2024-07-11T12:07:22,223 Created temporary directory: /tmp/pip-build-tracker-r3t0f_85 2024-07-11T12:07:22,224 Initialized build tracking at /tmp/pip-build-tracker-r3t0f_85 2024-07-11T12:07:22,224 Created build tracker: /tmp/pip-build-tracker-r3t0f_85 2024-07-11T12:07:22,225 Entered build tracker: /tmp/pip-build-tracker-r3t0f_85 2024-07-11T12:07:22,226 Created temporary directory: /tmp/pip-wheel-4_rdb_a8 2024-07-11T12:07:22,229 Created temporary directory: /tmp/pip-ephem-wheel-cache-3hu4ir25 2024-07-11T12:07:22,253 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-11T12:07:22,256 2 location(s) to search for versions of moleculekit: 2024-07-11T12:07:22,256 * https://pypi.org/simple/moleculekit/ 2024-07-11T12:07:22,256 * https://www.piwheels.org/simple/moleculekit/ 2024-07-11T12:07:22,257 Fetching project page and analyzing links: https://pypi.org/simple/moleculekit/ 2024-07-11T12:07:22,258 Getting page https://pypi.org/simple/moleculekit/ 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2024-07-11T12:07:22,721 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 2024-07-11T12:07:22,721 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 2024-07-11T12:07:22,722 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 2024-07-11T12:07:22,723 Found link https://files.pythonhosted.org/packages/38/d6/30462b4aeb3cb9ae0244bc9882779d3249e39393f5ea71c6abc2d36bb1ed/moleculekit-1.9.0.tar.gz (from https://pypi.org/simple/moleculekit/) (requires-python:>=3.8), version: 1.9.0 2024-07-11T12:07:22,724 Found link https://files.pythonhosted.org/packages/03/ac/c81679ee7481d8dd7e0fa576dafe3963c48c065ab2ca808b53f59693c211/moleculekit-1.9.1.tar.gz (from https://pypi.org/simple/moleculekit/) (requires-python:>=3.8), version: 1.9.1 2024-07-11T12:07:22,725 Fetching project page and analyzing links: https://www.piwheels.org/simple/moleculekit/ 2024-07-11T12:07:22,726 Getting page https://www.piwheels.org/simple/moleculekit/ 2024-07-11T12:07:22,727 Found index url https://www.piwheels.org/simple/ 2024-07-11T12:07:22,903 Fetched page https://www.piwheels.org/simple/moleculekit/ as text/html 2024-07-11T12:07:22,998 Skipping link: No binaries permitted for moleculekit: https://www.piwheels.org/simple/moleculekit/moleculekit-1.8.36-cp311-cp311-linux_armv6l.whl#sha256=e0fa24f661e395d9f38f9e1616422ff28e4ed401dd67c35c172ffccf1ea54038 (from https://www.piwheels.org/simple/moleculekit/) (requires-python:>=3.8) 2024-07-11T12:07:22,999 Skipping link: No binaries 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links for project 'moleculekit': discarding no candidates 2024-07-11T12:07:23,289 Collecting moleculekit==1.9.0 2024-07-11T12:07:23,292 Created temporary directory: /tmp/pip-unpack-t7ie1l20 2024-07-11T12:07:23,510 Downloading moleculekit-1.9.0.tar.gz (6.8 MB) 2024-07-11T12:07:25,992 Added moleculekit==1.9.0 from https://files.pythonhosted.org/packages/38/d6/30462b4aeb3cb9ae0244bc9882779d3249e39393f5ea71c6abc2d36bb1ed/moleculekit-1.9.0.tar.gz to build tracker '/tmp/pip-build-tracker-r3t0f_85' 2024-07-11T12:07:26,001 Created temporary directory: /tmp/pip-build-env-kqb5ac4z 2024-07-11T12:07:26,005 Installing build dependencies: started 2024-07-11T12:07:26,006 Running command pip subprocess to install build dependencies 2024-07-11T12:07:27,171 Using pip 24.0 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-07-11T12:07:27,709 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-11T12:07:29,157 Collecting setuptools 2024-07-11T12:07:29,172 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.3.0-py3-none-any.whl (931 kB) 2024-07-11T12:07:29,838 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) 2024-07-11T12:07:29,842 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) 2024-07-11T12:07:29,846 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) 2024-07-11T12:07:29,850 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) 2024-07-11T12:07:29,853 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) 2024-07-11T12:07:30,155 Collecting numpy>=1.18.5 2024-07-11T12:07:30,170 Using cached https://www.piwheels.org/simple/numpy/numpy-2.0.0-cp311-cp311-linux_armv7l.whl (5.9 MB) 2024-07-11T12:07:31,639 Collecting Cython>=0.29.21 2024-07-11T12:07:31,654 Using cached https://www.piwheels.org/simple/cython/Cython-3.0.10-cp311-cp311-linux_armv7l.whl (11.8 MB) 2024-07-11T12:07:32,057 Collecting toml 2024-07-11T12:07:32,073 Using cached https://www.piwheels.org/simple/toml/toml-0.10.2-py2.py3-none-any.whl (16 kB) 2024-07-11T12:07:32,266 Collecting versioneer==0.28 (from versioneer[toml]==0.28) 2024-07-11T12:07:32,283 Using cached https://www.piwheels.org/simple/versioneer/versioneer-0.28-py3-none-any.whl (45 kB) 2024-07-11T12:07:34,922 Installing collected packages: versioneer, toml, setuptools, numpy, Cython 2024-07-11T12:07:34,955 Creating /tmp/pip-build-env-kqb5ac4z/overlay/local/bin 2024-07-11T12:07:34,957 changing mode of /tmp/pip-build-env-kqb5ac4z/overlay/local/bin/versioneer to 755 2024-07-11T12:07:45,918 changing mode of /tmp/pip-build-env-kqb5ac4z/overlay/local/bin/f2py to 755 2024-07-11T12:07:45,920 changing mode of /tmp/pip-build-env-kqb5ac4z/overlay/local/bin/numpy-config to 755 2024-07-11T12:07:49,556 changing mode of /tmp/pip-build-env-kqb5ac4z/overlay/local/bin/cygdb to 755 2024-07-11T12:07:49,558 changing mode of /tmp/pip-build-env-kqb5ac4z/overlay/local/bin/cython to 755 2024-07-11T12:07:49,560 changing mode of /tmp/pip-build-env-kqb5ac4z/overlay/local/bin/cythonize to 755 2024-07-11T12:07:49,604 Successfully installed Cython-3.0.10 numpy-2.0.0 setuptools-70.3.0 toml-0.10.2 versioneer-0.28 2024-07-11T12:07:49,914 [notice] A new release of pip is available: 24.0 -> 24.1.2 2024-07-11T12:07:49,914 [notice] To update, run: python3 -m pip install --upgrade pip 2024-07-11T12:07:50,368 Installing build dependencies: finished with status 'done' 2024-07-11T12:07:50,371 Getting requirements to build wheel: started 2024-07-11T12:07:50,373 Running command Getting requirements to build wheel 2024-07-11T12:08:26,499 warning: moleculekit/wrapping/wrapping.pyx:47:4: Unreachable code 2024-07-11T12:08:35,126 Compiling moleculekit/interactions/hbonds/hbonds.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,126 Compiling moleculekit/interactions/pipi/pipi.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,127 Compiling moleculekit/interactions/cationpi/cationpi.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,128 Compiling moleculekit/interactions/sigmahole/sigmahole.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,128 Compiling moleculekit/wrapping/wrapping.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,129 Compiling moleculekit/bondguesser_utils/bondguesser_utils.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,130 Compiling moleculekit/atomselect_utils/atomselect_utils.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,130 Compiling moleculekit/distance_utils/distance_utils.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,131 Compiling moleculekit/occupancy_utils/occupancy_utils.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,132 Compiling moleculekit/cython_utils/cython_utils.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,132 Compiling moleculekit/fileformats/xtc/xtc.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-07-11T12:08:35,133 Compiling moleculekit/fileformats/xtc/trr.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-07-11T12:08:35,133 Compiling moleculekit/fileformats/dcd/dcd.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-07-11T12:08:35,134 Compiling moleculekit/fileformats/binpos/binpos.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-07-11T12:08:35,134 Compiling moleculekit/tmalign/tmalign_util.pyx because it depends on /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libcpp/vector.pxd. 2024-07-11T12:08:35,135 [ 1/15] Cythonizing moleculekit/atomselect_utils/atomselect_utils.pyx 2024-07-11T12:08:35,135 [ 2/15] Cythonizing moleculekit/bondguesser_utils/bondguesser_utils.pyx 2024-07-11T12:08:35,136 [ 3/15] Cythonizing moleculekit/cython_utils/cython_utils.pyx 2024-07-11T12:08:35,137 [ 4/15] Cythonizing moleculekit/distance_utils/distance_utils.pyx 2024-07-11T12:08:35,137 [ 5/15] Cythonizing moleculekit/fileformats/dcd/dcd.pyx 2024-07-11T12:08:35,138 [ 6/15] Cythonizing moleculekit/interactions/cationpi/cationpi.pyx 2024-07-11T12:08:35,139 [ 7/15] Cythonizing moleculekit/interactions/hbonds/hbonds.pyx 2024-07-11T12:08:35,139 [ 8/15] Cythonizing moleculekit/interactions/pipi/pipi.pyx 2024-07-11T12:08:35,140 [ 9/15] Cythonizing moleculekit/interactions/sigmahole/sigmahole.pyx 2024-07-11T12:08:35,140 [10/15] Cythonizing moleculekit/occupancy_utils/occupancy_utils.pyx 2024-07-11T12:08:35,141 [11/15] Cythonizing moleculekit/tmalign/tmalign_util.pyx 2024-07-11T12:08:35,141 [12/15] Cythonizing moleculekit/wrapping/wrapping.pyx 2024-07-11T12:08:35,142 [13/15] Cythonizing moleculekit/fileformats/binpos/binpos.pyx 2024-07-11T12:08:35,142 [14/15] Cythonizing moleculekit/fileformats/xtc/trr.pyx 2024-07-11T12:08:35,143 [15/15] Cythonizing moleculekit/fileformats/xtc/xtc.pyx 2024-07-11T12:08:35,426 running egg_info 2024-07-11T12:08:35,432 writing moleculekit.egg-info/PKG-INFO 2024-07-11T12:08:35,435 writing dependency_links to moleculekit.egg-info/dependency_links.txt 2024-07-11T12:08:35,437 writing requirements to moleculekit.egg-info/requires.txt 2024-07-11T12:08:35,439 writing top-level names to moleculekit.egg-info/top_level.txt 2024-07-11T12:08:35,468 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:35,469 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:35,469 dependency 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won't be automatically included in the manifest: the path must be relative 2024-07-11T12:08:35,477 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:35,478 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:35,479 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:35,479 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:35,480 dependency 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won't be automatically included in the manifest: the path must be relative 2024-07-11T12:08:40,049 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,049 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,050 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,050 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,051 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,051 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,052 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,052 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,053 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,053 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,054 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,054 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,055 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,056 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,057 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,057 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,057 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,058 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,058 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,059 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:40,059 reading manifest file '/tmp/pip-modern-metadata-ihvlf913/moleculekit.egg-info/SOURCES.txt' 2024-07-11T12:08:40,060 reading manifest template 'MANIFEST.in' 2024-07-11T12:08:40,306 no previously-included directories found matching 'moleculekit/test-data' 2024-07-11T12:08:40,307 no previously-included directories found matching 'moleculekit/tests' 2024-07-11T12:08:40,308 no previously-included directories found matching 'package' 2024-07-11T12:08:40,309 adding license file 'LICENSE' 2024-07-11T12:08:40,321 writing manifest file '/tmp/pip-modern-metadata-ihvlf913/moleculekit.egg-info/SOURCES.txt' 2024-07-11T12:08:40,329 creating '/tmp/pip-modern-metadata-ihvlf913/moleculekit-1.9.0.dist-info' 2024-07-11T12:08:40,552 Preparing metadata (pyproject.toml): finished with status 'done' 2024-07-11T12:08:40,557 Source in /tmp/pip-wheel-4_rdb_a8/moleculekit_94184c94b91645d2aaad16f4e3482c52 has version 1.9.0, which satisfies requirement moleculekit==1.9.0 from https://files.pythonhosted.org/packages/38/d6/30462b4aeb3cb9ae0244bc9882779d3249e39393f5ea71c6abc2d36bb1ed/moleculekit-1.9.0.tar.gz 2024-07-11T12:08:40,558 Removed moleculekit==1.9.0 from https://files.pythonhosted.org/packages/38/d6/30462b4aeb3cb9ae0244bc9882779d3249e39393f5ea71c6abc2d36bb1ed/moleculekit-1.9.0.tar.gz from build tracker '/tmp/pip-build-tracker-r3t0f_85' 2024-07-11T12:08:40,563 Created temporary directory: /tmp/pip-unpack-hkoy5rti 2024-07-11T12:08:40,564 Created temporary directory: /tmp/pip-unpack-juh05o_j 2024-07-11T12:08:40,572 Building wheels for collected packages: moleculekit 2024-07-11T12:08:40,577 Created temporary directory: /tmp/pip-wheel-j63sbhe6 2024-07-11T12:08:40,577 Destination directory: /tmp/pip-wheel-j63sbhe6 2024-07-11T12:08:40,579 Building wheel for moleculekit (pyproject.toml): started 2024-07-11T12:08:40,581 Running command Building wheel for moleculekit (pyproject.toml) 2024-07-11T12:08:42,781 running bdist_wheel 2024-07-11T12:08:42,795 running build 2024-07-11T12:08:42,796 running build_py 2024-07-11T12:08:42,802 creating build 2024-07-11T12:08:42,802 creating build/lib.linux-armv7l-cpython-311 2024-07-11T12:08:42,803 creating build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,804 copying moleculekit/_version.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,806 copying moleculekit/distance.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,808 copying moleculekit/molecule.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,812 copying moleculekit/readers.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,816 copying moleculekit/config.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,818 copying moleculekit/align.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,820 copying moleculekit/writers.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,822 copying moleculekit/vmdgraphics.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,825 copying moleculekit/vmdviewer.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,827 copying moleculekit/util.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,829 copying moleculekit/opm.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,831 copying moleculekit/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,833 copying moleculekit/viewer.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,835 copying moleculekit/rdkitintegration.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,836 copying moleculekit/home.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,838 copying moleculekit/dihedral.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,840 copying moleculekit/periodictable.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,842 copying moleculekit/pymolgraphics.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,843 copying moleculekit/rcsb.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,845 copying moleculekit/bondguesser.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,848 copying moleculekit/version.py -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:42,850 creating build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,851 copying moleculekit/tools/autosegment.