapping 2024-07-02T14:49:58,714 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/wrapping/wrapping.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/wrapping/wrapping.o -O3 2024-07-02T14:49:59,031 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:49:59,032 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:49:59,033 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:49:59,034 from moleculekit/wrapping/wrapping.cpp:1265: 2024-07-02T14:49:59,034 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:49:59,035 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:49:59,036 | ^~~~~~~ 2024-07-02T14:49:59,925 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:49:59,925 from moleculekit/wrapping/wrapping.cpp:1269: 2024-07-02T14:49:59,926 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:49:59,927 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:49:59,927 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:49:59,928 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:29,314 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/wrapping/wrapping.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/wrapping.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:50:29,549 building 'moleculekit.bondguesser_utils' extension 2024-07-02T14:50:29,550 creating build/temp.linux-armv7l-cpython-311/moleculekit/bondguesser_utils 2024-07-02T14:50:29,551 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/bondguesser_utils/bondguesser_utils.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/bondguesser_utils/bondguesser_utils.o -O3 2024-07-02T14:50:29,910 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:50:29,911 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:50:29,912 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:50:29,913 from moleculekit/bondguesser_utils/bondguesser_utils.cpp:1265: 2024-07-02T14:50:29,913 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:50:29,914 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:50:29,915 | ^~~~~~~ 2024-07-02T14:50:30,790 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:50:30,791 from moleculekit/bondguesser_utils/bondguesser_utils.cpp:1269: 2024-07-02T14:50:30,791 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:50:30,792 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:50:30,793 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:50:30,794 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,436 moleculekit/bondguesser_utils/bondguesser_utils.cpp: In function ‘PyObject* __pyx_pf_11moleculekit_17bondguesser_utils_make_grid_neighborlist_nonperiodic(PyObject*, __Pyx_memviewslice, __pyx_t_11moleculekit_17bondguesser_utils_UINT32_t, __pyx_t_11moleculekit_17bondguesser_utils_UINT32_t, __pyx_t_11moleculekit_17bondguesser_utils_UINT32_t)’: 2024-07-02T14:50:32,436 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20255:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__pyx_t_11moleculekit_17bondguesser_utils_UINT32_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2024-07-02T14:50:32,437 20255 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2024-07-02T14:50:32,437 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-02T14:50:32,438 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20267:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__pyx_t_11moleculekit_17bondguesser_utils_UINT32_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2024-07-02T14:50:32,439 20267 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2024-07-02T14:50:32,439 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-02T14:50:32,440 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20279:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__pyx_t_11moleculekit_17bondguesser_utils_UINT32_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2024-07-02T14:50:32,441 20279 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2024-07-02T14:50:32,441 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-02T14:50:32,442 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20318:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,443 20318 | __pyx_t_12 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-02T14:50:32,443 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,444 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20357:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,445 20357 | __pyx_t_12 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-02T14:50:32,445 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,446 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20396:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,447 20396 | __pyx_t_12 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,447 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,448 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20435:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,449 20435 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-02T14:50:32,450 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,450 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20441:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,451 20441 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-02T14:50:32,451 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,452 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20482:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,452 20482 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-02T14:50:32,453 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,454 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20488:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,455 20488 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,456 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,457 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20529:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,457 20529 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-02T14:50:32,458 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,459 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20535:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,459 20535 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,460 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,461 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20576:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,462 20576 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-02T14:50:32,462 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,463 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20629:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,464 20629 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,465 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,466 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20676:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,467 20676 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,468 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,469 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20717:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,470 20717 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-02T14:50:32,471 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,472 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20723:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,473 20723 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-02T14:50:32,475 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,476 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20729:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,476 20729 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,477 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,477 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20776:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,478 20776 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-02T14:50:32,478 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,479 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20782:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,480 20782 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,480 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,481 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20823:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,482 20823 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-02T14:50:32,482 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,483 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20835:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,484 20835 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,485 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,485 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20888:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-02T14:50:32,486 20888 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-02T14:50:32,487 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,488 moleculekit/bondguesser_utils/bondguesser_utils.cpp: In function ‘PyObject* __pyx_pf_11moleculekit_17bondguesser_utils_2grid_bonds(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, float, int, __Pyx_memviewslice, __Pyx_memviewslice)’: 2024-07-02T14:50:32,489 moleculekit/bondguesser_utils/bondguesser_utils.cpp:21510:37: warning: comparison of integer expressions of different signedness: ‘__pyx_t_11moleculekit_17bondguesser_utils_UINT32_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-02T14:50:32,490 21510 | __pyx_t_6 = (__pyx_v_boxneigh == __pyx_v_n_boxes); 2024-07-02T14:50:32,491 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2024-07-02T14:50:32,491 moleculekit/bondguesser_utils/bondguesser_utils.cpp:21547:37: warning: comparison of integer expressions of different signedness: ‘__pyx_t_11moleculekit_17bondguesser_utils_UINT32_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-02T14:50:32,492 21547 | __pyx_t_6 = (__pyx_v_boxneigh == __pyx_v_boxidx); 2024-07-02T14:50:32,493 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-07-02T14:50:58,931 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/bondguesser_utils/bondguesser_utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:50:59,200 building 'moleculekit.atomselect_utils' extension 2024-07-02T14:50:59,200 creating build/temp.linux-armv7l-cpython-311/moleculekit/atomselect_utils 2024-07-02T14:50:59,201 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/atomselect_utils/atomselect_utils.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/atomselect_utils/atomselect_utils.o -O3 2024-07-02T14:50:59,509 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:50:59,510 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:50:59,510 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:50:59,511 from moleculekit/atomselect_utils/atomselect_utils.cpp:1282: 2024-07-02T14:50:59,511 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:50:59,512 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:50:59,512 | ^~~~~~~ 2024-07-02T14:51:00,383 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:51:00,384 from moleculekit/atomselect_utils/atomselect_utils.cpp:1286: 2024-07-02T14:51:00,384 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:51:00,385 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:51:00,386 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:51:00,386 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:51:02,472 moleculekit/atomselect_utils/atomselect_utils.cpp: In function ‘bool __pyx_f_11moleculekit_16atomselect_utils__find_connected_subfragment(int, int, const char*, const char*, const char*, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, std::vector >&, __Pyx_memviewslice, std::vector >&, std::vector >&, std::vector >&)’: 2024-07-02T14:51:02,473 moleculekit/atomselect_utils/atomselect_utils.cpp:23709:161: warning: comparison of integer expressions of different signedness: ‘__pyx_t_11moleculekit_16atomselect_utils_UINT32_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-02T14:51:02,474 23709 | __pyx_t_3 = ((*((__pyx_t_11moleculekit_16atomselect_utils_UINT32_t *) ( /* dim=0 */ (__pyx_v_uq_resid.data + __pyx_t_2 * __pyx_v_uq_resid.strides[0]) ))) != __pyx_v_resnum); 2024-07-02T14:51:02,474 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-07-02T14:51:02,480 moleculekit/atomselect_utils/atomselect_utils.cpp: In function ‘bool __pyx_f_11moleculekit_16atomselect_utils__find_subfragments(int, std::vector >&, std::vector >&, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, std::vector >&, __Pyx_memviewslice, std::vector >&)’: 2024-07-02T14:51:02,481 moleculekit/atomselect_utils/atomselect_utils.cpp:23961:163: warning: comparison of integer expressions of different signedness: ‘__pyx_t_11moleculekit_16atomselect_utils_UINT32_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-02T14:51:02,481 23961 | __pyx_t_6 = ((*((__pyx_t_11moleculekit_16atomselect_utils_UINT32_t *) ( /* dim=0 */ (__pyx_v_uq_resid.data + __pyx_t_5 * __pyx_v_uq_resid.strides[0]) ))) != __pyx_v_i); 2024-07-02T14:51:02,482 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-02T14:51:02,488 moleculekit/atomselect_utils/atomselect_utils.cpp: In function ‘bool __pyx_f_11moleculekit_16atomselect_utils__find_subfragments_topologically(int, std::vector >&, std::vector >&, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, std::vector >&, __Pyx_memviewslice, std::vector >&)’: 2024-07-02T14:51:02,488 moleculekit/atomselect_utils/atomselect_utils.cpp:24228:163: warning: comparison of integer expressions of different signedness: ‘__pyx_t_11moleculekit_16atomselect_utils_UINT32_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-02T14:51:02,489 24228 | __pyx_t_6 = ((*((__pyx_t_11moleculekit_16atomselect_utils_UINT32_t *) ( /* dim=0 */ (__pyx_v_uq_resid.data + __pyx_t_5 * __pyx_v_uq_resid.strides[0]) ))) != __pyx_v_i); 2024-07-02T14:51:02,489 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-02T14:51:36,582 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/atomselect_utils/atomselect_utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:51:36,871 building 'moleculekit.distance_utils' extension 2024-07-02T14:51:36,871 creating build/temp.linux-armv7l-cpython-311/moleculekit/distance_utils 2024-07-02T14:51:36,872 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/distance_utils/distance_utils.