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,854 copying moleculekit/tools/sequencestructuralalignment.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,856 copying moleculekit/tools/detect.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,858 copying moleculekit/tools/hhblitsprofile.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,860 copying moleculekit/tools/modelling.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,862 copying moleculekit/tools/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,864 copying moleculekit/tools/graphalignment.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,866 copying moleculekit/tools/docking.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,868 copying moleculekit/tools/preparation.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,871 copying moleculekit/tools/crystalpacking.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,873 copying moleculekit/tools/atomtyper.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,875 copying moleculekit/tools/voxeldescriptors.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,878 copying moleculekit/tools/preparation_customres.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,880 copying moleculekit/tools/moleculechecks.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools 2024-07-11T12:08:42,883 creating build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-11T12:08:42,884 copying moleculekit/atomselect/languageparser.py -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-11T12:08:42,886 copying moleculekit/atomselect/analyze.py -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-11T12:08:42,889 copying moleculekit/atomselect/atomselect.py -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-11T12:08:42,891 copying moleculekit/atomselect/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect 2024-07-11T12:08:42,893 creating build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,894 copying moleculekit/projections/metricrmsd.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,897 copying moleculekit/projections/projection.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,898 copying moleculekit/projections/metricsecondarystructure.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,900 copying moleculekit/projections/metriccoordinate.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,903 copying moleculekit/projections/util.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,905 copying moleculekit/projections/metricplumed2.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,907 copying moleculekit/projections/metricgyration.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,909 copying moleculekit/projections/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,911 copying moleculekit/projections/metricshell.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,913 copying moleculekit/projections/metrictmscore.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,916 copying moleculekit/projections/metricsasa.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,918 copying moleculekit/projections/metricfluctuation.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,920 copying moleculekit/projections/metricdihedral.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,923 copying moleculekit/projections/metricdistance.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,926 copying moleculekit/projections/metricsphericalcoordinate.py -> build/lib.linux-armv7l-cpython-311/moleculekit/projections 2024-07-11T12:08:42,929 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-11T12:08:42,930 copying moleculekit/fileformats/netcdf.py -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-11T12:08:42,933 copying moleculekit/fileformats/utils.py -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-11T12:08:42,935 copying moleculekit/fileformats/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-11T12:08:42,938 creating build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-11T12:08:42,939 copying moleculekit/smallmol/smallmol.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-11T12:08:42,942 copying moleculekit/smallmol/smallmollib.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-11T12:08:42,945 copying moleculekit/smallmol/smallmolcdp.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-11T12:08:42,947 copying moleculekit/smallmol/util.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-11T12:08:42,950 copying moleculekit/smallmol/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-11T12:08:42,952 copying moleculekit/smallmol/test_smallmollib.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-11T12:08:42,955 copying moleculekit/smallmol/test_smallmol.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol 2024-07-11T12:08:42,957 creating build/lib.linux-armv7l-cpython-311/moleculekit/pdbx 2024-07-11T12:08:42,959 copying moleculekit/pdbx/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx 2024-07-11T12:08:42,961 creating build/lib.linux-armv7l-cpython-311/moleculekit/ply 2024-07-11T12:08:42,962 copying moleculekit/ply/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/ply 2024-07-11T12:08:42,964 copying moleculekit/ply/lex.py -> build/lib.linux-armv7l-cpython-311/moleculekit/ply 2024-07-11T12:08:42,967 copying moleculekit/ply/yacc.py -> build/lib.linux-armv7l-cpython-311/moleculekit/ply 2024-07-11T12:08:42,971 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions 2024-07-11T12:08:42,972 copying moleculekit/interactions/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions 2024-07-11T12:08:42,974 copying moleculekit/interactions/interactions.py -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions 2024-07-11T12:08:42,978 creating build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools 2024-07-11T12:08:42,979 copying moleculekit/tools/obabel_tools/obabel_cli.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools 2024-07-11T12:08:42,981 copying moleculekit/tools/obabel_tools/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools 2024-07-11T12:08:42,984 creating build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-11T12:08:42,985 copying moleculekit/smallmol/tools/clustering.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-11T12:08:42,988 copying moleculekit/smallmol/tools/restrainedembed.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-11T12:08:42,990 copying moleculekit/smallmol/tools/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-11T12:08:42,991 copying moleculekit/smallmol/tools/test_tools.py -> build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools 2024-07-11T12:08:42,995 creating build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-11T12:08:42,996 copying moleculekit/pdbx/reader/PdbxReader.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-11T12:08:42,999 copying moleculekit/pdbx/reader/PdbxContainers.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-11T12:08:43,002 copying moleculekit/pdbx/reader/PdbxParser.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-11T12:08:43,005 copying moleculekit/pdbx/reader/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-11T12:08:43,007 copying moleculekit/pdbx/reader/BinaryCifReader.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader 2024-07-11T12:08:43,010 creating build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-11T12:08:43,011 copying moleculekit/pdbx/tests/PdbxReadWriteTests.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-11T12:08:43,014 copying moleculekit/pdbx/tests/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-11T12:08:43,016 copying moleculekit/pdbx/tests/PdbxReaderTests.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-11T12:08:43,018 copying moleculekit/pdbx/tests/PdbxWriterTests.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests 2024-07-11T12:08:43,021 creating build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer 2024-07-11T12:08:43,022 copying moleculekit/pdbx/writer/PdbxWriter.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer 2024-07-11T12:08:43,024 copying moleculekit/pdbx/writer/__init__.py -> build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer 2024-07-11T12:08:43,026 running egg_info 2024-07-11T12:08:43,031 writing moleculekit.egg-info/PKG-INFO 2024-07-11T12:08:43,035 writing dependency_links to moleculekit.egg-info/dependency_links.txt 2024-07-11T12:08:43,037 writing requirements to moleculekit.egg-info/requires.txt 2024-07-11T12:08:43,038 writing top-level names to moleculekit.egg-info/top_level.txt 2024-07-11T12:08:43,056 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,056 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,057 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,057 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,058 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,058 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,059 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,059 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,060 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,061 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,061 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,062 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,062 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,063 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,064 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,064 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,065 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,065 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,066 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,067 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,067 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,068 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,068 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,069 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,069 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,069 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,070 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,070 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,071 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,072 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,072 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,073 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,074 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,074 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,075 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,075 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,076 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,077 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,078 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,078 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,078 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,079 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,079 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,080 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,080 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,081 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,081 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,082 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,083 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,083 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,084 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,084 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,085 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,086 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,086 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,087 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,088 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,088 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,088 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,089 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,089 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,090 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,090 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,090 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,091 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,092 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,092 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,093 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,094 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,094 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,095 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,095 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,096 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,096 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,097 dependency /tmp/pip-build-env-kqb5ac4z/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 2024-07-11T12:08:43,098 reading manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-07-11T12:08:43,098 reading manifest template 'MANIFEST.in' 2024-07-11T12:08:43,341 no previously-included directories found matching 'moleculekit/test-data' 2024-07-11T12:08:43,342 no previously-included directories found matching 'moleculekit/tests' 2024-07-11T12:08:43,343 no previously-included directories found matching 'package' 2024-07-11T12:08:43,343 adding license file 'LICENSE' 2024-07-11T12:08:43,359 writing manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-07-11T12:08:43,397 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.atomselect_utils' is absent from the `packages` configuration. 2024-07-11T12:08:43,397 !! 2024-07-11T12:08:43,398 ******************************************************************************** 2024-07-11T12:08:43,399 ############################ 2024-07-11T12:08:43,399 # Package would be ignored # 2024-07-11T12:08:43,400 ############################ 2024-07-11T12:08:43,400 Python recognizes 'moleculekit.atomselect_utils' as an importable package[^1], 2024-07-11T12:08:43,401 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,402 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,402 package, please make sure that 'moleculekit.atomselect_utils' is explicitly added 2024-07-11T12:08:43,403 to the `packages` configuration field. 2024-07-11T12:08:43,404 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,405 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,406 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,407 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,408 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,410 If you don't want 'moleculekit.atomselect_utils' to be distributed and are 2024-07-11T12:08:43,410 already explicitly excluding 'moleculekit.atomselect_utils' via 2024-07-11T12:08:43,411 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,411 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,412 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,412 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,413 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,415 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,415 even if it does not contain any `.py` files. 2024-07-11T12:08:43,416 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,416 directory, all directories are treated like packages. 2024-07-11T12:08:43,417 ******************************************************************************** 2024-07-11T12:08:43,418 !! 2024-07-11T12:08:43,418 check.warn(importable) 2024-07-11T12:08:43,419 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.bondguesser_utils' is absent from the `packages` configuration. 2024-07-11T12:08:43,419 !! 2024-07-11T12:08:43,421 ******************************************************************************** 2024-07-11T12:08:43,421 ############################ 2024-07-11T12:08:43,422 # Package would be ignored # 2024-07-11T12:08:43,422 ############################ 2024-07-11T12:08:43,422 Python recognizes 'moleculekit.bondguesser_utils' as an importable package[^1], 2024-07-11T12:08:43,423 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,423 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,424 package, please make sure that 'moleculekit.bondguesser_utils' is explicitly added 2024-07-11T12:08:43,424 to the `packages` configuration field. 2024-07-11T12:08:43,425 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,425 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,425 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,426 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,427 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,427 If you don't want 'moleculekit.bondguesser_utils' to be distributed and are 2024-07-11T12:08:43,428 already explicitly excluding 'moleculekit.bondguesser_utils' via 2024-07-11T12:08:43,428 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,429 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,429 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,430 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,431 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,432 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,433 even if it does not contain any `.py` files. 2024-07-11T12:08:43,433 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,434 directory, all directories are treated like packages. 2024-07-11T12:08:43,434 ******************************************************************************** 2024-07-11T12:08:43,435 !! 2024-07-11T12:08:43,436 check.warn(importable) 2024-07-11T12:08:43,436 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.cython_utils' is absent from the `packages` configuration. 2024-07-11T12:08:43,437 !! 2024-07-11T12:08:43,438 ******************************************************************************** 2024-07-11T12:08:43,438 ############################ 2024-07-11T12:08:43,439 # Package would be ignored # 2024-07-11T12:08:43,439 ############################ 2024-07-11T12:08:43,440 Python recognizes 'moleculekit.cython_utils' as an importable package[^1], 2024-07-11T12:08:43,440 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,441 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,441 package, please make sure that 'moleculekit.cython_utils' is explicitly added 2024-07-11T12:08:43,442 to the `packages` configuration field. 2024-07-11T12:08:43,443 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,443 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,444 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,445 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,446 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,447 If you don't want 'moleculekit.cython_utils' to be distributed and are 2024-07-11T12:08:43,447 already explicitly excluding 'moleculekit.cython_utils' via 2024-07-11T12:08:43,447 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,448 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,448 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,449 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,450 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,451 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,451 even if it does not contain any `.py` files. 2024-07-11T12:08:43,451 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,452 directory, all directories are treated like packages. 2024-07-11T12:08:43,452 ******************************************************************************** 2024-07-11T12:08:43,453 !! 2024-07-11T12:08:43,453 check.warn(importable) 2024-07-11T12:08:43,454 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.distance_utils' is absent from the `packages` configuration. 2024-07-11T12:08:43,454 !! 2024-07-11T12:08:43,455 ******************************************************************************** 2024-07-11T12:08:43,456 ############################ 2024-07-11T12:08:43,456 # Package would be ignored # 2024-07-11T12:08:43,457 ############################ 2024-07-11T12:08:43,458 Python recognizes 'moleculekit.distance_utils' as an importable package[^1], 2024-07-11T12:08:43,458 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,459 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,459 package, please make sure that 'moleculekit.distance_utils' is explicitly added 2024-07-11T12:08:43,460 to the `packages` configuration field. 2024-07-11T12:08:43,461 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,461 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,462 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,463 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,464 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,465 If you don't want 'moleculekit.distance_utils' to be distributed and are 2024-07-11T12:08:43,465 already explicitly excluding 'moleculekit.distance_utils' via 2024-07-11T12:08:43,466 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,466 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,467 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,468 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,469 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,471 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,471 even if it does not contain any `.py` files. 2024-07-11T12:08:43,472 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,473 directory, all directories are treated like packages. 2024-07-11T12:08:43,474 ******************************************************************************** 2024-07-11T12:08:43,474 !! 2024-07-11T12:08:43,475 check.warn(importable) 2024-07-11T12:08:43,475 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.binpos' is absent from the `packages` configuration. 2024-07-11T12:08:43,475 !! 2024-07-11T12:08:43,476 ******************************************************************************** 2024-07-11T12:08:43,476 ############################ 2024-07-11T12:08:43,477 # Package would be ignored # 2024-07-11T12:08:43,477 ############################ 2024-07-11T12:08:43,477 Python recognizes 'moleculekit.fileformats.binpos' as an importable package[^1], 2024-07-11T12:08:43,478 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,478 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,479 package, please make sure that 'moleculekit.fileformats.binpos' is explicitly added 2024-07-11T12:08:43,479 to the `packages` configuration field. 2024-07-11T12:08:43,480 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,480 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,480 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,481 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,482 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,483 If you don't want 'moleculekit.fileformats.binpos' to be distributed and are 2024-07-11T12:08:43,483 already explicitly excluding 'moleculekit.fileformats.binpos' via 2024-07-11T12:08:43,484 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,484 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,485 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,486 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,487 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,489 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,489 even if it does not contain any `.py` files. 2024-07-11T12:08:43,490 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,491 directory, all directories are treated like packages. 2024-07-11T12:08:43,492 ******************************************************************************** 2024-07-11T12:08:43,493 !! 2024-07-11T12:08:43,493 check.warn(importable) 2024-07-11T12:08:43,494 /tmp/pip-build-env-kqb5ac4z/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. 2024-07-11T12:08:43,494 !! 2024-07-11T12:08:43,495 ******************************************************************************** 2024-07-11T12:08:43,496 ############################ 2024-07-11T12:08:43,496 # Package would be ignored # 2024-07-11T12:08:43,497 ############################ 2024-07-11T12:08:43,498 Python recognizes 'moleculekit.fileformats.binpos.include' as an importable package[^1], 2024-07-11T12:08:43,498 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,499 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,500 package, please make sure that 'moleculekit.fileformats.binpos.include' is explicitly added 2024-07-11T12:08:43,501 to the `packages` configuration field. 2024-07-11T12:08:43,502 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,502 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,503 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,504 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,504 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,505 If you don't want 'moleculekit.fileformats.binpos.include' to be distributed and are 2024-07-11T12:08:43,505 already explicitly excluding 'moleculekit.fileformats.binpos.include' via 2024-07-11T12:08:43,506 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,506 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,507 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,507 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,508 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,509 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,509 even if it does not contain any `.py` files. 2024-07-11T12:08:43,510 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,510 directory, all directories are treated like packages. 2024-07-11T12:08:43,511 ******************************************************************************** 2024-07-11T12:08:43,512 !! 2024-07-11T12:08:43,513 check.warn(importable) 2024-07-11T12:08:43,513 /tmp/pip-build-env-kqb5ac4z/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. 2024-07-11T12:08:43,514 !! 2024-07-11T12:08:43,515 ******************************************************************************** 2024-07-11T12:08:43,515 ############################ 2024-07-11T12:08:43,516 # Package would be ignored # 2024-07-11T12:08:43,517 ############################ 2024-07-11T12:08:43,517 Python recognizes 'moleculekit.fileformats.binpos.src' as an importable package[^1], 2024-07-11T12:08:43,518 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,519 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,519 package, please make sure that 'moleculekit.fileformats.binpos.src' is explicitly added 2024-07-11T12:08:43,519 to the `packages` configuration field. 2024-07-11T12:08:43,520 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,521 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,521 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,522 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,523 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,524 If you don't want 'moleculekit.fileformats.binpos.src' to be distributed and are 2024-07-11T12:08:43,525 already explicitly excluding 'moleculekit.fileformats.binpos.src' via 2024-07-11T12:08:43,525 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,526 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,526 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,527 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,528 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,529 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,529 even if it does not contain any `.py` files. 2024-07-11T12:08:43,530 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,530 directory, all directories are treated like packages. 2024-07-11T12:08:43,530 ******************************************************************************** 2024-07-11T12:08:43,531 !! 2024-07-11T12:08:43,531 check.warn(importable) 2024-07-11T12:08:43,532 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.dcd' is absent from the `packages` configuration. 2024-07-11T12:08:43,532 !! 2024-07-11T12:08:43,533 ******************************************************************************** 2024-07-11T12:08:43,533 ############################ 2024-07-11T12:08:43,533 # Package would be ignored # 2024-07-11T12:08:43,534 ############################ 2024-07-11T12:08:43,534 Python recognizes 'moleculekit.fileformats.dcd' as an importable package[^1], 2024-07-11T12:08:43,534 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,535 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,536 package, please make sure that 'moleculekit.fileformats.dcd' is explicitly added 2024-07-11T12:08:43,537 to the `packages` configuration field. 2024-07-11T12:08:43,538 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,538 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,539 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,540 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,541 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,542 If you don't want 'moleculekit.fileformats.dcd' to be distributed and are 2024-07-11T12:08:43,543 already explicitly excluding 'moleculekit.fileformats.dcd' via 2024-07-11T12:08:43,543 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,544 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,544 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,545 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,546 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,547 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,548 even if it does not contain any `.py` files. 2024-07-11T12:08:43,548 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,549 directory, all directories are treated like packages. 2024-07-11T12:08:43,549 ******************************************************************************** 2024-07-11T12:08:43,550 !! 2024-07-11T12:08:43,551 check.warn(importable) 2024-07-11T12:08:43,551 /tmp/pip-build-env-kqb5ac4z/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. 2024-07-11T12:08:43,552 !! 2024-07-11T12:08:43,553 ******************************************************************************** 2024-07-11T12:08:43,553 ############################ 2024-07-11T12:08:43,554 # Package would be ignored # 2024-07-11T12:08:43,554 ############################ 2024-07-11T12:08:43,554 Python recognizes 'moleculekit.fileformats.dcd.include' as an importable package[^1], 2024-07-11T12:08:43,555 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,555 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,556 package, please make sure that 'moleculekit.fileformats.dcd.include' is explicitly added 2024-07-11T12:08:43,556 to the `packages` configuration field. 