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/distance_utils/distance_utils.o -O3 2024-07-02T14:51:37,176 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:51:37,177 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:51:37,177 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:51:37,178 from moleculekit/distance_utils/distance_utils.cpp:1265: 2024-07-02T14:51:37,178 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:51:37,179 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:51:37,180 | ^~~~~~~ 2024-07-02T14:51:38,052 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:51:38,052 from moleculekit/distance_utils/distance_utils.cpp:1269: 2024-07-02T14:51:38,053 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:51:38,054 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:51:38,055 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:51:38,055 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:51:39,562 moleculekit/distance_utils/distance_utils.cpp: In function ‘PyObject* __pyx_pf_11moleculekit_14distance_utils_2get_collisions(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, float)’: 2024-07-02T14:51:39,563 moleculekit/distance_utils/distance_utils.cpp:21813:33: warning: comparison of integer expressions of different signedness: ‘__pyx_t_11moleculekit_14distance_utils_UINT32_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-02T14:51:39,564 21813 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2024-07-02T14:51:39,564 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-02T14:51:39,565 moleculekit/distance_utils/distance_utils.cpp:21825:35: warning: comparison of integer expressions of different signedness: ‘__pyx_t_11moleculekit_14distance_utils_UINT32_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-02T14:51:39,565 21825 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2024-07-02T14:51:39,566 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-02T14:52:16,785 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/distance_utils/distance_utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:52:17,075 building 'moleculekit.occupancy_utils' extension 2024-07-02T14:52:17,076 creating build/temp.linux-armv7l-cpython-311/moleculekit/occupancy_utils 2024-07-02T14:52:17,076 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/occupancy_utils/occupancy_utils.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/occupancy_utils/occupancy_utils.o -O3 2024-07-02T14:52:17,385 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:52:17,386 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:52:17,386 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:52:17,387 from moleculekit/occupancy_utils/occupancy_utils.cpp:1265: 2024-07-02T14:52:17,387 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:52:17,388 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:52:17,388 | ^~~~~~~ 2024-07-02T14:52:18,243 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:52:18,244 from moleculekit/occupancy_utils/occupancy_utils.cpp:1269: 2024-07-02T14:52:18,244 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:52:18,245 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:52:18,246 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:52:18,247 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:52:44,717 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/occupancy_utils/occupancy_utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:52:44,906 building 'moleculekit.cython_utils' extension 2024-07-02T14:52:44,907 creating build/temp.linux-armv7l-cpython-311/moleculekit/cython_utils 2024-07-02T14:52:44,907 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-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/cython_utils/cython_utils.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/cython_utils/cython_utils.o -O3 2024-07-02T14:52:45,213 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:52:45,214 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:52:45,214 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:52:45,215 from moleculekit/cython_utils/cython_utils.cpp:1265: 2024-07-02T14:52:45,215 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:52:45,216 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:52:45,217 | ^~~~~~~ 2024-07-02T14:52:46,068 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-02T14:52:46,069 from moleculekit/cython_utils/cython_utils.cpp:1269: 2024-07-02T14:52:46,070 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-02T14:52:46,070 /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-07-02T14:52:46,071 405 | return ((longdouble_t *) &z)[0]; 2024-07-02T14:52:46,072 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:53:15,109 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/cython_utils/cython_utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:53:15,391 building 'moleculekit.xtc' extension 2024-07-02T14:53:15,392 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-02T14:53:15,392 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-02T14:53:15,393 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-02T14:53:15,395 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/xtc -Imoleculekit/fileformats/xtc/include/ -Imoleculekit/fileformats/xtc/ -I/tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/fileformats/xtc/src/xdrfile.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile.o 2024-07-02T14:53:16,032 moleculekit/fileformats/xtc/src/xdrfile.cpp:66:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,033 66 | "OK", 2024-07-02T14:53:16,034 | ^~~~ 2024-07-02T14:53:16,034 moleculekit/fileformats/xtc/src/xdrfile.cpp:67:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,035 67 | "Header", 2024-07-02T14:53:16,035 | ^~~~~~~~ 2024-07-02T14:53:16,035 moleculekit/fileformats/xtc/src/xdrfile.cpp:68:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,036 68 | "String", 2024-07-02T14:53:16,036 | ^~~~~~~~ 2024-07-02T14:53:16,037 moleculekit/fileformats/xtc/src/xdrfile.cpp:69:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,037 69 | "Double", 2024-07-02T14:53:16,038 | ^~~~~~~~ 2024-07-02T14:53:16,038 moleculekit/fileformats/xtc/src/xdrfile.cpp:70:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,039 70 | "Integer", 2024-07-02T14:53:16,039 | ^~~~~~~~~ 2024-07-02T14:53:16,040 moleculekit/fileformats/xtc/src/xdrfile.cpp:71:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,040 71 | "Float", 2024-07-02T14:53:16,041 | ^~~~~~~ 2024-07-02T14:53:16,041 moleculekit/fileformats/xtc/src/xdrfile.cpp:72:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,042 72 | "Unsigned integer", 2024-07-02T14:53:16,042 | ^~~~~~~~~~~~~~~~~~ 2024-07-02T14:53:16,043 moleculekit/fileformats/xtc/src/xdrfile.cpp:73:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,043 73 | "Compressed 3D coordinate", 2024-07-02T14:53:16,044 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:53:16,044 moleculekit/fileformats/xtc/src/xdrfile.cpp:74:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,045 74 | "Closing file", 2024-07-02T14:53:16,045 | ^~~~~~~~~~~~~~ 2024-07-02T14:53:16,046 moleculekit/fileformats/xtc/src/xdrfile.cpp:75:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,046 75 | "Magic number", 2024-07-02T14:53:16,047 | ^~~~~~~~~~~~~~ 2024-07-02T14:53:16,048 moleculekit/fileformats/xtc/src/xdrfile.cpp:76:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,048 76 | "Not enough memory", 2024-07-02T14:53:16,049 | ^~~~~~~~~~~~~~~~~~~ 2024-07-02T14:53:16,050 moleculekit/fileformats/xtc/src/xdrfile.cpp:77:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,050 77 | "End of file", 2024-07-02T14:53:16,051 | ^~~~~~~~~~~~~ 2024-07-02T14:53:16,051 moleculekit/fileformats/xtc/src/xdrfile.cpp:78:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-02T14:53:16,052 78 | "File not found" 2024-07-02T14:53:16,052 | ^~~~~~~~~~~~~~~~ 2024-07-02T14:53:16,061 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofint(int)’: 2024-07-02T14:53:16,062 moleculekit/fileformats/xtc/src/xdrfile.cpp:459:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,063 459 | while (size >= num && num_of_bits < 32) 2024-07-02T14:53:16,063 | ~~~~~^~~~~~ 2024-07-02T14:53:16,065 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofints(int, unsigned int*)’: 2024-07-02T14:53:16,066 moleculekit/fileformats/xtc/src/xdrfile.cpp:505:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:16,067 505 | while (bytes[num_of_bytes] >= num) 2024-07-02T14:53:16,067 | ~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-07-02T14:53:16,070 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘void encodeints(int*, int, int, unsigned int*, unsigned int*)’: 2024-07-02T14:53:16,071 moleculekit/fileformats/xtc/src/xdrfile.cpp:614:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,071 614 | if (num_of_bits >= num_of_bytes * 8) 2024-07-02T14:53:16,072 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-07-02T14:53:16,072 moleculekit/fileformats/xtc/src/xdrfile.cpp:616:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,073 616 | for (i = 0; i < num_of_bytes; i++) 2024-07-02T14:53:16,073 | ~~^~~~~~~~~~~~~~ 2024-07-02T14:53:16,074 moleculekit/fileformats/xtc/src/xdrfile.cpp:624:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,074 624 | for (i = 0; i < num_of_bytes-1; i++) 2024-07-02T14:53:16,075 | ~~^~~~~~~~~~~~~~~~ 2024-07-02T14:53:16,077 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int decodebits(int*, int)’: 2024-07-02T14:53:16,078 moleculekit/fileformats/xtc/src/xdrfile.cpp:664:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:16,078 664 | if (lastbits < num_of_bits) 2024-07-02T14:53:16,079 | ~~~~~~~~~^~~~~~~~~~~~~ 2024-07-02T14:53:16,083 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_decompress_coord_float(float*, int*, float*, XDRFILE*)’: 2024-07-02T14:53:16,084 moleculekit/fileformats/xtc/src/xdrfile.cpp:785:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:16,085 785 | if(size3>xfp->buf1size) 2024-07-02T14:53:16,086 | ~~~~~^~~~~~~~~~~~~~ 2024-07-02T14:53:16,087 moleculekit/fileformats/xtc/src/xdrfile.cpp:842:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:16,088 842 | maxidx = (LASTIDX= size3 ) { return -1; } 2024-07-02T14:53:16,093 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:16,093 moleculekit/fileformats/xtc/src/xdrfile.cpp:935:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,094 935 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:16,094 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:16,095 moleculekit/fileformats/xtc/src/xdrfile.cpp:938:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,096 938 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:16,097 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:16,097 moleculekit/fileformats/xtc/src/xdrfile.cpp:945:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,098 945 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:16,099 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:16,099 moleculekit/fileformats/xtc/src/xdrfile.cpp:948:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,100 948 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:16,100 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:16,101 moleculekit/fileformats/xtc/src/xdrfile.cpp:951:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,101 951 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:16,102 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:16,103 moleculekit/fileformats/xtc/src/xdrfile.cpp:756:24: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-07-02T14:53:16,103 756 | int smallidx, minidx, maxidx; 2024-07-02T14:53:16,104 | ^~~~~~ 2024-07-02T14:53:16,104 moleculekit/fileformats/xtc/src/xdrfile.cpp:759:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-07-02T14:53:16,105 759 | int smallnum, smaller, larger, i, is_smaller, run; 2024-07-02T14:53:16,105 | ^~~~~~ 2024-07-02T14:53:16,106 moleculekit/fileformats/xtc/src/xdrfile.cpp:763:13: warning: unused variable ‘errval’ [-Wunused-variable] 2024-07-02T14:53:16,107 763 | int errval=1; 2024-07-02T14:53:16,108 | ^~~~~~ 2024-07-02T14:53:16,108 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_compress_coord_float(float*, int, float, XDRFILE*)’: 2024-07-02T14:53:16,109 moleculekit/fileformats/xtc/src/xdrfile.cpp:1011:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:16,110 1011 | if(size3>xfp->buf1size) 2024-07-02T14:53:16,111 | ~~~~~^~~~~~~~~~~~~~ 2024-07-02T14:53:16,111 moleculekit/fileformats/xtc/src/xdrfile.cpp:1068:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,112 1068 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-02T14:53:16,113 | ~~~~~~~~^~~~~~~ 2024-07-02T14:53:16,113 moleculekit/fileformats/xtc/src/xdrfile.cpp:1084:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,114 1084 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-02T14:53:16,115 | ~~~~~~~~^~~~~~~ 2024-07-02T14:53:16,115 moleculekit/fileformats/xtc/src/xdrfile.cpp:1098:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,116 1098 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-02T14:53:16,117 | ~~~~~~~~^~~~~~~ 2024-07-02T14:53:16,117 moleculekit/fileformats/xtc/src/xdrfile.cpp:1137:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,118 1137 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2024-07-02T14:53:16,119 | ^ 2024-07-02T14:53:16,120 moleculekit/fileformats/xtc/src/xdrfile.cpp:1143:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:16,120 1143 | maxidx = (LASTIDXxfp->buf1size) 2024-07-02T14:53:16,127 | ~~~~~^~~~~~~~~~~~~~ 2024-07-02T14:53:16,127 moleculekit/fileformats/xtc/src/xdrfile.cpp:1377:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:16,128 1377 | maxidx = (LASTIDXxfp->buf1size) { 2024-07-02T14:53:16,137 | ~~~~~^~~~~~~~~~~~~~ 2024-07-02T14:53:16,138 moleculekit/fileformats/xtc/src/xdrfile.cpp:1628:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:16,138 1628 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2024-07-02T14:53:16,139 | ^ 2024-07-02T14:53:16,140 moleculekit/fileformats/xtc/src/xdrfile.cpp:1633:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:16,140 1633 | maxidx = (LASTIDX= num && num_of_bits < 32) 2024-07-02T14:53:46,355 | ~~~~~^~~~~~ 2024-07-02T14:53:46,356 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofints(int, unsigned int*)’: 2024-07-02T14:53:46,357 moleculekit/fileformats/xtc/src/xdrfile.cpp:505:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:46,357 505 | while (bytes[num_of_bytes] >= num) 2024-07-02T14:53:46,358 | ~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-07-02T14:53:46,359 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘void encodeints(int*, int, int, unsigned int*, unsigned int*)’: 2024-07-02T14:53:46,360 moleculekit/fileformats/xtc/src/xdrfile.cpp:614:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,361 614 | if (num_of_bits >= num_of_bytes * 8) 2024-07-02T14:53:46,362 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-07-02T14:53:46,362 moleculekit/fileformats/xtc/src/xdrfile.cpp:616:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,363 616 | for (i = 0; i < num_of_bytes; i++) 2024-07-02T14:53:46,363 | ~~^~~~~~~~~~~~~~ 2024-07-02T14:53:46,364 moleculekit/fileformats/xtc/src/xdrfile.cpp:624:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,364 624 | for (i = 0; i < num_of_bytes-1; i++) 2024-07-02T14:53:46,365 | ~~^~~~~~~~~~~~~~~~ 2024-07-02T14:53:46,365 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int decodebits(int*, int)’: 2024-07-02T14:53:46,366 moleculekit/fileformats/xtc/src/xdrfile.cpp:664:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:46,367 664 | if (lastbits < num_of_bits) 2024-07-02T14:53:46,367 | ~~~~~~~~~^~~~~~~~~~~~~ 2024-07-02T14:53:46,368 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_decompress_coord_float(float*, int*, float*, XDRFILE*)’: 2024-07-02T14:53:46,368 moleculekit/fileformats/xtc/src/xdrfile.cpp:785:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:46,369 785 | if(size3>xfp->buf1size) 2024-07-02T14:53:46,370 | ~~~~~^~~~~~~~~~~~~~ 2024-07-02T14:53:46,371 moleculekit/fileformats/xtc/src/xdrfile.cpp:842:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:46,371 842 | maxidx = (LASTIDX= size3 ) { return -1; } 2024-07-02T14:53:46,376 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:46,377 