2024-07-11T12:08:43,557 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,557 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,557 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,558 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,559 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,559 If you don't want 'moleculekit.fileformats.dcd.include' to be distributed and are 2024-07-11T12:08:43,560 already explicitly excluding 'moleculekit.fileformats.dcd.include' via 2024-07-11T12:08:43,560 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,561 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,561 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,563 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,564 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,566 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,566 even if it does not contain any `.py` files. 2024-07-11T12:08:43,567 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,567 directory, all directories are treated like packages. 2024-07-11T12:08:43,568 ******************************************************************************** 2024-07-11T12:08:43,569 !! 2024-07-11T12:08:43,570 check.warn(importable) 2024-07-11T12:08:43,570 /tmp/pip-build-env-kqb5ac4z/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. 2024-07-11T12:08:43,571 !! 2024-07-11T12:08:43,572 ******************************************************************************** 2024-07-11T12:08:43,572 ############################ 2024-07-11T12:08:43,573 # Package would be ignored # 2024-07-11T12:08:43,574 ############################ 2024-07-11T12:08:43,574 Python recognizes 'moleculekit.fileformats.dcd.src' as an importable package[^1], 2024-07-11T12:08:43,575 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,576 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,577 package, please make sure that 'moleculekit.fileformats.dcd.src' is explicitly added 2024-07-11T12:08:43,577 to the `packages` configuration field. 2024-07-11T12:08:43,578 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,579 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,580 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,581 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,582 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,583 If you don't want 'moleculekit.fileformats.dcd.src' to be distributed and are 2024-07-11T12:08:43,583 already explicitly excluding 'moleculekit.fileformats.dcd.src' via 2024-07-11T12:08:43,584 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,584 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,585 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,586 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,587 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,588 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,589 even if it does not contain any `.py` files. 2024-07-11T12:08:43,589 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,589 directory, all directories are treated like packages. 2024-07-11T12:08:43,590 ******************************************************************************** 2024-07-11T12:08:43,591 !! 2024-07-11T12:08:43,591 check.warn(importable) 2024-07-11T12:08:43,592 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.xtc' is absent from the `packages` configuration. 2024-07-11T12:08:43,592 !! 2024-07-11T12:08:43,594 ******************************************************************************** 2024-07-11T12:08:43,594 ############################ 2024-07-11T12:08:43,595 # Package would be ignored # 2024-07-11T12:08:43,596 ############################ 2024-07-11T12:08:43,598 Python recognizes 'moleculekit.fileformats.xtc' as an importable package[^1], 2024-07-11T12:08:43,600 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,609 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,610 package, please make sure that 'moleculekit.fileformats.xtc' is explicitly added 2024-07-11T12:08:43,611 to the `packages` configuration field. 2024-07-11T12:08:43,612 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,612 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,613 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,614 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,615 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,616 If you don't want 'moleculekit.fileformats.xtc' to be distributed and are 2024-07-11T12:08:43,617 already explicitly excluding 'moleculekit.fileformats.xtc' via 2024-07-11T12:08:43,618 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,618 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,619 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,620 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,621 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,626 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,627 even if it does not contain any `.py` files. 2024-07-11T12:08:43,632 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,635 directory, all directories are treated like packages. 2024-07-11T12:08:43,636 ******************************************************************************** 2024-07-11T12:08:43,637 !! 2024-07-11T12:08:43,637 check.warn(importable) 2024-07-11T12:08:43,638 /tmp/pip-build-env-kqb5ac4z/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. 2024-07-11T12:08:43,638 !! 2024-07-11T12:08:43,639 ******************************************************************************** 2024-07-11T12:08:43,640 ############################ 2024-07-11T12:08:43,640 # Package would be ignored # 2024-07-11T12:08:43,641 ############################ 2024-07-11T12:08:43,641 Python recognizes 'moleculekit.fileformats.xtc.include' as an importable package[^1], 2024-07-11T12:08:43,641 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,642 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,643 package, please make sure that 'moleculekit.fileformats.xtc.include' is explicitly added 2024-07-11T12:08:43,645 to the `packages` configuration field. 2024-07-11T12:08:43,646 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,647 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,647 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,649 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,659 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,661 If you don't want 'moleculekit.fileformats.xtc.include' to be distributed and are 2024-07-11T12:08:43,661 already explicitly excluding 'moleculekit.fileformats.xtc.include' via 2024-07-11T12:08:43,662 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,663 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,663 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,664 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,665 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,667 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,668 even if it does not contain any `.py` files. 2024-07-11T12:08:43,668 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,669 directory, all directories are treated like packages. 2024-07-11T12:08:43,670 ******************************************************************************** 2024-07-11T12:08:43,671 !! 2024-07-11T12:08:43,671 check.warn(importable) 2024-07-11T12:08:43,676 /tmp/pip-build-env-kqb5ac4z/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. 2024-07-11T12:08:43,678 !! 2024-07-11T12:08:43,685 ******************************************************************************** 2024-07-11T12:08:43,687 ############################ 2024-07-11T12:08:43,688 # Package would be ignored # 2024-07-11T12:08:43,689 ############################ 2024-07-11T12:08:43,690 Python recognizes 'moleculekit.fileformats.xtc.src' as an importable package[^1], 2024-07-11T12:08:43,690 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,691 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,692 package, please make sure that 'moleculekit.fileformats.xtc.src' is explicitly added 2024-07-11T12:08:43,692 to the `packages` configuration field. 2024-07-11T12:08:43,693 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,695 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,696 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,697 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,697 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,698 If you don't want 'moleculekit.fileformats.xtc.src' to be distributed and are 2024-07-11T12:08:43,699 already explicitly excluding 'moleculekit.fileformats.xtc.src' via 2024-07-11T12:08:43,700 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,703 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,709 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,711 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,712 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,714 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,714 even if it does not contain any `.py` files. 2024-07-11T12:08:43,715 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,715 directory, all directories are treated like packages. 2024-07-11T12:08:43,716 ******************************************************************************** 2024-07-11T12:08:43,716 !! 2024-07-11T12:08:43,717 check.warn(importable) 2024-07-11T12:08:43,717 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.cationpi' is absent from the `packages` configuration. 2024-07-11T12:08:43,718 !! 2024-07-11T12:08:43,719 ******************************************************************************** 2024-07-11T12:08:43,719 ############################ 2024-07-11T12:08:43,720 # Package would be ignored # 2024-07-11T12:08:43,720 ############################ 2024-07-11T12:08:43,721 Python recognizes 'moleculekit.interactions.cationpi' as an importable package[^1], 2024-07-11T12:08:43,721 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,722 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,723 package, please make sure that 'moleculekit.interactions.cationpi' is explicitly added 2024-07-11T12:08:43,723 to the `packages` configuration field. 2024-07-11T12:08:43,724 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,725 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,726 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,727 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,728 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,729 If you don't want 'moleculekit.interactions.cationpi' to be distributed and are 2024-07-11T12:08:43,730 already explicitly excluding 'moleculekit.interactions.cationpi' via 2024-07-11T12:08:43,730 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,731 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,732 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,733 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,734 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,735 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,736 even if it does not contain any `.py` files. 2024-07-11T12:08:43,736 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,736 directory, all directories are treated like packages. 2024-07-11T12:08:43,737 ******************************************************************************** 2024-07-11T12:08:43,738 !! 2024-07-11T12:08:43,738 check.warn(importable) 2024-07-11T12:08:43,739 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.hbonds' is absent from the `packages` configuration. 2024-07-11T12:08:43,739 !! 2024-07-11T12:08:43,740 ******************************************************************************** 2024-07-11T12:08:43,740 ############################ 2024-07-11T12:08:43,741 # Package would be ignored # 2024-07-11T12:08:43,741 ############################ 2024-07-11T12:08:43,742 Python recognizes 'moleculekit.interactions.hbonds' as an importable package[^1], 2024-07-11T12:08:43,742 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,743 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,744 package, please make sure that 'moleculekit.interactions.hbonds' is explicitly added 2024-07-11T12:08:43,744 to the `packages` configuration field. 2024-07-11T12:08:43,746 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,746 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,747 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,748 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,750 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,751 If you don't want 'moleculekit.interactions.hbonds' to be distributed and are 2024-07-11T12:08:43,752 already explicitly excluding 'moleculekit.interactions.hbonds' via 2024-07-11T12:08:43,752 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,753 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,754 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,755 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,756 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,758 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,758 even if it does not contain any `.py` files. 2024-07-11T12:08:43,759 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,759 directory, all directories are treated like packages. 2024-07-11T12:08:43,760 ******************************************************************************** 2024-07-11T12:08:43,761 !! 2024-07-11T12:08:43,762 check.warn(importable) 2024-07-11T12:08:43,762 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.pipi' is absent from the `packages` configuration. 2024-07-11T12:08:43,763 !! 2024-07-11T12:08:43,764 ******************************************************************************** 2024-07-11T12:08:43,765 ############################ 2024-07-11T12:08:43,765 # Package would be ignored # 2024-07-11T12:08:43,766 ############################ 2024-07-11T12:08:43,766 Python recognizes 'moleculekit.interactions.pipi' as an importable package[^1], 2024-07-11T12:08:43,767 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,767 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,768 package, please make sure that 'moleculekit.interactions.pipi' is explicitly added 2024-07-11T12:08:43,768 to the `packages` configuration field. 2024-07-11T12:08:43,769 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,770 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,770 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,771 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,772 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,773 If you don't want 'moleculekit.interactions.pipi' to be distributed and are 2024-07-11T12:08:43,773 already explicitly excluding 'moleculekit.interactions.pipi' via 2024-07-11T12:08:43,774 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,774 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,775 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,776 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,777 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,779 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,780 even if it does not contain any `.py` files. 2024-07-11T12:08:43,781 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,781 directory, all directories are treated like packages. 2024-07-11T12:08:43,782 ******************************************************************************** 2024-07-11T12:08:43,812 !! 2024-07-11T12:08:43,814 check.warn(importable) 2024-07-11T12:08:43,816 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.sigmahole' is absent from the `packages` configuration. 2024-07-11T12:08:43,821 !! 