moleculekit/fileformats/xtc/src/xdrfile.cpp:935:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,378 935 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:46,379 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:46,379 moleculekit/fileformats/xtc/src/xdrfile.cpp:938:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,380 938 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:46,380 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:46,381 moleculekit/fileformats/xtc/src/xdrfile.cpp:945:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,382 945 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:46,383 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:46,383 moleculekit/fileformats/xtc/src/xdrfile.cpp:948:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,384 948 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:46,385 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:46,386 moleculekit/fileformats/xtc/src/xdrfile.cpp:951:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,386 951 | if(countmjh >= size3 ) { return -1; } 2024-07-02T14:53:46,387 | ~~~~~~~~~^~~~~~~~ 2024-07-02T14:53:46,387 moleculekit/fileformats/xtc/src/xdrfile.cpp:756:24: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-07-02T14:53:46,388 756 | int smallidx, minidx, maxidx; 2024-07-02T14:53:46,388 | ^~~~~~ 2024-07-02T14:53:46,389 moleculekit/fileformats/xtc/src/xdrfile.cpp:759:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-07-02T14:53:46,389 759 | int smallnum, smaller, larger, i, is_smaller, run; 2024-07-02T14:53:46,390 | ^~~~~~ 2024-07-02T14:53:46,391 moleculekit/fileformats/xtc/src/xdrfile.cpp:763:13: warning: unused variable ‘errval’ [-Wunused-variable] 2024-07-02T14:53:46,391 763 | int errval=1; 2024-07-02T14:53:46,392 | ^~~~~~ 2024-07-02T14:53:46,392 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_compress_coord_float(float*, int, float, XDRFILE*)’: 2024-07-02T14:53:46,393 moleculekit/fileformats/xtc/src/xdrfile.cpp:1011:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:46,393 1011 | if(size3>xfp->buf1size) 2024-07-02T14:53:46,394 | ~~~~~^~~~~~~~~~~~~~ 2024-07-02T14:53:46,395 moleculekit/fileformats/xtc/src/xdrfile.cpp:1068:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,395 1068 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-02T14:53:46,396 | ~~~~~~~~^~~~~~~ 2024-07-02T14:53:46,396 moleculekit/fileformats/xtc/src/xdrfile.cpp:1084:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,397 1084 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-02T14:53:46,398 | ~~~~~~~~^~~~~~~ 2024-07-02T14:53:46,399 moleculekit/fileformats/xtc/src/xdrfile.cpp:1098:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,399 1098 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-02T14:53:46,400 | ~~~~~~~~^~~~~~~ 2024-07-02T14:53:46,401 moleculekit/fileformats/xtc/src/xdrfile.cpp:1137:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,402 1137 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2024-07-02T14:53:46,402 | ^ 2024-07-02T14:53:46,403 moleculekit/fileformats/xtc/src/xdrfile.cpp:1143:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:46,404 1143 | maxidx = (LASTIDXxfp->buf1size) 2024-07-02T14:53:46,411 | ~~~~~^~~~~~~~~~~~~~ 2024-07-02T14:53:46,411 moleculekit/fileformats/xtc/src/xdrfile.cpp:1377:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:46,412 1377 | maxidx = (LASTIDXxfp->buf1size) { 2024-07-02T14:53:46,421 | ~~~~~^~~~~~~~~~~~~~ 2024-07-02T14:53:46,422 moleculekit/fileformats/xtc/src/xdrfile.cpp:1628:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:53:46,422 1628 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2024-07-02T14:53:46,423 | ^ 2024-07-02T14:53:46,424 moleculekit/fileformats/xtc/src/xdrfile.cpp:1633:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:53:46,425 1633 | maxidx = (LASTIDX= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; 2024-07-02T14:54:26,702 | ^ 2024-07-02T14:54:26,711 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2024-07-02T14:54:26,712 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-07-02T14:54:26,712 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,722 moleculekit/fileformats/xtc/trr.c:12009:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,723 12009 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-02T14:54:26,723 | ^ 2024-07-02T14:54:26,732 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2024-07-02T14:54:26,733 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-07-02T14:54:26,733 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,734 moleculekit/fileformats/xtc/trr.c:2485:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,735 2485 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-07-02T14:54:26,735 | ^ 2024-07-02T14:54:26,745 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-07-02T14:54:26,745 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-07-02T14:54:26,746 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,756 moleculekit/fileformats/xtc/trr.c:12003:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,756 12003 | __pyx_t_28 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-07-02T14:54:26,757 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-07-02T14:54:26,766 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2024-07-02T14:54:26,766 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-07-02T14:54:26,767 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,777 moleculekit/fileformats/xtc/trr.c:11956:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,777 11956 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; 2024-07-02T14:54:26,778 | ^ 2024-07-02T14:54:26,787 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2024-07-02T14:54:26,787 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-07-02T14:54:26,788 | ^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,798 moleculekit/fileformats/xtc/trr.c:11952:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,798 11952 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-02T14:54:26,799 | ^ 2024-07-02T14:54:26,808 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2024-07-02T14:54:26,808 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-07-02T14:54:26,809 | ^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,810 moleculekit/fileformats/xtc/trr.c:2485:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,810 2485 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-07-02T14:54:26,811 | ^ 2024-07-02T14:54:26,820 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-07-02T14:54:26,820 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-07-02T14:54:26,821 | ^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,831 moleculekit/fileformats/xtc/trr.c:11946:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,831 11946 | __pyx_t_28 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-07-02T14:54:26,832 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-07-02T14:54:26,841 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2024-07-02T14:54:26,842 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-07-02T14:54:26,842 | ^~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,853 moleculekit/fileformats/xtc/trr.c:12345:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,853 12345 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-02T14:54:26,854 | ^ 2024-07-02T14:54:26,863 moleculekit/fileformats/xtc/trr.c:10567:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2024-07-02T14:54:26,864 10567 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-07-02T14:54:26,864 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,875 moleculekit/fileformats/xtc/trr.c:12341:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,876 12341 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-07-02T14:54:26,876 | ^ 2024-07-02T14:54:26,886 moleculekit/fileformats/xtc/trr.c:10567:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2024-07-02T14:54:26,886 10567 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-07-02T14:54:26,887 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,897 moleculekit/fileformats/xtc/trr.c:12186:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,897 12186 | } else if (unlikely(__pyx_t_35 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-02T14:54:26,898 | ^ 2024-07-02T14:54:26,907 moleculekit/fileformats/xtc/trr.c:10563:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2024-07-02T14:54:26,908 10563 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-07-02T14:54:26,908 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,918 moleculekit/fileformats/xtc/trr.c:12182:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,919 12182 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-07-02T14:54:26,919 | ^ 2024-07-02T14:54:26,928 moleculekit/fileformats/xtc/trr.c:10563:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2024-07-02T14:54:26,929 10563 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-07-02T14:54:26,930 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,940 moleculekit/fileformats/xtc/trr.c:12238:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,940 12238 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-02T14:54:26,941 | ^ 2024-07-02T14:54:26,950 moleculekit/fileformats/xtc/trr.c:10547:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2024-07-02T14:54:26,951 10547 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-07-02T14:54:26,951 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:26,961 moleculekit/fileformats/xtc/trr.c:12234:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:26,962 12234 | } else if (unlikely(__pyx_t_35 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-07-02T14:54:26,962 | ^ 2024-07-02T14:54:26,971 moleculekit/fileformats/xtc/trr.c:10547:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2024-07-02T14:54:26,972 10547 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-07-02T14:54:26,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-02T14:54:33,484 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/trr.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/trr.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:54:33,638 building 'moleculekit.dcd' extension 2024-07-02T14:54:33,638 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-02T14:54:33,639 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src 2024-07-02T14:54:33,640 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/dcd -Imoleculekit/fileformats/dcd/include/ -Imoleculekit/fileformats/dcd/ -I/tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/fileformats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/dcd.o 2024-07-02T14:54:34,081 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:54:34,081 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:54:34,082 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:54:34,083 from moleculekit/fileformats/dcd/dcd.c:1256: 2024-07-02T14:54:34,083 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:54:34,084 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:54:34,084 | ^~~~~~~ 2024-07-02T14:54:35,359 In file included from moleculekit/fileformats/dcd/include/dcdplugin.h:1, 2024-07-02T14:54:35,360 from moleculekit/fileformats/dcd/dcd.c:1262: 2024-07-02T14:54:35,360 moleculekit/fileformats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2024-07-02T14:54:35,361 474 | static int fio_write_str(fio_fd fd, const char *str) { 2024-07-02T14:54:35,362 | ^~~~~~~~~~~~~ 2024-07-02T14:54:35,362 moleculekit/fileformats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2024-07-02T14:54:35,363 470 | static int fio_read_int32(fio_fd fd, int *i) { 2024-07-02T14:54:35,364 | ^~~~~~~~~~~~~~ 2024-07-02T14:54:35,365 moleculekit/fileformats/dcd/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 2024-07-02T14:54:35,365 466 | static int fio_write_int32(fio_fd fd, int i) { 2024-07-02T14:54:35,366 | ^~~~~~~~~~~~~~~ 2024-07-02T14:54:35,366 moleculekit/fileformats/dcd/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2024-07-02T14:54:35,367 457 | static fio_size_t fio_ftell(fio_fd fd) { 2024-07-02T14:54:35,367 | ^~~~~~~~~ 2024-07-02T14:54:35,368 moleculekit/fileformats/dcd/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 2024-07-02T14:54:35,368 450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { 2024-07-02T14:54:35,369 | ^~~~~~~~~ 2024-07-02T14:54:35,369 moleculekit/fileformats/dcd/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 2024-07-02T14:54:35,370 415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { 2024-07-02T14:54:35,371 | ^~~~~~~~~ 2024-07-02T14:54:35,371 moleculekit/fileformats/dcd/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2024-07-02T14:54:35,372 394 | static int fio_fclose(fio_fd fd) { 2024-07-02T14:54:35,373 | ^~~~~~~~~~ 2024-07-02T14:54:35,374 moleculekit/fileformats/dcd/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2024-07-02T14:54:35,374 366 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2024-07-02T14:54:35,375 | ^~~~~~~~ 2024-07-02T14:54:49,794 moleculekit/fileformats/dcd/dcd.c: In function ‘__pyx_pf_11moleculekit_3dcd_17DCDTrajectoryFile_18read’: 2024-07-02T14:54:49,795 moleculekit/fileformats/dcd/dcd.c:1158:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:54:49,795 1158 | #define PyInt_FromLong PyLong_FromLong 2024-07-02T14:54:49,796 | ^~~~~~~~~~~~~~~ 2024-07-02T14:54:49,802 moleculekit/fileformats/dcd/dcd.c:8476:7: note: ‘__pyx_v_i’ was declared here 2024-07-02T14:54:49,803 8476 | int __pyx_v_i; 2024-07-02T14:54:49,804 | ^~~~~~~~~ 2024-07-02T14:54:53,144 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/dcd -Imoleculekit/fileformats/dcd/include/ -Imoleculekit/fileformats/dcd/ -I/tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/fileformats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src/dcdplugin.o 2024-07-02T14:54:53,362 moleculekit/fileformats/dcd/src/dcdplugin.c: In function ‘read_dcdheader’: 2024-07-02T14:54:53,363 moleculekit/fileformats/dcd/src/dcdplugin.c:150:55: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:54:53,364 150 | else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) 2024-07-02T14:54:53,364 | ^~ 2024-07-02T14:54:53,365 moleculekit/fileformats/dcd/src/dcdplugin.c:173:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:54:53,366 173 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) 2024-07-02T14:54:53,366 | ^~ 2024-07-02T14:54:53,367 moleculekit/fileformats/dcd/src/dcdplugin.c:194:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:54:53,368 194 | if (input_integer[0] != dcdcordmagic) 2024-07-02T14:54:53,369 | ^~ 2024-07-02T14:54:53,369 moleculekit/fileformats/dcd/src/dcdplugin.c:409:47: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:54:53,370 409 | if ((input_integer[0] + input_integer[1]) != ((*N) - (*NAMNF)) * 4) 2024-07-02T14:54:53,370 | ^~ 2024-07-02T14:54:53,371 moleculekit/fileformats/dcd/src/dcdplugin.c:428:47: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-02T14:54:53,371 428 | if ((input_integer[0] + input_integer[1]) != ((*N) - (*NAMNF)) * 4) 2024-07-02T14:54:53,372 | ^~ 2024-07-02T14:54:53,375 moleculekit/fileformats/dcd/src/dcdplugin.c: In function ‘read_dcdstep’: 2024-07-02T14:54:53,375 moleculekit/fileformats/dcd/src/dcdplugin.c:651:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:54:53,376 651 | if (tmpbuf[i] != sizeof(float) * N) 2024-07-02T14:54:53,376 | ^~ 2024-07-02T14:54:53,377 moleculekit/fileformats/dcd/src/dcdplugin.c:659:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-02T14:54:53,377 659 | if ((tmpbuf[2 * i] + tmpbuf[2 * i + 1]) != sizeof(float) * N) 2024-07-02T14:54:53,378 | ^~ 2024-07-02T14:54:53,404 In file included from moleculekit/fileformats/dcd/src/dcdplugin.c:55: 2024-07-02T14:54:53,405 moleculekit/fileformats/dcd/include/endianswap.h: At top level: 2024-07-02T14:54:53,405 moleculekit/fileformats/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2024-07-02T14:54:53,406 96 | static void swap2_aligned(void *v, long ndata) { 2024-07-02T14:54:53,407 | ^~~~~~~~~~~~~ 2024-07-02T14:54:53,408 moleculekit/fileformats/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2024-07-02T14:54:53,408 32 | static void swap2_unaligned(void *v, long ndata) { 2024-07-02T14:54:53,409 | ^~~~~~~~~~~~~~~ 2024-07-02T14:54:53,410 In file included from moleculekit/fileformats/dcd/src/dcdplugin.c:46: 2024-07-02T14:54:53,410 moleculekit/fileformats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2024-07-02T14:54:53,411 474 | static int fio_write_str(fio_fd fd, const char *str) { 2024-07-02T14:54:53,411 | ^~~~~~~~~~~~~ 2024-07-02T14:54:53,412 moleculekit/fileformats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2024-07-02T14:54:53,413 470 | static int fio_read_int32(fio_fd fd, int *i) { 2024-07-02T14:54:53,413 | ^~~~~~~~~~~~~~ 2024-07-02T14:54:54,687 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/dcd.o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src/dcdplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/dcd.