2024-07-11T12:08:43,872 ******************************************************************************** 2024-07-11T12:08:43,906 ############################ 2024-07-11T12:08:43,925 # Package would be ignored # 2024-07-11T12:08:43,926 ############################ 2024-07-11T12:08:43,926 Python recognizes 'moleculekit.interactions.sigmahole' as an importable package[^1], 2024-07-11T12:08:43,927 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,929 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,929 package, please make sure that 'moleculekit.interactions.sigmahole' is explicitly added 2024-07-11T12:08:43,930 to the `packages` configuration field. 2024-07-11T12:08:43,931 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,932 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,933 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,934 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,935 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,936 If you don't want 'moleculekit.interactions.sigmahole' to be distributed and are 2024-07-11T12:08:43,936 already explicitly excluding 'moleculekit.interactions.sigmahole' via 2024-07-11T12:08:43,937 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,937 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,937 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,938 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,939 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,940 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,940 even if it does not contain any `.py` files. 2024-07-11T12:08:43,941 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,941 directory, all directories are treated like packages. 2024-07-11T12:08:43,942 ******************************************************************************** 2024-07-11T12:08:43,943 !! 2024-07-11T12:08:43,943 check.warn(importable) 2024-07-11T12:08:43,943 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.occupancy_utils' is absent from the `packages` configuration. 2024-07-11T12:08:43,944 !! 2024-07-11T12:08:43,945 ******************************************************************************** 2024-07-11T12:08:43,945 ############################ 2024-07-11T12:08:43,946 # Package would be ignored # 2024-07-11T12:08:43,946 ############################ 2024-07-11T12:08:43,947 Python recognizes 'moleculekit.occupancy_utils' as an importable package[^1], 2024-07-11T12:08:43,947 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,948 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,949 package, please make sure that 'moleculekit.occupancy_utils' is explicitly added 2024-07-11T12:08:43,949 to the `packages` configuration field. 2024-07-11T12:08:43,950 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,951 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,951 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,952 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,953 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,954 If you don't want 'moleculekit.occupancy_utils' to be distributed and are 2024-07-11T12:08:43,955 already explicitly excluding 'moleculekit.occupancy_utils' via 2024-07-11T12:08:43,955 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,956 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,956 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,957 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,958 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,960 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,960 even if it does not contain any `.py` files. 2024-07-11T12:08:43,961 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,962 directory, all directories are treated like packages. 2024-07-11T12:08:43,962 ******************************************************************************** 2024-07-11T12:08:43,963 !! 2024-07-11T12:08:43,963 check.warn(importable) 2024-07-11T12:08:43,964 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.share' is absent from the `packages` configuration. 2024-07-11T12:08:43,964 !! 2024-07-11T12:08:43,965 ******************************************************************************** 2024-07-11T12:08:43,965 ############################ 2024-07-11T12:08:43,966 # Package would be ignored # 2024-07-11T12:08:43,966 ############################ 2024-07-11T12:08:43,967 Python recognizes 'moleculekit.share' as an importable package[^1], 2024-07-11T12:08:43,967 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,968 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,968 package, please make sure that 'moleculekit.share' is explicitly added 2024-07-11T12:08:43,969 to the `packages` configuration field. 2024-07-11T12:08:43,970 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,970 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,971 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,972 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,972 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,973 If you don't want 'moleculekit.share' to be distributed and are 2024-07-11T12:08:43,974 already explicitly excluding 'moleculekit.share' via 2024-07-11T12:08:43,974 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,975 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,975 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,976 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,977 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,979 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,979 even if it does not contain any `.py` files. 2024-07-11T12:08:43,980 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,981 directory, all directories are treated like packages. 2024-07-11T12:08:43,981 ******************************************************************************** 2024-07-11T12:08:43,982 !! 2024-07-11T12:08:43,982 check.warn(importable) 2024-07-11T12:08:43,983 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.share.atomselect' is absent from the `packages` configuration. 2024-07-11T12:08:43,983 !! 2024-07-11T12:08:43,984 ******************************************************************************** 2024-07-11T12:08:43,985 ############################ 2024-07-11T12:08:43,985 # Package would be ignored # 2024-07-11T12:08:43,986 ############################ 2024-07-11T12:08:43,986 Python recognizes 'moleculekit.share.atomselect' as an importable package[^1], 2024-07-11T12:08:43,987 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:43,988 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:43,988 package, please make sure that 'moleculekit.share.atomselect' is explicitly added 2024-07-11T12:08:43,989 to the `packages` configuration field. 2024-07-11T12:08:43,990 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:43,990 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:43,991 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:43,991 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:43,992 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:43,993 If you don't want 'moleculekit.share.atomselect' to be distributed and are 2024-07-11T12:08:43,993 already explicitly excluding 'moleculekit.share.atomselect' via 2024-07-11T12:08:43,994 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:43,994 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:43,995 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:43,996 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:43,997 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:43,998 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:43,998 even if it does not contain any `.py` files. 2024-07-11T12:08:43,998 On the other hand, currently there is no concept of package data 2024-07-11T12:08:43,999 directory, all directories are treated like packages. 2024-07-11T12:08:43,999 ******************************************************************************** 2024-07-11T12:08:44,000 !! 2024-07-11T12:08:44,001 check.warn(importable) 2024-07-11T12:08:44,001 /tmp/pip-build-env-kqb5ac4z/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. 2024-07-11T12:08:44,002 !! 2024-07-11T12:08:44,003 ******************************************************************************** 2024-07-11T12:08:44,003 ############################ 2024-07-11T12:08:44,004 # Package would be ignored # 2024-07-11T12:08:44,004 ############################ 2024-07-11T12:08:44,004 Python recognizes 'moleculekit.share.pdb2pqr.residues' as an importable package[^1], 2024-07-11T12:08:44,005 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:44,006 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:44,006 package, please make sure that 'moleculekit.share.pdb2pqr.residues' is explicitly added 2024-07-11T12:08:44,007 to the `packages` configuration field. 2024-07-11T12:08:44,008 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:44,008 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:44,009 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:44,010 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:44,011 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:44,012 If you don't want 'moleculekit.share.pdb2pqr.residues' to be distributed and are 2024-07-11T12:08:44,012 already explicitly excluding 'moleculekit.share.pdb2pqr.residues' via 2024-07-11T12:08:44,013 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:44,013 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:44,014 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:44,015 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:44,015 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:44,017 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:44,017 even if it does not contain any `.py` files. 2024-07-11T12:08:44,018 On the other hand, currently there is no concept of package data 2024-07-11T12:08:44,018 directory, all directories are treated like packages. 2024-07-11T12:08:44,019 ******************************************************************************** 2024-07-11T12:08:44,019 !! 2024-07-11T12:08:44,020 check.warn(importable) 2024-07-11T12:08:44,020 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign' is absent from the `packages` configuration. 2024-07-11T12:08:44,020 !! 2024-07-11T12:08:44,021 ******************************************************************************** 2024-07-11T12:08:44,022 ############################ 2024-07-11T12:08:44,022 # Package would be ignored # 2024-07-11T12:08:44,023 ############################ 2024-07-11T12:08:44,023 Python recognizes 'moleculekit.tmalign' as an importable package[^1], 2024-07-11T12:08:44,024 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:44,024 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:44,025 package, please make sure that 'moleculekit.tmalign' is explicitly added 2024-07-11T12:08:44,025 to the `packages` configuration field. 2024-07-11T12:08:44,026 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:44,027 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:44,027 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:44,028 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:44,029 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:44,030 If you don't want 'moleculekit.tmalign' to be distributed and are 2024-07-11T12:08:44,030 already explicitly excluding 'moleculekit.tmalign' via 2024-07-11T12:08:44,031 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:44,031 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:44,032 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:44,033 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:44,034 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:44,035 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:44,036 even if it does not contain any `.py` files. 2024-07-11T12:08:44,036 On the other hand, currently there is no concept of package data 2024-07-11T12:08:44,037 directory, all directories are treated like packages. 2024-07-11T12:08:44,037 ******************************************************************************** 2024-07-11T12:08:44,038 !! 2024-07-11T12:08:44,039 check.warn(importable) 2024-07-11T12:08:44,039 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign.include' is absent from the `packages` configuration. 2024-07-11T12:08:44,040 !! 2024-07-11T12:08:44,041 ******************************************************************************** 2024-07-11T12:08:44,041 ############################ 2024-07-11T12:08:44,042 # Package would be ignored # 2024-07-11T12:08:44,043 ############################ 2024-07-11T12:08:44,043 Python recognizes 'moleculekit.tmalign.include' as an importable package[^1], 2024-07-11T12:08:44,043 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:44,044 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:44,044 package, please make sure that 'moleculekit.tmalign.include' is explicitly added 2024-07-11T12:08:44,045 to the `packages` configuration field. 2024-07-11T12:08:44,046 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:44,046 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:44,047 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:44,047 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:44,048 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:44,049 If you don't want 'moleculekit.tmalign.include' to be distributed and are 2024-07-11T12:08:44,050 already explicitly excluding 'moleculekit.tmalign.include' via 2024-07-11T12:08:44,050 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:44,051 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:44,051 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:44,052 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:44,053 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:44,054 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:44,055 even if it does not contain any `.py` files. 2024-07-11T12:08:44,055 On the other hand, currently there is no concept of package data 2024-07-11T12:08:44,056 directory, all directories are treated like packages. 2024-07-11T12:08:44,057 ******************************************************************************** 2024-07-11T12:08:44,057 !! 2024-07-11T12:08:44,058 check.warn(importable) 2024-07-11T12:08:44,058 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign.src' is absent from the `packages` configuration. 2024-07-11T12:08:44,059 !! 2024-07-11T12:08:44,060 ******************************************************************************** 2024-07-11T12:08:44,060 ############################ 2024-07-11T12:08:44,061 # Package would be ignored # 2024-07-11T12:08:44,061 ############################ 2024-07-11T12:08:44,062 Python recognizes 'moleculekit.tmalign.src' as an importable package[^1], 2024-07-11T12:08:44,062 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:44,063 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:44,064 package, please make sure that 'moleculekit.tmalign.src' is explicitly added 2024-07-11T12:08:44,065 to the `packages` configuration field. 2024-07-11T12:08:44,066 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:44,066 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:44,067 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:44,068 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:44,069 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:44,070 If you don't want 'moleculekit.tmalign.src' to be distributed and are 2024-07-11T12:08:44,071 already explicitly excluding 'moleculekit.tmalign.src' via 2024-07-11T12:08:44,071 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:44,071 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:44,072 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:44,073 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:44,073 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:44,074 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:44,075 even if it does not contain any `.py` files. 2024-07-11T12:08:44,075 On the other hand, currently there is no concept of package data 2024-07-11T12:08:44,076 directory, all directories are treated like packages. 2024-07-11T12:08:44,076 ******************************************************************************** 2024-07-11T12:08:44,077 !! 2024-07-11T12:08:44,077 check.warn(importable) 2024-07-11T12:08:44,078 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.wrapping' is absent from the `packages` configuration. 2024-07-11T12:08:44,078 !! 2024-07-11T12:08:44,079 ******************************************************************************** 2024-07-11T12:08:44,080 ############################ 2024-07-11T12:08:44,080 # Package would be ignored # 2024-07-11T12:08:44,081 ############################ 2024-07-11T12:08:44,081 Python recognizes 'moleculekit.wrapping' as an importable package[^1], 2024-07-11T12:08:44,082 but it is absent from setuptools' `packages` configuration. 2024-07-11T12:08:44,083 This leads to an ambiguous overall configuration. If you want to distribute this 2024-07-11T12:08:44,084 package, please make sure that 'moleculekit.wrapping' is explicitly added 2024-07-11T12:08:44,084 to the `packages` configuration field. 2024-07-11T12:08:44,085 Alternatively, you can also rely on setuptools' discovery methods 2024-07-11T12:08:44,086 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-07-11T12:08:44,086 instead of `find_packages(...)`/`find:`). 2024-07-11T12:08:44,087 You can read more about "package discovery" on setuptools documentation page: 2024-07-11T12:08:44,088 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-07-11T12:08:44,089 If you don't want 'moleculekit.wrapping' to be distributed and are 2024-07-11T12:08:44,089 already explicitly excluding 'moleculekit.wrapping' via 2024-07-11T12:08:44,090 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-07-11T12:08:44,090 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-07-11T12:08:44,091 combination with a more fine grained `package-data` configuration. 2024-07-11T12:08:44,092 You can read more about "package data files" on setuptools documentation page: 2024-07-11T12:08:44,093 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-07-11T12:08:44,094 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-07-11T12:08:44,095 even if it does not contain any `.py` files. 2024-07-11T12:08:44,095 On the other hand, currently there is no concept of package data 2024-07-11T12:08:44,096 directory, all directories are treated like packages. 2024-07-11T12:08:44,096 ******************************************************************************** 2024-07-11T12:08:44,098 !! 2024-07-11T12:08:44,098 check.warn(importable) 2024-07-11T12:08:44,099 copying moleculekit/logging.ini -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:44,099 copying moleculekit/vmd_wrapper -> build/lib.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:44,099 creating build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils 2024-07-11T12:08:44,100 copying moleculekit/atomselect_utils/atomselect_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils 2024-07-11T12:08:44,100 copying moleculekit/atomselect_utils/atomselect_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils 2024-07-11T12:08:44,101 creating build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils 2024-07-11T12:08:44,101 copying moleculekit/bondguesser_utils/bondguesser_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils 2024-07-11T12:08:44,102 copying moleculekit/bondguesser_utils/bondguesser_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils 2024-07-11T12:08:44,102 creating build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils 2024-07-11T12:08:44,102 copying moleculekit/cython_utils/cython_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils 2024-07-11T12:08:44,103 copying moleculekit/cython_utils/cython_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils 2024-07-11T12:08:44,103 creating build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils 2024-07-11T12:08:44,104 copying moleculekit/distance_utils/distance_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils 2024-07-11T12:08:44,104 copying moleculekit/distance_utils/distance_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils 2024-07-11T12:08:44,104 creating build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils 2024-07-11T12:08:44,105 copying moleculekit/occupancy_utils/occupancy_utils.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils 2024-07-11T12:08:44,105 copying moleculekit/occupancy_utils/occupancy_utils.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils 2024-07-11T12:08:44,106 creating build/lib.linux-armv7l-cpython-311/moleculekit/share 2024-07-11T12:08:44,106 copying moleculekit/share/ALA.cif -> build/lib.linux-armv7l-cpython-311/moleculekit/share 2024-07-11T12:08:44,107 copying moleculekit/share/backbone.cif -> build/lib.linux-armv7l-cpython-311/moleculekit/share 2024-07-11T12:08:44,107 copying moleculekit/share/opm_sequences.json -> build/lib.linux-armv7l-cpython-311/moleculekit/share 2024-07-11T12:08:44,108 creating build/lib.linux-armv7l-cpython-311/moleculekit/share/atomselect 2024-07-11T12:08:44,108 copying moleculekit/share/atomselect/atomselect.json -> build/lib.linux-armv7l-cpython-311/moleculekit/share/atomselect 2024-07-11T12:08:44,109 creating build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr 2024-07-11T12:08:44,109 creating build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,109 copying moleculekit/share/pdb2pqr/residues/.gitkeep -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,110 copying moleculekit/share/pdb2pqr/residues/004.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,110 copying moleculekit/share/pdb2pqr/residues/004.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,111 copying moleculekit/share/pdb2pqr/residues/03Y.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,111 copying moleculekit/share/pdb2pqr/residues/03Y.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,112 copying moleculekit/share/pdb2pqr/residues/0A1.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,112 copying moleculekit/share/pdb2pqr/residues/0A1.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,113 copying moleculekit/share/pdb2pqr/residues/0AF.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,114 copying moleculekit/share/pdb2pqr/residues/0AF.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,114 copying moleculekit/share/pdb2pqr/residues/0BN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,114 copying moleculekit/share/pdb2pqr/residues/0BN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,115 copying moleculekit/share/pdb2pqr/residues/1MH.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,115 copying moleculekit/share/pdb2pqr/residues/1MH.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,116 copying moleculekit/share/pdb2pqr/residues/2AS.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,116 copying moleculekit/share/pdb2pqr/residues/2AS.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,117 copying moleculekit/share/pdb2pqr/residues/2GX.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,117 copying moleculekit/share/pdb2pqr/residues/2GX.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,117 copying moleculekit/share/pdb2pqr/residues/2ML.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,118 copying moleculekit/share/pdb2pqr/residues/2ML.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,118 copying moleculekit/share/pdb2pqr/residues/2MR.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,119 copying moleculekit/share/pdb2pqr/residues/2MR.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,119 copying moleculekit/share/pdb2pqr/residues/4IN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,120 copying moleculekit/share/pdb2pqr/residues/4IN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,120 copying moleculekit/share/pdb2pqr/residues/4PH.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,121 copying moleculekit/share/pdb2pqr/residues/4PH.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,121 copying moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,121 copying moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,122 copying moleculekit/share/pdb2pqr/residues/5JP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,122 copying moleculekit/share/pdb2pqr/residues/5JP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,123 copying moleculekit/share/pdb2pqr/residues/AA4.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,124 copying moleculekit/share/pdb2pqr/residues/AA4.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,124 copying moleculekit/share/pdb2pqr/residues/ABA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,125 copying moleculekit/share/pdb2pqr/residues/ABA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,125 copying moleculekit/share/pdb2pqr/residues/AHP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,126 copying moleculekit/share/pdb2pqr/residues/AHP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,126 copying moleculekit/share/pdb2pqr/residues/ALC.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,127 copying moleculekit/share/pdb2pqr/residues/ALC.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,127 copying moleculekit/share/pdb2pqr/residues/ALN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,127 copying moleculekit/share/pdb2pqr/residues/ALN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,128 copying moleculekit/share/pdb2pqr/residues/ALY.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,128 copying moleculekit/share/pdb2pqr/residues/ALY.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,129 copying moleculekit/share/pdb2pqr/residues/APD.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,129 copying moleculekit/share/pdb2pqr/residues/APD.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,130 copying moleculekit/share/pdb2pqr/residues/BB8.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,130 copying moleculekit/share/pdb2pqr/residues/BB8.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,130 copying moleculekit/share/pdb2pqr/residues/BCS.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,131 copying moleculekit/share/pdb2pqr/residues/BCS.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,131 copying moleculekit/share/pdb2pqr/residues/BTK.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,132 copying moleculekit/share/pdb2pqr/residues/BTK.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,132 copying moleculekit/share/pdb2pqr/residues/CCS.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,132 copying moleculekit/share/pdb2pqr/residues/CCS.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,133 copying moleculekit/share/pdb2pqr/residues/CGU.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,133 copying moleculekit/share/pdb2pqr/residues/CGU.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,134 copying moleculekit/share/pdb2pqr/residues/CSA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,134 copying moleculekit/share/pdb2pqr/residues/CSA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,135 copying moleculekit/share/pdb2pqr/residues/CSO.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,135 copying moleculekit/share/pdb2pqr/residues/CSO.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,136 copying moleculekit/share/pdb2pqr/residues/CSP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,136 copying moleculekit/share/pdb2pqr/residues/CSP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,137 copying moleculekit/share/pdb2pqr/residues/CSS.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,137 copying moleculekit/share/pdb2pqr/residues/CSS.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,138 copying moleculekit/share/pdb2pqr/residues/D4P.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,139 copying moleculekit/share/pdb2pqr/residues/D4P.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,139 copying moleculekit/share/pdb2pqr/residues/DA2.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,139 copying moleculekit/share/pdb2pqr/residues/DA2.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,140 copying moleculekit/share/pdb2pqr/residues/DAB.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,140 copying moleculekit/share/pdb2pqr/residues/DAB.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,141 copying moleculekit/share/pdb2pqr/residues/DAH.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,141 copying moleculekit/share/pdb2pqr/residues/DAH.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,142 copying moleculekit/share/pdb2pqr/residues/DPP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,142 copying moleculekit/share/pdb2pqr/residues/DPP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,142 copying moleculekit/share/pdb2pqr/residues/ESC.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,143 copying moleculekit/share/pdb2pqr/residues/ESC.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,143 copying moleculekit/share/pdb2pqr/residues/FGL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,144 copying moleculekit/share/pdb2pqr/residues/FGL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,144 copying moleculekit/share/pdb2pqr/residues/GHG.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,145 copying moleculekit/share/pdb2pqr/residues/GHG.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,145 copying moleculekit/share/pdb2pqr/residues/GME.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,146 copying moleculekit/share/pdb2pqr/residues/GME.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,146 copying moleculekit/share/pdb2pqr/residues/GNC.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,147 copying moleculekit/share/pdb2pqr/residues/GNC.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,147 copying moleculekit/share/pdb2pqr/residues/HHK.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,148 copying moleculekit/share/pdb2pqr/residues/HHK.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,148 copying moleculekit/share/pdb2pqr/residues/HLU.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,149 copying moleculekit/share/pdb2pqr/residues/HLU.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,149 copying moleculekit/share/pdb2pqr/residues/HLX.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,150 copying moleculekit/share/pdb2pqr/residues/HLX.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,150 copying moleculekit/share/pdb2pqr/residues/HOX.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,151 copying moleculekit/share/pdb2pqr/residues/HOX.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,151 copying moleculekit/share/pdb2pqr/residues/HPE.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,152 copying moleculekit/share/pdb2pqr/residues/HPE.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,152 copying moleculekit/share/pdb2pqr/residues/HQA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,153 copying moleculekit/share/pdb2pqr/residues/HQA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,154 copying moleculekit/share/pdb2pqr/residues/HTR.