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:54:54,812 building 'moleculekit.binpos' extension 2024-07-02T14:54:54,813 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-02T14:54:54,814 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src 2024-07-02T14:54:54,816 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/binpos -Imoleculekit/fileformats/binpos/include/ -Imoleculekit/fileformats/binpos/ -I/tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/fileformats/binpos/binpos.c -o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/binpos.o 2024-07-02T14:54:55,226 In file included from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-02T14:54:55,226 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-02T14:54:55,227 from /tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-02T14:54:55,227 from moleculekit/fileformats/binpos/binpos.c:1256: 2024-07-02T14:54:55,228 /tmp/pip-build-env-i6d6y4aa/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] 2024-07-02T14:54:55,229 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-02T14:54:55,229 | ^~~~~~~ 2024-07-02T14:55:09,759 In function ‘__pyx_pf_11moleculekit_6binpos_20BINPOSTrajectoryFile_6_read’, 2024-07-02T14:55:09,760 inlined from ‘__pyx_pw_11moleculekit_6binpos_20BINPOSTrajectoryFile_7_read’ at moleculekit/fileformats/binpos/binpos.c:7958:13: 2024-07-02T14:55:09,767 moleculekit/fileformats/binpos/binpos.c:8499:6: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:55:09,768 8499 | if (__pyx_t_1) { 2024-07-02T14:55:09,769 | ^ 2024-07-02T14:55:09,769 moleculekit/fileformats/binpos/binpos.c: In function ‘__pyx_pw_11moleculekit_6binpos_20BINPOSTrajectoryFile_7_read’: 2024-07-02T14:55:09,775 moleculekit/fileformats/binpos/binpos.c:7976:7: note: ‘__pyx_v_status’ was declared here 2024-07-02T14:55:09,776 7976 | int __pyx_v_status; 2024-07-02T14:55:09,777 | ^~~~~~~~~~~~~~ 2024-07-02T14:55:09,777 moleculekit/fileformats/binpos/binpos.c:1158:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-02T14:55:09,778 1158 | #define PyInt_FromLong PyLong_FromLong 2024-07-02T14:55:09,779 | ^~~~~~~~~~~~~~~ 2024-07-02T14:55:09,784 moleculekit/fileformats/binpos/binpos.c:7973:7: note: ‘__pyx_v_i’ was declared here 2024-07-02T14:55:09,785 7973 | int __pyx_v_i; 2024-07-02T14:55:09,785 | ^~~~~~~~~ 2024-07-02T14:55:13,241 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/binpos -Imoleculekit/fileformats/binpos/include/ -Imoleculekit/fileformats/binpos/ -I/tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/fileformats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src/binposplugin.o 2024-07-02T14:55:13,571 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/binpos.o build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src/binposplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/binpos.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:55:13,698 building 'moleculekit.tmalign' extension 2024-07-02T14:55:13,699 creating build/temp.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-02T14:55:13,700 creating build/temp.linux-armv7l-cpython-311/moleculekit/tmalign/src 2024-07-02T14:55:13,701 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/tmalign -Imoleculekit/tmalign/include/ -Imoleculekit/tmalign/ -I/tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/tmalign/src/TMAlign.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/tmalign/src/TMAlign.o -w 2024-07-02T14:55:47,474 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/tmalign -Imoleculekit/tmalign/include/ -Imoleculekit/tmalign/ -I/tmp/pip-build-env-i6d6y4aa/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c moleculekit/tmalign/tmalign_util.cpp -o build/temp.linux-armv7l-cpython-311/moleculekit/tmalign/tmalign_util.o -w 2024-07-02T14:56:10,006 In file included from /usr/include/c++/12/vector:70, 2024-07-02T14:56:10,007 from moleculekit/tmalign/tmalign_util.cpp:1280: 2024-07-02T14:56:10,008 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2024-07-02T14:56:10,008 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-07-02T14:56:10,009 439 | vector<_Tp, _Alloc>:: 2024-07-02T14:56:10,010 | ^~~~~~~~~~~~~~~~~~~ 2024-07-02T14:56:10,810 In file included from /usr/include/c++/12/vector:64: 2024-07-02T14:56:10,810 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-07-02T14:56:10,811 inlined from ‘PyObject* __pyx_pf_11moleculekit_7tmalign_tmalign(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, std::string, std::string)’ at moleculekit/tmalign/tmalign_util.cpp:21233:32, 2024-07-02T14:56:10,812 inlined from ‘PyObject* __pyx_pw_11moleculekit_7tmalign_1tmalign(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at moleculekit/tmalign/tmalign_util.cpp:20718:52: 2024-07-02T14:56:10,812 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-07-02T14:56:10,813 1287 | _M_realloc_insert(end(), __x); 2024-07-02T14:56:10,814 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-02T14:56:10,815 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-07-02T14:56:10,815 inlined from ‘PyObject* __pyx_pf_11moleculekit_7tmalign_tmalign(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, std::string, std::string)’ at moleculekit/tmalign/tmalign_util.cpp:21247:33, 2024-07-02T14:56:10,816 inlined from ‘PyObject* __pyx_pw_11moleculekit_7tmalign_1tmalign(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at moleculekit/tmalign/tmalign_util.cpp:20718:52: 2024-07-02T14:56:10,817 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-07-02T14:56:10,818 1287 | _M_realloc_insert(end(), __x); 2024-07-02T14:56:10,818 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-02T14:56:10,819 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-07-02T14:56:10,820 inlined from ‘PyObject* __pyx_pf_11moleculekit_7tmalign_tmalign(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, std::string, std::string)’ at moleculekit/tmalign/tmalign_util.cpp:21332:34, 2024-07-02T14:56:10,821 inlined from ‘PyObject* __pyx_pw_11moleculekit_7tmalign_1tmalign(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at moleculekit/tmalign/tmalign_util.cpp:20718:52: 2024-07-02T14:56:10,821 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-07-02T14:56:10,822 1287 | _M_realloc_insert(end(), __x); 2024-07-02T14:56:10,823 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-02T14:56:13,185 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/moleculekit/tmalign/src/TMAlign.o build/temp.linux-armv7l-cpython-311/moleculekit/tmalign/tmalign_util.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/moleculekit/tmalign.cpython-311-arm-linux-gnueabihf.so 2024-07-02T14:56:13,570 UPDATING build/lib.linux-armv7l-cpython-311/moleculekit/_version.py 2024-07-02T14:56:13,570 set build/lib.linux-armv7l-cpython-311/moleculekit/_version.py to '1.8.36' 2024-07-02T14:56:13,571 installing to build/bdist.linux-armv7l/wheel 2024-07-02T14:56:13,571 running install 2024-07-02T14:56:13,596 running install_lib 2024-07-02T14:56:13,602 creating build/bdist.linux-armv7l 2024-07-02T14:56:13,602 creating build/bdist.linux-armv7l/wheel 2024-07-02T14:56:13,605 creating build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:13,607 copying build/lib.linux-armv7l-cpython-311/moleculekit/util.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:13,610 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-07-02T14:56:13,612 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign/include 2024-07-02T14:56:13,613 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/include/TMAlign.h -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign/include 2024-07-02T14:56:13,616 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/tmalignlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-07-02T14:56:13,618 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/tmalign_util.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-07-02T14:56:13,641 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign/src 2024-07-02T14:56:13,642 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/src/TMAlign.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign/src 2024-07-02T14:56:13,654 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/tmalign_util.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-07-02T14:56:13,657 creating build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-02T14:56:13,658 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/util.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-02T14:56:13,661 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/smallmollib.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-02T14:56:13,664 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/smallmol.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-02T14:56:13,668 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/test_smallmol.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-02T14:56:13,671 creating build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-02T14:56:13,672 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools/restrainedembed.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-02T14:56:13,674 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools/test_tools.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-02T14:56:13,677 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools/clustering.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-02T14:56:13,680 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-02T14:56:13,682 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-02T14:56:13,684 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/smallmolcdp.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-02T14:56:13,687 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/test_smallmollib.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-02T14:56:13,690 copying build/lib.linux-armv7l-cpython-311/moleculekit/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:13,721 copying build/lib.linux-armv7l-cpython-311/moleculekit/binpos.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:13,733 copying build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:13,735 copying build/lib.linux-armv7l-cpython-311/moleculekit/align.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:13,738 copying build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:13,757 creating build/bdist.linux-armv7l/wheel/moleculekit/share 2024-07-02T14:56:13,758 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/opm_sequences.json -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-07-02T14:56:13,958 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/ALA.cif -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-07-02T14:56:13,960 creating build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr 2024-07-02T14:56:13,964 creating build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,966 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DAB.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,968 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0BN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,969 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BB8.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,971 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/I2M.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,973 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2MR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,975 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/KYN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,977 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/YNM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,979 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2AS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,980 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ONL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,982 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/.gitkeep -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,984 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/M3L.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,985 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PTR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,987 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,989 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TY2.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,991 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PTR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,993 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CGU.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,995 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,996 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/D4P.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:13,998 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ABA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,000 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HOX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,002 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CCS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,004 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/OMX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,005 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NVA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,007 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HHK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,009 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/P1L.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,012 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BCS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,014 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HOX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,015 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/AHP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,017 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NCY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,019 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PRK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,021 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HQA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,022 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HTR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,025 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GHG.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,026 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/APD.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,029 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/D4P.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,030 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TPO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,032 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IML.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,034 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,036 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2MR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,038 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,040 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NLE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,041 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DA2.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,043 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4PH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,045 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/YNM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,047 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NAL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,049 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,051 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/5JP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,052 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/1MH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,054 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,056 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,058 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/OMX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,060 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HHK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,062 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CCS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:14,064 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,718 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TPO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,722 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TRO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,726 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ME0.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,730 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PRK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,734 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DA2.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,739 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,743 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BB8.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,746 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,750 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BTK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,754 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,758 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,762 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/1MH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,765 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/OCY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,769 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NZC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,773 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/P1L.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,777 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,781 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NVA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,784 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IGL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,788 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HLU.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,792 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0A1.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,796 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/FGL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,800 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/KYN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,804 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,808 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ORM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,812 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/004.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,822 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,825 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ONL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,829 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HLX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,832 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0A1.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,842 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IGL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,844 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,847 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IIL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,850 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BCS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,853 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/AA4.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,857 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,859 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2ML.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,862 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ME0.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,865 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2GX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,869 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/FGL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,872 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NLE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,880 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,883 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TRO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,887 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/SEP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,896 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2GX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,899 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HPE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,902 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/004.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,905 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,909 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/I2M.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,912 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CGU.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,916 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HYP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,919 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GNC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,923 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,926 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ABA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,930 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NCY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,933 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MMO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,937 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/YCM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,940 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IIL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,943 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PCA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,946 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BTK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,949 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,952 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,956 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,959 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HTR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,963 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/OCY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,966 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DPP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,978 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NAL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,981 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/M3L.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,984 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,987 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MVA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,990 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2ML.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,993 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NZC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,996 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HQA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:15,999 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ORM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,002 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PCA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,005 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GNC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,008 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0AF.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,011 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HPE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,014 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/5JP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,017 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HLX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,020 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,023 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,027 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,030 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,033 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2AS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,035 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/SEP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,038 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DPP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,041 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/YCM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,044 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HYP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,046 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4PH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,050 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,052 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/03Y.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,056 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TY2.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,059 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,062 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0AF.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,065 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0BN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,068 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,073 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,077 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,080 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,083 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DAH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,086 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MMO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,089 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/AA4.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,093 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,096 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,099 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/AHP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,102 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ESC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,105 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4IN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,108 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,111 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ESC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,114 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DAH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,117 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/03Y.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,120 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,123 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DAB.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,126 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4IN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,129 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HLU.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,132 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MVA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,135 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/APD.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,138 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GHG.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,141 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,144 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,146 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IML.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-02T14:56:16,150 creating build/bdist.linux-armv7l/wheel/moleculekit/share/atomselect 2024-07-02T14:56:16,152 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/atomselect/atomselect.json -> build/bdist.linux-armv7l/wheel/moleculekit/share/atomselect 2024-07-02T14:56:16,154 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/backbone.cif -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-07-02T14:56:16,158 copying build/lib.linux-armv7l-cpython-311/moleculekit/home.