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,156 copying moleculekit/share/pdb2pqr/residues/HTR.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,158 copying moleculekit/share/pdb2pqr/residues/HYP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,160 copying moleculekit/share/pdb2pqr/residues/HYP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,162 copying moleculekit/share/pdb2pqr/residues/I2M.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,164 copying moleculekit/share/pdb2pqr/residues/I2M.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,166 copying moleculekit/share/pdb2pqr/residues/IGL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,167 copying moleculekit/share/pdb2pqr/residues/IGL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,170 copying moleculekit/share/pdb2pqr/residues/IIL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,172 copying moleculekit/share/pdb2pqr/residues/IIL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,174 copying moleculekit/share/pdb2pqr/residues/IML.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,175 copying moleculekit/share/pdb2pqr/residues/IML.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,178 copying moleculekit/share/pdb2pqr/residues/KYN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,180 copying moleculekit/share/pdb2pqr/residues/KYN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,182 copying moleculekit/share/pdb2pqr/residues/LME.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,184 copying moleculekit/share/pdb2pqr/residues/LME.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,186 copying moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,187 copying moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,190 copying moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,192 copying moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,194 copying moleculekit/share/pdb2pqr/residues/M3L.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,196 copying moleculekit/share/pdb2pqr/residues/M3L.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,198 copying moleculekit/share/pdb2pqr/residues/ME0.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,200 copying moleculekit/share/pdb2pqr/residues/ME0.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,203 copying moleculekit/share/pdb2pqr/residues/MEA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,204 copying moleculekit/share/pdb2pqr/residues/MEA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,206 copying moleculekit/share/pdb2pqr/residues/MEN.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,208 copying moleculekit/share/pdb2pqr/residues/MEN.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,210 copying moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,212 copying moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,214 copying moleculekit/share/pdb2pqr/residues/MLE.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,216 copying moleculekit/share/pdb2pqr/residues/MLE.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,218 copying moleculekit/share/pdb2pqr/residues/MLY.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,220 copying moleculekit/share/pdb2pqr/residues/MLY.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,222 copying moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,224 copying moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,227 copying moleculekit/share/pdb2pqr/residues/MME.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,229 copying moleculekit/share/pdb2pqr/residues/MME.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,231 copying moleculekit/share/pdb2pqr/residues/MMO.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,233 copying moleculekit/share/pdb2pqr/residues/MMO.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,235 copying moleculekit/share/pdb2pqr/residues/MVA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,237 copying moleculekit/share/pdb2pqr/residues/MVA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,239 copying moleculekit/share/pdb2pqr/residues/NAL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,241 copying moleculekit/share/pdb2pqr/residues/NAL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,243 copying moleculekit/share/pdb2pqr/residues/NCY.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,245 copying moleculekit/share/pdb2pqr/residues/NCY.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,247 copying moleculekit/share/pdb2pqr/residues/NLE.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,249 copying moleculekit/share/pdb2pqr/residues/NLE.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,251 copying moleculekit/share/pdb2pqr/residues/NVA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,253 copying moleculekit/share/pdb2pqr/residues/NVA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,255 copying moleculekit/share/pdb2pqr/residues/NZC.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,257 copying moleculekit/share/pdb2pqr/residues/NZC.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,259 copying moleculekit/share/pdb2pqr/residues/OCY.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,261 copying moleculekit/share/pdb2pqr/residues/OCY.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,263 copying moleculekit/share/pdb2pqr/residues/OMX.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,265 copying moleculekit/share/pdb2pqr/residues/OMX.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,267 copying moleculekit/share/pdb2pqr/residues/ONL.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,269 copying moleculekit/share/pdb2pqr/residues/ONL.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,271 copying moleculekit/share/pdb2pqr/residues/ORM.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,272 copying moleculekit/share/pdb2pqr/residues/ORM.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,274 copying moleculekit/share/pdb2pqr/residues/P1L.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,276 copying moleculekit/share/pdb2pqr/residues/P1L.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,279 copying moleculekit/share/pdb2pqr/residues/PCA.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,280 copying moleculekit/share/pdb2pqr/residues/PCA.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,283 copying moleculekit/share/pdb2pqr/residues/PRK.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,285 copying moleculekit/share/pdb2pqr/residues/PRK.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,287 copying moleculekit/share/pdb2pqr/residues/PTR.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,289 copying moleculekit/share/pdb2pqr/residues/PTR.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,291 copying moleculekit/share/pdb2pqr/residues/SEP.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,293 copying moleculekit/share/pdb2pqr/residues/SEP.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,296 copying moleculekit/share/pdb2pqr/residues/TPO.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,298 copying moleculekit/share/pdb2pqr/residues/TPO.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,300 copying moleculekit/share/pdb2pqr/residues/TRO.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,302 copying moleculekit/share/pdb2pqr/residues/TRO.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,304 copying moleculekit/share/pdb2pqr/residues/TY2.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,306 copying moleculekit/share/pdb2pqr/residues/TY2.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,308 copying moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,310 copying moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,312 copying moleculekit/share/pdb2pqr/residues/YCM.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,314 copying moleculekit/share/pdb2pqr/residues/YCM.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,316 copying moleculekit/share/pdb2pqr/residues/YNM.dat -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,318 copying moleculekit/share/pdb2pqr/residues/YNM.xml -> build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues 2024-07-11T12:08:44,320 creating build/lib.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-11T12:08:44,321 copying moleculekit/tmalign/tmalign_util.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-11T12:08:44,340 copying moleculekit/tmalign/tmalign_util.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-11T12:08:44,342 copying moleculekit/tmalign/tmalignlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-11T12:08:44,344 creating build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/include 2024-07-11T12:08:44,344 copying moleculekit/tmalign/include/TMAlign.h -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/include 2024-07-11T12:08:44,347 creating build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/src 2024-07-11T12:08:44,347 copying moleculekit/tmalign/src/TMAlign.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/src 2024-07-11T12:08:44,353 creating build/lib.linux-armv7l-cpython-311/moleculekit/wrapping 2024-07-11T12:08:44,354 copying moleculekit/wrapping/wrapping.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/wrapping 2024-07-11T12:08:44,375 copying moleculekit/wrapping/wrapping.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/wrapping 2024-07-11T12:08:44,377 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-11T12:08:44,378 copying moleculekit/fileformats/binpos/binpos.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-11T12:08:44,392 copying moleculekit/fileformats/binpos/binpos.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-11T12:08:44,395 copying moleculekit/fileformats/binpos/binposlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-11T12:08:44,397 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include 2024-07-11T12:08:44,399 copying moleculekit/fileformats/binpos/include/binposplugin.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include 2024-07-11T12:08:44,401 copying moleculekit/fileformats/binpos/include/largefiles.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include 2024-07-11T12:08:44,403 copying moleculekit/fileformats/binpos/include/molfile_plugin.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include 2024-07-11T12:08:44,407 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src 2024-07-11T12:08:44,408 copying moleculekit/fileformats/binpos/src/binposplugin.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src 2024-07-11T12:08:44,411 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-11T12:08:44,412 copying moleculekit/fileformats/dcd/dcd.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-11T12:08:44,429 copying moleculekit/fileformats/dcd/dcd.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-11T12:08:44,432 copying moleculekit/fileformats/dcd/dcdlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-11T12:08:44,434 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-11T12:08:44,435 copying moleculekit/fileformats/dcd/include/dcdplugin.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-11T12:08:44,437 copying moleculekit/fileformats/dcd/include/endianswap.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-11T12:08:44,439 copying moleculekit/fileformats/dcd/include/fastio.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-11T12:08:44,442 copying moleculekit/fileformats/dcd/include/largefiles.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-11T12:08:44,443 copying moleculekit/fileformats/dcd/include/molfile_plugin.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include 2024-07-11T12:08:44,447 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src 2024-07-11T12:08:44,447 copying moleculekit/fileformats/dcd/src/dcdplugin.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src 2024-07-11T12:08:44,450 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:08:44,451 copying moleculekit/fileformats/xtc/trr.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:08:44,473 copying moleculekit/fileformats/xtc/trr.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:08:44,476 copying moleculekit/fileformats/xtc/trrlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:08:44,478 copying moleculekit/fileformats/xtc/xdrlib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:08:44,479 copying moleculekit/fileformats/xtc/xtc.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:08:44,499 copying moleculekit/fileformats/xtc/xtc.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:08:44,501 copying moleculekit/fileformats/xtc/xtclib.pxd -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:08:44,503 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-11T12:08:44,504 copying moleculekit/fileformats/xtc/include/trr_header.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-11T12:08:44,506 copying moleculekit/fileformats/xtc/include/xdr_seek.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-11T12:08:44,507 copying moleculekit/fileformats/xtc/include/xdrfile.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-11T12:08:44,510 copying moleculekit/fileformats/xtc/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-11T12:08:44,512 copying moleculekit/fileformats/xtc/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-11T12:08:44,514 copying moleculekit/fileformats/xtc/include/xtc.h -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include 2024-07-11T12:08:44,516 creating build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-11T12:08:44,517 copying moleculekit/fileformats/xtc/src/xdr_seek.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-11T12:08:44,519 copying moleculekit/fileformats/xtc/src/xdrfile.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-11T12:08:44,522 copying moleculekit/fileformats/xtc/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-11T12:08:44,525 copying moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-11T12:08:44,527 copying moleculekit/fileformats/xtc/src/xtc.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-11T12:08:44,529 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi 2024-07-11T12:08:44,530 copying moleculekit/interactions/cationpi/cationpi.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi 2024-07-11T12:08:44,549 copying moleculekit/interactions/cationpi/cationpi.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi 2024-07-11T12:08:44,552 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds 2024-07-11T12:08:44,553 copying moleculekit/interactions/hbonds/hbonds.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds 2024-07-11T12:08:44,573 copying moleculekit/interactions/hbonds/hbonds.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds 2024-07-11T12:08:44,576 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi 2024-07-11T12:08:44,577 copying moleculekit/interactions/pipi/pipi.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi 2024-07-11T12:08:44,596 copying moleculekit/interactions/pipi/pipi.