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,161 copying build/lib.linux-armv7l-cpython-311/moleculekit/vmdgraphics.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,164 copying build/lib.linux-armv7l-cpython-311/moleculekit/config.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,167 copying build/lib.linux-armv7l-cpython-311/moleculekit/vmd_wrapper -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,171 creating build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-07-02T14:56:16,172 copying build/lib.linux-armv7l-cpython-311/moleculekit/wrapping/wrapping.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-07-02T14:56:16,214 copying build/lib.linux-armv7l-cpython-311/moleculekit/wrapping/wrapping.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-07-02T14:56:16,218 creating build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-07-02T14:56:16,219 copying build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils/distance_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-07-02T14:56:16,286 copying build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils/distance_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-07-02T14:56:16,291 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-07-02T14:56:16,293 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-07-02T14:56:16,295 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/dcd.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-07-02T14:56:16,299 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-02T14:56:16,300 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/fastio.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-02T14:56:16,304 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/largefiles.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-02T14:56:16,307 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/molfile_plugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-02T14:56:16,311 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/dcdplugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-02T14:56:16,314 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/endianswap.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-02T14:56:16,317 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/src 2024-07-02T14:56:16,318 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src/dcdplugin.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/src 2024-07-02T14:56:16,324 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/dcd.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-07-02T14:56:16,343 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/dcdlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-07-02T14:56:16,346 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/utils.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-07-02T14:56:16,350 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/netcdf.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-07-02T14:56:16,353 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-02T14:56:16,354 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/trr.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-02T14:56:16,357 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-02T14:56:16,398 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-02T14:56:16,399 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xtc.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-02T14:56:16,401 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-02T14:56:16,404 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-02T14:56:16,406 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/trr_header.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-02T14:56:16,408 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-02T14:56:16,410 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xdr_seek.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-02T14:56:16,412 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/trr.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-02T14:56:16,441 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/xdrlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-02T14:56:16,442 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/xtclib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-02T14:56:16,445 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/trrlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-02T14:56:16,447 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-02T14:56:16,448 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdr_seek.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-02T14:56:16,451 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-02T14:56:16,453 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-02T14:56:16,457 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-02T14:56:16,459 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-02T14:56:16,462 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/xtc.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-02T14:56:16,464 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-07-02T14:56:16,467 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-07-02T14:56:16,468 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/binposlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-07-02T14:56:16,471 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-07-02T14:56:16,472 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include/binposplugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-07-02T14:56:16,474 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include/largefiles.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-07-02T14:56:16,476 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include/molfile_plugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-07-02T14:56:16,479 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/binpos.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-07-02T14:56:16,482 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/src 2024-07-02T14:56:16,484 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src/binposplugin.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/src 2024-07-02T14:56:16,487 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/binpos.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-07-02T14:56:16,501 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,549 creating build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-07-02T14:56:16,550 copying build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils/occupancy_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-07-02T14:56:16,570 copying build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils/occupancy_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-07-02T14:56:16,572 copying build/lib.linux-armv7l-cpython-311/moleculekit/writers.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,576 copying build/lib.linux-armv7l-cpython-311/moleculekit/version.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,578 copying build/lib.linux-armv7l-cpython-311/moleculekit/wrapping.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,597 copying build/lib.linux-armv7l-cpython-311/moleculekit/molecule.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,602 creating build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-07-02T14:56:16,603 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils/atomselect_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-07-02T14:56:16,632 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils/atomselect_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-07-02T14:56:16,636 creating build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,637 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/docking.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,639 creating build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-07-02T14:56:16,640 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools/obabel_cli.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-07-02T14:56:16,643 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-07-02T14:56:16,645 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/preparation_customres.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,648 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/voxeldescriptors.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,650 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/sequencestructuralalignment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,653 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/preparation.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,656 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/modelling.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,658 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/hhblitsprofile.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,660 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/moleculechecks.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,662 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/autosegment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,665 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/crystalpacking.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,667 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/detect.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,669 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/atomtyper.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,671 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,673 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/graphalignment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-02T14:56:16,676 creating build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-07-02T14:56:16,677 copying build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils/cython_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-07-02T14:56:16,697 copying build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils/cython_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-07-02T14:56:16,700 copying build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,726 copying build/lib.linux-armv7l-cpython-311/moleculekit/vmdviewer.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,729 copying build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,749 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx 2024-07-02T14:56:16,750 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-07-02T14:56:16,751 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-07-02T14:56:16,753 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer/PdbxWriter.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-07-02T14:56:16,756 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-02T14:56:16,757 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests/PdbxWriterTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-02T14:56:16,759 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests/PdbxReaderTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-02T14:56:16,761 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests/PdbxReadWriteTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-02T14:56:16,763 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-02T14:56:16,765 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx 2024-07-02T14:56:16,767 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-02T14:56:16,768 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/PdbxParser.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-02T14:56:16,771 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-02T14:56:16,772 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/PdbxContainers.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-02T14:56:16,775 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/PdbxReader.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-02T14:56:16,778 copying build/lib.linux-armv7l-cpython-311/moleculekit/rcsb.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,781 creating build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-02T14:56:16,782 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect/atomselect.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-02T14:56:16,785 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect/languageparser.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-02T14:56:16,787 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-02T14:56:16,789 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect/analyze.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-02T14:56:16,792 copying build/lib.linux-armv7l-cpython-311/moleculekit/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,794 copying build/lib.linux-armv7l-cpython-311/moleculekit/viewer.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,796 copying build/lib.linux-armv7l-cpython-311/moleculekit/periodictable.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,799 creating build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-07-02T14:56:16,801 copying build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils/bondguesser_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-07-02T14:56:16,803 copying build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils/bondguesser_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-07-02T14:56:16,827 copying build/lib.linux-armv7l-cpython-311/moleculekit/rdkitintegration.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,829 copying build/lib.linux-armv7l-cpython-311/moleculekit/readers.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:16,834 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-02T14:56:16,835 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-07-02T14:56:16,836 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds/hbonds.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-07-02T14:56:16,839 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds/hbonds.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-07-02T14:56:16,860 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-07-02T14:56:16,861 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi/pipi.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-07-02T14:56:16,881 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi/pipi.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-07-02T14:56:16,883 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/interactions.py -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-02T14:56:16,886 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-02T14:56:16,908 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-02T14:56:16,937 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-02T14:56:16,940 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-07-02T14:56:16,941 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole/sigmahole.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-07-02T14:56:16,944 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole/sigmahole.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-07-02T14:56:16,980 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-02T14:56:17,017 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-02T14:56:17,039 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-07-02T14:56:17,039 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi/cationpi.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-07-02T14:56:17,066 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi/cationpi.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-07-02T14:56:17,069 creating build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,070 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/util.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,073 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricshell.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,075 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricsasa.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,078 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricrmsd.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,080 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/projection.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,082 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricsecondarystructure.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,085 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricsphericalcoordinate.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,087 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricgyration.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,089 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricfluctuation.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,092 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metriccoordinate.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,094 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricdistance.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,097 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricdihedral.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,100 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,101 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metrictmscore.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,104 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricplumed2.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-02T14:56:17,107 copying build/lib.linux-armv7l-cpython-311/moleculekit/logging.ini -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,108 copying build/lib.linux-armv7l-cpython-311/moleculekit/distance.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,110 copying build/lib.linux-armv7l-cpython-311/moleculekit/dihedral.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,112 creating build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-07-02T14:56:17,113 copying build/lib.linux-armv7l-cpython-311/moleculekit/ply/yacc.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-07-02T14:56:17,117 copying build/lib.linux-armv7l-cpython-311/moleculekit/ply/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-07-02T14:56:17,118 copying build/lib.linux-armv7l-cpython-311/moleculekit/ply/lex.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-07-02T14:56:17,121 copying build/lib.linux-armv7l-cpython-311/moleculekit/pymolgraphics.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,123 copying build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,157 copying build/lib.linux-armv7l-cpython-311/moleculekit/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,179 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,223 copying build/lib.linux-armv7l-cpython-311/moleculekit/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,255 copying build/lib.linux-armv7l-cpython-311/moleculekit/opm.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,257 copying build/lib.linux-armv7l-cpython-311/moleculekit/_version.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-02T14:56:17,259 running install_egg_info 2024-07-02T14:56:17,264 Copying moleculekit.egg-info to build/bdist.linux-armv7l/wheel/moleculekit-1.8.36-py3.11.egg-info 2024-07-02T14:56:17,277 running install_scripts 2024-07-02T14:56:17,324 creating build/bdist.linux-armv7l/wheel/moleculekit-1.8.36.dist-info/WHEEL 2024-07-02T14:56:17,327 creating '/tmp/pip-wheel-4lop_2xt/.tmp-3sts3sga/moleculekit-1.8.36-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-02T14:56:17,330 adding 'moleculekit/__init__.py' 2024-07-02T14:56:17,331 adding 'moleculekit/_version.py' 2024-07-02T14:56:17,333 adding 'moleculekit/align.py' 2024-07-02T14:56:17,654 adding 'moleculekit/atomselect_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:17,813 adding 'moleculekit/binpos.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:17,819 adding 'moleculekit/bondguesser.py' 2024-07-02T14:56:18,063 adding 'moleculekit/bondguesser_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:18,071 adding 'moleculekit/config.py' 2024-07-02T14:56:18,330 adding 'moleculekit/cython_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:18,490 adding 'moleculekit/dcd.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:18,495 adding 'moleculekit/dihedral.py' 2024-07-02T14:56:18,497 adding 'moleculekit/distance.py' 2024-07-02T14:56:18,814 adding 'moleculekit/distance_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:18,824 adding 'moleculekit/home.py' 2024-07-02T14:56:18,826 adding 'moleculekit/logging.ini' 2024-07-02T14:56:18,840 adding 'moleculekit/molecule.py' 2024-07-02T14:56:19,068 adding 'moleculekit/occupancy_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:19,076 adding 'moleculekit/opm.py' 2024-07-02T14:56:19,078 adding 'moleculekit/periodictable.py' 2024-07-02T14:56:19,079 adding 'moleculekit/pymolgraphics.py' 2024-07-02T14:56:19,081 adding 'moleculekit/rcsb.py' 2024-07-02T14:56:19,082 adding 'moleculekit/rdkitintegration.py' 2024-07-02T14:56:19,096 adding 'moleculekit/readers.py' 2024-07-02T14:56:19,692 adding 'moleculekit/tmalign.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:19,995 adding 'moleculekit/trr.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:20,206 adding 'moleculekit/util.py' 2024-07-02T14:56:20,207 adding 'moleculekit/version.py' 2024-07-02T14:56:20,209 adding 'moleculekit/viewer.py' 2024-07-02T14:56:20,211 adding 'moleculekit/vmd_wrapper' 2024-07-02T14:56:20,212 adding 'moleculekit/vmdgraphics.py' 2024-07-02T14:56:20,215 adding 'moleculekit/vmdviewer.py' 2024-07-02T14:56:20,483 adding 'moleculekit/wrapping.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:20,497 adding 'moleculekit/writers.py' 2024-07-02T14:56:20,757 adding 'moleculekit/xtc.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:20,766 adding 'moleculekit/atomselect/__init__.py' 2024-07-02T14:56:20,767 adding 'moleculekit/atomselect/analyze.py' 2024-07-02T14:56:20,770 adding 'moleculekit/atomselect/atomselect.py' 2024-07-02T14:56:20,772 adding 'moleculekit/atomselect/languageparser.py' 2024-07-02T14:56:20,876 adding 'moleculekit/atomselect_utils/atomselect_utils.cpp' 2024-07-02T14:56:20,887 adding 'moleculekit/atomselect_utils/atomselect_utils.pyx' 2024-07-02T14:56:20,978 adding 'moleculekit/bondguesser_utils/bondguesser_utils.cpp' 2024-07-02T14:56:20,987 adding 'moleculekit/bondguesser_utils/bondguesser_utils.pyx' 2024-07-02T14:56:21,076 adding 'moleculekit/cython_utils/cython_utils.cpp' 2024-07-02T14:56:21,085 adding 'moleculekit/cython_utils/cython_utils.pyx' 2024-07-02T14:56:21,188 adding 'moleculekit/distance_utils/distance_utils.cpp' 2024-07-02T14:56:21,198 adding 'moleculekit/distance_utils/distance_utils.pyx' 2024-07-02T14:56:21,200 adding 'moleculekit/fileformats/__init__.py' 2024-07-02T14:56:21,205 adding 'moleculekit/fileformats/netcdf.py' 2024-07-02T14:56:21,207 adding 'moleculekit/fileformats/utils.py' 2024-07-02T14:56:21,269 adding 'moleculekit/fileformats/binpos/binpos.c' 2024-07-02T14:56:21,276 adding 'moleculekit/fileformats/binpos/binpos.pyx' 2024-07-02T14:56:21,277 adding 'moleculekit/fileformats/binpos/binposlib.pxd' 2024-07-02T14:56:21,279 adding 'moleculekit/fileformats/binpos/include/binposplugin.h' 2024-07-02T14:56:21,280 adding 'moleculekit/fileformats/binpos/include/largefiles.h' 2024-07-02T14:56:21,286 adding 'moleculekit/fileformats/binpos/include/molfile_plugin.h' 2024-07-02T14:56:21,288 adding 'moleculekit/fileformats/binpos/src/binposplugin.c' 2024-07-02T14:56:21,352 adding 'moleculekit/fileformats/dcd/dcd.c' 2024-07-02T14:56:21,359 adding 'moleculekit/fileformats/dcd/dcd.pyx' 2024-07-02T14:56:21,361 adding 'moleculekit/fileformats/dcd/dcdlib.pxd' 2024-07-02T14:56:21,363 adding 'moleculekit/fileformats/dcd/include/dcdplugin.h' 2024-07-02T14:56:21,365 adding 'moleculekit/fileformats/dcd/include/endianswap.h' 2024-07-02T14:56:21,366 adding 'moleculekit/fileformats/dcd/include/fastio.h' 2024-07-02T14:56:21,368 adding 'moleculekit/fileformats/dcd/include/largefiles.h' 2024-07-02T14:56:21,373 adding 'moleculekit/fileformats/dcd/include/molfile_plugin.h' 2024-07-02T14:56:21,378 adding 'moleculekit/fileformats/dcd/src/dcdplugin.c' 2024-07-02T14:56:21,474 adding 'moleculekit/fileformats/xtc/trr.c' 2024-07-02T14:56:21,485 adding 'moleculekit/fileformats/xtc/trr.pyx' 2024-07-02T14:56:21,486 adding 'moleculekit/fileformats/xtc/trrlib.pxd' 2024-07-02T14:56:21,488 adding 'moleculekit/fileformats/xtc/xdrlib.pxd' 2024-07-02T14:56:21,577 adding 'moleculekit/fileformats/xtc/xtc.cpp' 2024-07-02T14:56:21,586 adding 'moleculekit/fileformats/xtc/xtc.pyx' 2024-07-02T14:56:21,587 adding 'moleculekit/fileformats/xtc/xtclib.pxd' 2024-07-02T14:56:21,588 adding 'moleculekit/fileformats/xtc/include/trr_header.h' 2024-07-02T14:56:21,589 adding 'moleculekit/fileformats/xtc/include/xdr_seek.h' 2024-07-02T14:56:21,592 adding 'moleculekit/fileformats/xtc/include/xdrfile.h' 2024-07-02T14:56:21,593 adding 'moleculekit/fileformats/xtc/include/xdrfile_trr.h' 2024-07-02T14:56:21,594 adding 'moleculekit/fileformats/xtc/include/xdrfile_xtc.h' 2024-07-02T14:56:21,596 adding 'moleculekit/fileformats/xtc/include/xtc.h' 2024-07-02T14:56:21,597 adding 'moleculekit/fileformats/xtc/src/xdr_seek.c' 2024-07-02T14:56:21,604 adding 'moleculekit/fileformats/xtc/src/xdrfile.cpp' 2024-07-02T14:56:21,606 adding 'moleculekit/fileformats/xtc/src/xdrfile_trr.c' 2024-07-02T14:56:21,608 adding 'moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp' 2024-07-02T14:56:21,610 adding 'moleculekit/fileformats/xtc/src/xtc.cpp' 2024-07-02T14:56:21,612 adding 'moleculekit/interactions/__init__.py' 2024-07-02T14:56:21,891 adding 'moleculekit/interactions/cationpi.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:22,156 adding 'moleculekit/interactions/hbonds.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:22,167 adding 'moleculekit/interactions/interactions.py' 2024-07-02T14:56:22,444 adding 'moleculekit/interactions/pipi.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:22,726 adding 'moleculekit/interactions/sigmahole.cpython-311-arm-linux-gnueabihf.so' 2024-07-02T14:56:22,827 adding 'moleculekit/interactions/cationpi/cationpi.cpp' 2024-07-02T14:56:22,837 adding 'moleculekit/interactions/cationpi/cationpi.pyx' 2024-07-02T14:56:22,928 adding 'moleculekit/interactions/hbonds/hbonds.cpp' 2024-07-02T14:56:22,937 adding 'moleculekit/interactions/hbonds/hbonds.pyx' 2024-07-02T14:56:23,029 adding 'moleculekit/interactions/pipi/pipi.cpp' 2024-07-02T14:56:23,039 adding 'moleculekit/interactions/pipi/pipi.pyx' 2024-07-02T14:56:23,131 adding 'moleculekit/interactions/sigmahole/sigmahole.cpp' 2024-07-02T14:56:23,140 adding 'moleculekit/interactions/sigmahole/sigmahole.pyx' 2024-07-02T14:56:23,227 adding 'moleculekit/occupancy_utils/occupancy_utils.cpp' 2024-07-02T14:56:23,236 adding 'moleculekit/occupancy_utils/occupancy_utils.pyx' 2024-07-02T14:56:23,237 adding 'moleculekit/pdbx/__init__.py' 2024-07-02T14:56:23,241 adding 'moleculekit/pdbx/reader/PdbxContainers.py' 2024-07-02T14:56:23,244 adding 'moleculekit/pdbx/reader/PdbxParser.py' 2024-07-02T14:56:23,246 adding 'moleculekit/pdbx/reader/PdbxReader.py' 2024-07-02T14:56:23,247 adding 'moleculekit/pdbx/reader/__init__.py' 2024-07-02T14:56:23,249 adding 'moleculekit/pdbx/tests/PdbxReadWriteTests.py' 2024-07-02T14:56:23,251 adding 'moleculekit/pdbx/tests/PdbxReaderTests.py' 2024-07-02T14:56:23,252 adding 'moleculekit/pdbx/tests/PdbxWriterTests.py' 2024-07-02T14:56:23,253 adding 'moleculekit/pdbx/tests/__init__.py' 2024-07-02T14:56:23,255 adding 'moleculekit/pdbx/writer/PdbxWriter.py' 2024-07-02T14:56:23,256 adding 'moleculekit/pdbx/writer/__init__.py' 2024-07-02T14:56:23,258 adding 'moleculekit/ply/__init__.py' 2024-07-02T14:56:23,262 adding 'moleculekit/ply/lex.py' 2024-07-02T14:56:23,274 adding 'moleculekit/ply/yacc.py' 2024-07-02T14:56:23,276 adding 'moleculekit/projections/__init__.py' 2024-07-02T14:56:23,278 adding 'moleculekit/projections/metriccoordinate.py' 2024-07-02T14:56:23,281 adding 'moleculekit/projections/metricdihedral.py' 2024-07-02T14:56:23,285 adding 'moleculekit/projections/metricdistance.py' 2024-07-02T14:56:23,287 adding 'moleculekit/projections/metricfluctuation.py' 2024-07-02T14:56:23,289 adding 'moleculekit/projections/metricgyration.py' 2024-07-02T14:56:23,293 adding 'moleculekit/projections/metricplumed2.py' 2024-07-02T14:56:23,295 adding 'moleculekit/projections/metricrmsd.py' 2024-07-02T14:56:23,297 adding 'moleculekit/projections/metricsasa.py' 2024-07-02T14:56:23,298 adding 'moleculekit/projections/metricsecondarystructure.py' 2024-07-02T14:56:23,300 adding 'moleculekit/projections/metricshell.py' 2024-07-02T14:56:23,301 adding 'moleculekit/projections/metricsphericalcoordinate.py' 2024-07-02T14:56:23,303 adding 'moleculekit/projections/metrictmscore.py' 2024-07-02T14:56:23,304 adding 'moleculekit/projections/projection.py' 2024-07-02T14:56:23,306 adding 'moleculekit/projections/util.py' 2024-07-02T14:56:23,308 adding 'moleculekit/share/ALA.cif' 2024-07-02T14:56:23,309 adding 'moleculekit/share/backbone.cif' 2024-07-02T14:56:24,605 adding 'moleculekit/share/opm_sequences.json' 2024-07-02T14:56:24,690 adding 'moleculekit/share/atomselect/atomselect.json' 2024-07-02T14:56:24,694 adding 'moleculekit/share/pdb2pqr/residues/.gitkeep' 2024-07-02T14:56:24,695 adding 'moleculekit/share/pdb2pqr/residues/004.dat' 2024-07-02T14:56:24,697 adding 'moleculekit/share/pdb2pqr/residues/004.xml' 2024-07-02T14:56:24,698 adding 'moleculekit/share/pdb2pqr/residues/03Y.dat' 2024-07-02T14:56:24,699 adding 'moleculekit/share/pdb2pqr/residues/03Y.xml' 2024-07-02T14:56:24,700 adding 'moleculekit/share/pdb2pqr/residues/0A1.dat' 2024-07-02T14:56:24,701 adding 'moleculekit/share/pdb2pqr/residues/0A1.xml' 2024-07-02T14:56:24,703 adding 'moleculekit/share/pdb2pqr/residues/0AF.dat' 2024-07-02T14:56:24,704 adding 'moleculekit/share/pdb2pqr/residues/0AF.xml' 2024-07-02T14:56:24,705 adding 'moleculekit/share/pdb2pqr/residues/0BN.dat' 2024-07-02T14:56:24,706 adding 'moleculekit/share/pdb2pqr/residues/0BN.xml' 2024-07-02T14:56:24,707 adding 'moleculekit/share/pdb2pqr/residues/1MH.dat' 2024-07-02T14:56:24,709 adding 'moleculekit/share/pdb2pqr/residues/1MH.xml' 2024-07-02T14:56:24,710 adding 'moleculekit/share/pdb2pqr/residues/2AS.dat' 2024-07-02T14:56:24,711 adding 'moleculekit/share/pdb2pqr/residues/2AS.xml' 2024-07-02T14:56:24,713 adding 'moleculekit/share/pdb2pqr/residues/2GX.dat' 2024-07-02T14:56:24,714 adding 'moleculekit/share/pdb2pqr/residues/2GX.xml' 2024-07-02T14:56:24,715 adding 'moleculekit/share/pdb2pqr/residues/2ML.dat' 2024-07-02T14:56:24,716 adding 'moleculekit/share/pdb2pqr/residues/2ML.xml' 2024-07-02T14:56:24,718 adding 'moleculekit/share/pdb2pqr/residues/2MR.dat' 2024-07-02T14:56:24,719 adding 'moleculekit/share/pdb2pqr/residues/2MR.xml' 2024-07-02T14:56:24,720 adding 'moleculekit/share/pdb2pqr/residues/4IN.dat' 2024-07-02T14:56:24,721 adding 'moleculekit/share/pdb2pqr/residues/4IN.xml' 2024-07-02T14:56:24,723 adding 'moleculekit/share/pdb2pqr/residues/4PH.dat' 2024-07-02T14:56:24,724 adding 'moleculekit/share/pdb2pqr/residues/4PH.xml' 2024-07-02T14:56:24,725 adding 'moleculekit/share/pdb2pqr/residues/4PQ.dat' 2024-07-02T14:56:24,726 adding 'moleculekit/share/pdb2pqr/residues/4PQ.xml' 2024-07-02T14:56:24,728 adding 'moleculekit/share/pdb2pqr/residues/5JP.dat' 2024-07-02T14:56:24,729 adding 'moleculekit/share/pdb2pqr/residues/5JP.xml' 2024-07-02T14:56:24,730 adding 'moleculekit/share/pdb2pqr/residues/AA4.dat' 2024-07-02T14:56:24,731 adding 'moleculekit/share/pdb2pqr/residues/AA4.xml' 2024-07-02T14:56:24,732 adding 'moleculekit/share/pdb2pqr/residues/ABA.dat' 2024-07-02T14:56:24,734 adding 'moleculekit/share/pdb2pqr/residues/ABA.xml' 2024-07-02T14:56:24,735 adding 'moleculekit/share/pdb2pqr/residues/AHP.dat' 2024-07-02T14:56:24,736 adding 'moleculekit/share/pdb2pqr/residues/AHP.xml' 2024-07-02T14:56:24,737 adding 'moleculekit/share/pdb2pqr/residues/ALC.dat' 2024-07-02T14:56:24,739 adding 'moleculekit/share/pdb2pqr/residues/ALC.xml' 2024-07-02T14:56:24,740 adding 'moleculekit/share/pdb2pqr/residues/ALN.dat' 2024-07-02T14:56:24,741 adding 'moleculekit/share/pdb2pqr/residues/ALN.xml' 2024-07-02T14:56:24,743 adding 'moleculekit/share/pdb2pqr/residues/ALY.dat' 2024-07-02T14:56:24,744 adding 'moleculekit/share/pdb2pqr/residues/ALY.xml' 2024-07-02T14:56:24,745 adding 'moleculekit/share/pdb2pqr/residues/APD.dat' 2024-07-02T14:56:24,747 adding 'moleculekit/share/pdb2pqr/residues/APD.xml' 2024-07-02T14:56:24,748 adding 'moleculekit/share/pdb2pqr/residues/BB8.dat' 2024-07-02T14:56:24,749 adding 'moleculekit/share/pdb2pqr/residues/BB8.xml' 2024-07-02T14:56:24,750 adding 'moleculekit/share/pdb2pqr/residues/BCS.dat' 2024-07-02T14:56:24,751 adding 'moleculekit/share/pdb2pqr/residues/BCS.xml' 2024-07-02T14:56:24,753 adding 'moleculekit/share/pdb2pqr/residues/BTK.dat' 2024-07-02T14:56:24,754 adding 'moleculekit/share/pdb2pqr/residues/BTK.xml' 2024-07-02T14:56:24,755 adding 'moleculekit/share/pdb2pqr/residues/CCS.dat' 2024-07-02T14:56:24,756 adding 'moleculekit/share/pdb2pqr/residues/CCS.xml' 2024-07-02T14:56:24,757 adding 'moleculekit/share/pdb2pqr/residues/CGU.dat' 2024-07-02T14:56:24,758 adding 'moleculekit/share/pdb2pqr/residues/CGU.xml' 2024-07-02T14:56:24,760 adding 'moleculekit/share/pdb2pqr/residues/CSA.dat' 2024-07-02T14:56:24,761 adding 'moleculekit/share/pdb2pqr/residues/CSA.xml' 2024-07-02T14:56:24,762 adding 'moleculekit/share/pdb2pqr/residues/CSO.dat' 2024-07-02T14:56:24,763 adding 'moleculekit/share/pdb2pqr/residues/CSO.xml' 2024-07-02T14:56:24,764 adding 'moleculekit/share/pdb2pqr/residues/CSP.dat' 2024-07-02T14:56:24,766 adding 'moleculekit/share/pdb2pqr/residues/CSP.xml' 2024-07-02T14:56:24,767 adding 'moleculekit/share/pdb2pqr/residues/CSS.dat' 2024-07-02T14:56:24,768 adding 'moleculekit/share/pdb2pqr/residues/CSS.xml' 2024-07-02T14:56:24,769 adding 'moleculekit/share/pdb2pqr/residues/D4P.dat' 2024-07-02T14:56:24,770 adding 'moleculekit/share/pdb2pqr/residues/D4P.xml' 2024-07-02T14:56:24,771 adding 'moleculekit/share/pdb2pqr/residues/DA2.dat' 2024-07-02T14:56:24,773 adding 'moleculekit/share/pdb2pqr/residues/DA2.xml' 2024-07-02T14:56:24,774 adding 'moleculekit/share/pdb2pqr/residues/DAB.dat' 2024-07-02T14:56:24,775 adding 'moleculekit/share/pdb2pqr/residues/DAB.xml' 2024-07-02T14:56:24,776 adding 'moleculekit/share/pdb2pqr/residues/DAH.dat' 2024-07-02T14:56:24,778 adding 'moleculekit/share/pdb2pqr/residues/DAH.xml' 2024-07-02T14:56:24,779 adding 'moleculekit/share/pdb2pqr/residues/DPP.dat' 2024-07-02T14:56:24,780 adding 'moleculekit/share/pdb2pqr/residues/DPP.xml' 2024-07-02T14:56:24,781 adding 'moleculekit/share/pdb2pqr/residues/ESC.dat' 2024-07-02T14:56:24,783 adding 'moleculekit/share/pdb2pqr/residues/ESC.xml' 2024-07-02T14:56:24,784 adding 'moleculekit/share/pdb2pqr/residues/FGL.dat' 2024-07-02T14:56:24,785 adding 'moleculekit/share/pdb2pqr/residues/FGL.xml' 2024-07-02T14:56:24,786 adding 'moleculekit/share/pdb2pqr/residues/GHG.dat' 2024-07-02T14:56:24,787 adding 'moleculekit/share/pdb2pqr/residues/GHG.xml' 2024-07-02T14:56:24,789 adding 'moleculekit/share/pdb2pqr/residues/GME.dat' 2024-07-02T14:56:24,790 adding 'moleculekit/share/pdb2pqr/residues/GME.xml' 2024-07-02T14:56:24,791 adding 'moleculekit/share/pdb2pqr/residues/GNC.dat' 2024-07-02T14:56:24,792 adding 'moleculekit/share/pdb2pqr/residues/GNC.xml' 2024-07-02T14:56:24,794 adding 'moleculekit/share/pdb2pqr/residues/HHK.dat' 2024-07-02T14:56:24,795 adding 'moleculekit/share/pdb2pqr/residues/HHK.xml' 2024-07-02T14:56:24,796 adding 'moleculekit/share/pdb2pqr/residues/HLU.dat' 2024-07-02T14:56:24,797 adding 'moleculekit/share/pdb2pqr/residues/HLU.xml' 2024-07-02T14:56:24,799 adding 'moleculekit/share/pdb2pqr/residues/HLX.dat' 2024-07-02T14:56:24,800 adding 'moleculekit/share/pdb2pqr/residues/HLX.xml' 2024-07-02T14:56:24,801 adding 'moleculekit/share/pdb2pqr/residues/HOX.dat' 2024-07-02T14:56:24,802 adding 'moleculekit/share/pdb2pqr/residues/HOX.xml' 2024-07-02T14:56:24,803 adding 'moleculekit/share/pdb2pqr/residues/HPE.dat' 2024-07-02T14:56:24,805 adding 'moleculekit/share/pdb2pqr/residues/HPE.xml' 2024-07-02T14:56:24,806 adding 'moleculekit/share/pdb2pqr/residues/HQA.dat' 2024-07-02T14:56:24,807 adding 'moleculekit/share/pdb2pqr/residues/HQA.xml' 2024-07-02T14:56:24,808 adding 'moleculekit/share/pdb2pqr/residues/HTR.dat' 2024-07-02T14:56:24,810 adding 'moleculekit/share/pdb2pqr/residues/HTR.xml' 2024-07-02T14:56:24,811 adding 'moleculekit/share/pdb2pqr/residues/HYP.dat' 2024-07-02T14:56:24,812 adding 'moleculekit/share/pdb2pqr/residues/HYP.xml' 2024-07-02T14:56:24,813 adding 'moleculekit/share/pdb2pqr/residues/I2M.dat' 2024-07-02T14:56:24,814 adding 'moleculekit/share/pdb2pqr/residues/I2M.xml' 2024-07-02T14:56:24,815 adding 'moleculekit/share/pdb2pqr/residues/IGL.dat' 2024-07-02T14:56:24,817 adding 'moleculekit/share/pdb2pqr/residues/IGL.xml' 2024-07-02T14:56:24,818 adding 'moleculekit/share/pdb2pqr/residues/IIL.dat' 2024-07-02T14:56:24,819 adding 'moleculekit/share/pdb2pqr/residues/IIL.xml' 2024-07-02T14:56:24,820 adding 'moleculekit/share/pdb2pqr/residues/IML.dat' 2024-07-02T14:56:24,822 adding 'moleculekit/share/pdb2pqr/residues/IML.xml' 2024-07-02T14:56:24,823 adding 'moleculekit/share/pdb2pqr/residues/KYN.dat' 2024-07-02T14:56:24,824 adding 'moleculekit/share/pdb2pqr/residues/KYN.xml' 2024-07-02T14:56:24,825 adding 'moleculekit/share/pdb2pqr/residues/LME.dat' 2024-07-02T14:56:24,826 adding 'moleculekit/share/pdb2pqr/residues/LME.xml' 2024-07-02T14:56:24,828 adding 'moleculekit/share/pdb2pqr/residues/LMQ.dat' 2024-07-02T14:56:24,829 adding 'moleculekit/share/pdb2pqr/residues/LMQ.xml' 2024-07-02T14:56:24,830 adding 'moleculekit/share/pdb2pqr/residues/LYZ.dat' 2024-07-02T14:56:24,831 adding 'moleculekit/share/pdb2pqr/residues/LYZ.xml' 2024-07-02T14:56:24,832 adding 'moleculekit/share/pdb2pqr/residues/M3L.dat' 2024-07-02T14:56:24,834 adding 'moleculekit/share/pdb2pqr/residues/M3L.xml' 2024-07-02T14:56:24,835 adding 'moleculekit/share/pdb2pqr/residues/ME0.dat' 2024-07-02T14:56:24,837 adding 'moleculekit/share/pdb2pqr/residues/ME0.xml' 2024-07-02T14:56:24,838 adding 'moleculekit/share/pdb2pqr/residues/MEA.dat' 2024-07-02T14:56:24,839 adding 'moleculekit/share/pdb2pqr/residues/MEA.xml' 2024-07-02T14:56:24,840 adding 'moleculekit/share/pdb2pqr/residues/MEN.dat' 2024-07-02T14:56:24,842 adding 'moleculekit/share/pdb2pqr/residues/MEN.xml' 2024-07-02T14:56:24,843 adding 'moleculekit/share/pdb2pqr/residues/MEQ.dat' 2024-07-02T14:56:24,844 adding 'moleculekit/share/pdb2pqr/residues/MEQ.xml' 2024-07-02T14:56:24,845 adding 'moleculekit/share/pdb2pqr/residues/MLE.dat' 2024-07-02T14:56:24,847 adding 'moleculekit/share/pdb2pqr/residues/MLE.xml' 2024-07-02T14:56:24,848 adding 'moleculekit/share/pdb2pqr/residues/MLY.dat' 2024-07-02T14:56:24,849 adding 'moleculekit/share/pdb2pqr/residues/MLY.xml' 2024-07-02T14:56:24,850 adding 'moleculekit/share/pdb2pqr/residues/MLZ.dat' 2024-07-02T14:56:24,852 adding 'moleculekit/share/pdb2pqr/residues/MLZ.xml' 2024-07-02T14:56:24,853 adding 'moleculekit/share/pdb2pqr/residues/MME.dat' 2024-07-02T14:56:24,854 adding 'moleculekit/share/pdb2pqr/residues/MME.xml' 2024-07-02T14:56:24,855 adding 'moleculekit/share/pdb2pqr/residues/MMO.dat' 2024-07-02T14:56:24,857 adding 'moleculekit/share/pdb2pqr/residues/MMO.xml' 2024-07-02T14:56:24,858 adding 'moleculekit/share/pdb2pqr/residues/MVA.dat' 2024-07-02T14:56:24,859 adding 'moleculekit/share/pdb2pqr/residues/MVA.xml' 2024-07-02T14:56:24,860 adding 'moleculekit/share/pdb2pqr/residues/NAL.dat' 2024-07-02T14:56:24,862 adding 'moleculekit/share/pdb2pqr/residues/NAL.xml' 2024-07-02T14:56:24,863 adding 'moleculekit/share/pdb2pqr/residues/NCY.dat' 2024-07-02T14:56:24,864 adding 'moleculekit/share/pdb2pqr/residues/NCY.xml' 2024-07-02T14:56:24,865 adding 'moleculekit/share/pdb2pqr/residues/NLE.dat' 2024-07-02T14:56:24,867 adding 'moleculekit/share/pdb2pqr/residues/NLE.xml' 2024-07-02T14:56:24,868 adding 'moleculekit/share/pdb2pqr/residues/NVA.dat' 2024-07-02T14:56:24,869 adding 'moleculekit/share/pdb2pqr/residues/NVA.xml' 2024-07-02T14:56:24,870 adding 'moleculekit/share/pdb2pqr/residues/NZC.dat' 2024-07-02T14:56:24,871 adding 'moleculekit/share/pdb2pqr/residues/NZC.xml' 2024-07-02T14:56:24,873 adding 'moleculekit/share/pdb2pqr/residues/OCY.dat' 2024-07-02T14:56:24,874 adding 'moleculekit/share/pdb2pqr/residues/OCY.xml' 2024-07-02T14:56:24,875 adding 'moleculekit/share/pdb2pqr/residues/OMX.dat' 2024-07-02T14:56:24,876 adding 'moleculekit/share/pdb2pqr/residues/OMX.xml' 2024-07-02T14:56:24,877 adding 'moleculekit/share/pdb2pqr/residues/ONL.dat' 2024-07-02T14:56:24,879 adding 'moleculekit/share/pdb2pqr/residues/ONL.xml' 2024-07-02T14:56:24,880 adding 'moleculekit/share/pdb2pqr/residues/ORM.dat' 2024-07-02T14:56:24,881 adding 'moleculekit/share/pdb2pqr/residues/ORM.xml' 2024-07-02T14:56:24,882 adding 'moleculekit/share/pdb2pqr/residues/P1L.dat' 2024-07-02T14:56:24,884 adding 'moleculekit/share/pdb2pqr/residues/P1L.xml' 2024-07-02T14:56:24,885 adding 'moleculekit/share/pdb2pqr/residues/PCA.dat' 2024-07-02T14:56:24,886 adding 'moleculekit/share/pdb2pqr/residues/PCA.xml' 2024-07-02T14:56:24,887 adding 'moleculekit/share/pdb2pqr/residues/PRK.dat' 2024-07-02T14:56:24,889 adding 'moleculekit/share/pdb2pqr/residues/PRK.xml' 2024-07-02T14:56:24,890 adding 'moleculekit/share/pdb2pqr/residues/PTR.dat' 2024-07-02T14:56:24,891 adding 'moleculekit/share/pdb2pqr/residues/PTR.xml' 2024-07-02T14:56:24,892 adding 'moleculekit/share/pdb2pqr/residues/SEP.dat' 2024-07-02T14:56:24,894 adding 'moleculekit/share/pdb2pqr/residues/SEP.xml' 2024-07-02T14:56:24,895 adding 'moleculekit/share/pdb2pqr/residues/TPO.dat' 2024-07-02T14:56:24,896 adding 'moleculekit/share/pdb2pqr/residues/TPO.xml' 2024-07-02T14:56:24,897 adding 'moleculekit/share/pdb2pqr/residues/TRO.dat' 2024-07-02T14:56:24,899 adding 'moleculekit/share/pdb2pqr/residues/TRO.xml' 2024-07-02T14:56:24,900 adding 'moleculekit/share/pdb2pqr/residues/TY2.dat' 2024-07-02T14:56:24,901 adding 'moleculekit/share/pdb2pqr/residues/TY2.xml' 2024-07-02T14:56:24,902 adding 'moleculekit/share/pdb2pqr/residues/TYQ.dat' 2024-07-02T14:56:24,904 adding 'moleculekit/share/pdb2pqr/residues/TYQ.xml' 2024-07-02T14:56:24,905 adding 'moleculekit/share/pdb2pqr/residues/YCM.dat' 2024-07-02T14:56:24,906 adding 'moleculekit/share/pdb2pqr/residues/YCM.xml' 2024-07-02T14:56:24,907 adding 'moleculekit/share/pdb2pqr/residues/YNM.dat' 2024-07-02T14:56:24,909 adding 'moleculekit/share/pdb2pqr/residues/YNM.xml' 2024-07-02T14:56:24,911 adding 'moleculekit/smallmol/__init__.py' 2024-07-02T14:56:24,916 adding 'moleculekit/smallmol/smallmol.py' 2024-07-02T14:56:24,918 adding 'moleculekit/smallmol/smallmolcdp.py' 2024-07-02T14:56:24,920 adding 'moleculekit/smallmol/smallmollib.py' 2024-07-02T14:56:24,922 adding 'moleculekit/smallmol/test_smallmol.py' 2024-07-02T14:56:24,923 adding 'moleculekit/smallmol/test_smallmollib.py' 2024-07-02T14:56:24,925 adding 'moleculekit/smallmol/util.py' 2024-07-02T14:56:24,927 adding 'moleculekit/smallmol/tools/__init__.py' 2024-07-02T14:56:24,929 adding 'moleculekit/smallmol/tools/clustering.py' 2024-07-02T14:56:24,931 adding 'moleculekit/smallmol/tools/restrainedembed.py' 2024-07-02T14:56:24,932 adding 'moleculekit/smallmol/tools/test_tools.py' 2024-07-02T14:56:25,023 adding 'moleculekit/tmalign/tmalign_util.cpp' 2024-07-02T14:56:25,032 adding 'moleculekit/tmalign/tmalign_util.pyx' 2024-07-02T14:56:25,033 adding 'moleculekit/tmalign/tmalignlib.pxd' 2024-07-02T14:56:25,035 adding 'moleculekit/tmalign/include/TMAlign.h' 2024-07-02T14:56:25,052 adding 'moleculekit/tmalign/src/TMAlign.cpp' 2024-07-02T14:56:25,055 adding 'moleculekit/tools/__init__.py' 2024-07-02T14:56:25,057 adding 'moleculekit/tools/atomtyper.py' 2024-07-02T14:56:25,059 adding 'moleculekit/tools/autosegment.py' 2024-07-02T14:56:25,061 adding 'moleculekit/tools/crystalpacking.py' 2024-07-02T14:56:25,065 adding 'moleculekit/tools/detect.py' 2024-07-02T14:56:25,067 adding 'moleculekit/tools/docking.py' 2024-07-02T14:56:25,069 adding 'moleculekit/tools/graphalignment.py' 2024-07-02T14:56:25,071 adding 'moleculekit/tools/hhblitsprofile.py' 2024-07-02T14:56:25,072 adding 'moleculekit/tools/modelling.py' 2024-07-02T14:56:25,074 adding 'moleculekit/tools/moleculechecks.py' 2024-07-02T14:56:25,080 adding 'moleculekit/tools/preparation.py' 2024-07-02T14:56:25,083 adding 'moleculekit/tools/preparation_customres.py' 2024-07-02T14:56:25,084 adding 'moleculekit/tools/sequencestructuralalignment.py' 2024-07-02T14:56:25,087 adding 'moleculekit/tools/voxeldescriptors.py' 2024-07-02T14:56:25,089 adding 'moleculekit/tools/obabel_tools/__init__.py' 2024-07-02T14:56:25,090 adding 'moleculekit/tools/obabel_tools/obabel_cli.py' 2024-07-02T14:56:25,182 adding 'moleculekit/wrapping/wrapping.cpp' 2024-07-02T14:56:25,192 adding 'moleculekit/wrapping/wrapping.pyx' 2024-07-02T14:56:25,194 adding 'moleculekit-1.8.36.dist-info/LICENSE' 2024-07-02T14:56:25,195 adding 'moleculekit-1.8.36.dist-info/METADATA' 2024-07-02T14:56:25,196 adding 'moleculekit-1.8.36.dist-info/WHEEL' 2024-07-02T14:56:25,197 adding 'moleculekit-1.8.36.dist-info/top_level.txt' 2024-07-02T14:56:25,202 adding 'moleculekit-1.8.36.dist-info/RECORD' 2024-07-02T14:56:25,365 removing build/bdist.linux-armv7l/wheel 2024-07-02T14:56:25,659 Building wheel for moleculekit (pyproject.toml): finished with status 'done' 2024-07-02T14:56:26,004 Created wheel for moleculekit: filename=moleculekit-1.8.36-cp311-cp311-linux_armv7l.whl size=15296020 sha256=e0fa24f661e395d9f38f9e1616422ff28e4ed401dd67c35c172ffccf1ea54038 2024-07-02T14:56:26,005 Stored in directory: /tmp/pip-ephem-wheel-cache-gw4j272b/wheels/88/63/97/ea5c9007def8d0c921c72f908d2bb60ad96b96488b2e4cfdf6 2024-07-02T14:56:26,031 Successfully built moleculekit 2024-07-02T14:56:26,644 Removed build tracker: '/tmp/pip-build-tracker-ft_geqt3'