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi 2024-07-11T12:08:44,599 creating build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole 2024-07-11T12:08:44,599 copying moleculekit/interactions/sigmahole/sigmahole.cpp -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole 2024-07-11T12:08:44,622 copying moleculekit/interactions/sigmahole/sigmahole.pyx -> build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole 2024-07-11T12:08:44,633 UPDATING build/lib.linux-armv7l-cpython-311/moleculekit/_version.py 2024-07-11T12:08:44,633 set build/lib.linux-armv7l-cpython-311/moleculekit/_version.py to '1.9.0' 2024-07-11T12:08:44,634 running build_ext 2024-07-11T12:08:44,646 building 'moleculekit.interactions.hbonds' extension 2024-07-11T12:08:44,646 creating build/temp.linux-armv7l-cpython-311 2024-07-11T12:08:44,647 creating build/temp.linux-armv7l-cpython-311/moleculekit 2024-07-11T12:08:44,648 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions 2024-07-11T12:08:44,649 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions/hbonds 2024-07-11T12:08:44,650 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-kqb5ac4z/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 2024-07-11T12:08:44,999 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:08:45,000 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:08:45,001 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:08:45,001 from moleculekit/interactions/hbonds/hbonds.cpp:1265: 2024-07-11T12:08:45,002 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:08:45,002 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:08:45,003 | ^~~~~~~ 2024-07-11T12:08:45,873 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:08:45,874 from moleculekit/interactions/hbonds/hbonds.cpp:1269: 2024-07-11T12:08:45,875 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:08:45,875 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:08:45,876 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:08:45,877 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:09:12,531 In function ‘PyObject* __pyx_pf_11moleculekit_12interactions_6hbonds_calculate(PyObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, float, float, bool, bool)’, 2024-07-11T12:09:12,531 inlined from ‘PyObject* __pyx_pw_11moleculekit_12interactions_6hbonds_1calculate(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at moleculekit/interactions/hbonds/hbonds.cpp:20443:68: 2024-07-11T12:09:12,532 moleculekit/interactions/hbonds/hbonds.cpp:21469:52: warning: ‘__pyx_v_d_idx_h’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:09:12,532 21469 | (__pyx_v_results[__pyx_v_f]).push_back(__pyx_v_d_idx_h); 2024-07-11T12:09:12,533 | ^~~~~~~~~~~~~~~ 2024-07-11T12:09:12,534 moleculekit/interactions/hbonds/hbonds.cpp: In function ‘PyObject* __pyx_pw_11moleculekit_12interactions_6hbonds_1calculate(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’: 2024-07-11T12:09:12,534 moleculekit/interactions/hbonds/hbonds.cpp:20486:57: note: ‘__pyx_v_d_idx_h’ was declared here 2024-07-11T12:09:12,535 20486 | __pyx_t_11moleculekit_12interactions_6hbonds_UINT32_t __pyx_v_d_idx_h; 2024-07-11T12:09:12,535 | ^~~~~~~~~~~~~~~ 2024-07-11T12:09:15,581 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 2024-07-11T12:09:15,865 building 'moleculekit.interactions.pipi' extension 2024-07-11T12:09:15,866 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions/pipi 2024-07-11T12:09:15,866 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-kqb5ac4z/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 2024-07-11T12:09:16,167 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:09:16,168 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:09:16,169 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:09:16,169 from moleculekit/interactions/pipi/pipi.cpp:1265: 2024-07-11T12:09:16,170 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:09:16,170 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:09:16,171 | ^~~~~~~ 2024-07-11T12:09:17,028 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:09:17,028 from moleculekit/interactions/pipi/pipi.cpp:1269: 2024-07-11T12:09:17,029 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:09:17,030 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:09:17,030 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:09:17,031 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:09:49,060 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 2024-07-11T12:09:49,340 building 'moleculekit.interactions.cationpi' extension 2024-07-11T12:09:49,341 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions/cationpi 2024-07-11T12:09:49,341 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-kqb5ac4z/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 2024-07-11T12:09:49,650 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:09:49,651 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:09:49,651 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:09:49,652 from moleculekit/interactions/cationpi/cationpi.cpp:1265: 2024-07-11T12:09:49,652 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:09:49,653 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:09:49,654 | ^~~~~~~ 2024-07-11T12:09:50,511 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:09:50,512 from moleculekit/interactions/cationpi/cationpi.cpp:1269: 2024-07-11T12:09:50,512 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:09:50,513 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:09:50,514 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:09:50,515 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:10:21,850 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 2024-07-11T12:10:22,145 building 'moleculekit.interactions.sigmahole' extension 2024-07-11T12:10:22,146 creating build/temp.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole 2024-07-11T12:10:22,147 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-kqb5ac4z/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 2024-07-11T12:10:22,459 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:10:22,459 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:10:22,461 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:10:22,461 from moleculekit/interactions/sigmahole/sigmahole.cpp:1265: 2024-07-11T12:10:22,462 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:10:22,462 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:10:22,463 | ^~~~~~~ 2024-07-11T12:10:23,325 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:10:23,326 from moleculekit/interactions/sigmahole/sigmahole.cpp:1269: 2024-07-11T12:10:23,326 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:10:23,327 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:10:23,328 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:10:23,328 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:10:54,401 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 2024-07-11T12:10:54,690 building 'moleculekit.wrapping' extension 2024-07-11T12:10:54,690 creating build/temp.linux-armv7l-cpython-311/moleculekit/wrapping 2024-07-11T12:10:54,691 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-kqb5ac4z/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 2024-07-11T12:10:55,003 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:10:55,004 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:10:55,005 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:10:55,006 from moleculekit/wrapping/wrapping.cpp:1265: 2024-07-11T12:10:55,006 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:10:55,007 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:10:55,007 | ^~~~~~~ 2024-07-11T12:10:55,866 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:10:55,866 from moleculekit/wrapping/wrapping.cpp:1269: 2024-07-11T12:10:55,867 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:10:55,868 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:10:55,869 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:10:55,869 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:25,179 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 2024-07-11T12:11:25,367 building 'moleculekit.bondguesser_utils' extension 2024-07-11T12:11:25,368 creating build/temp.linux-armv7l-cpython-311/moleculekit/bondguesser_utils 2024-07-11T12:11:25,368 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-kqb5ac4z/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 2024-07-11T12:11:25,674 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:11:25,674 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:11:25,675 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:11:25,675 from moleculekit/bondguesser_utils/bondguesser_utils.cpp:1265: 2024-07-11T12:11:25,676 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:11:25,677 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:11:25,678 | ^~~~~~~ 2024-07-11T12:11:26,532 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:11:26,532 from moleculekit/bondguesser_utils/bondguesser_utils.cpp:1269: 2024-07-11T12:11:26,533 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:11:26,534 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:11:26,534 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:11:26,535 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,964 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)’: 2024-07-11T12:11:27,965 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] 2024-07-11T12:11:27,966 20255 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2024-07-11T12:11:27,966 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-11T12:11:27,967 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] 2024-07-11T12:11:27,968 20267 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2024-07-11T12:11:27,969 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-11T12:11:27,969 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] 2024-07-11T12:11:27,970 20279 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2024-07-11T12:11:27,970 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-11T12:11:27,971 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20318:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,971 20318 | __pyx_t_12 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-11T12:11:27,972 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,973 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20357:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,973 20357 | __pyx_t_12 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-11T12:11:27,974 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,974 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20396:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,975 20396 | __pyx_t_12 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:27,975 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,976 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20435:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,977 20435 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-11T12:11:27,977 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,978 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20441:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,979 20441 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-11T12:11:27,980 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,980 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20482:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,981 20482 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-11T12:11:27,982 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,983 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20488:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,983 20488 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:27,984 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,985 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20529:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,985 20529 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-11T12:11:27,986 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,987 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20535:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,988 20535 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:27,989 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,989 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20576:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,990 20576 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-11T12:11:27,990 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,991 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20629:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,991 20629 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:27,992 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,993 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20676:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,993 20676 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:27,994 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,994 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20717:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,995 20717 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-11T12:11:27,996 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,996 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20723:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,997 20723 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-11T12:11:27,998 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:27,999 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20729:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:27,999 20729 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:28,000 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:28,001 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20776:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:28,001 20776 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-07-11T12:11:28,002 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:28,003 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20782:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:28,003 20782 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:28,004 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:28,005 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20823:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:28,005 20823 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-07-11T12:11:28,006 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:28,007 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20835:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:28,008 20835 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:28,008 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:28,009 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20888:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-07-11T12:11:28,010 20888 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-07-11T12:11:28,011 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:28,011 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)’: 2024-07-11T12:11:28,012 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] 2024-07-11T12:11:28,013 21510 | __pyx_t_6 = (__pyx_v_boxneigh == __pyx_v_n_boxes); 2024-07-11T12:11:28,013 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:28,014 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] 2024-07-11T12:11:28,014 21547 | __pyx_t_6 = (__pyx_v_boxneigh == __pyx_v_boxidx); 2024-07-11T12:11:28,015 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-07-11T12:11:54,465 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 2024-07-11T12:11:54,734 building 'moleculekit.atomselect_utils' extension 2024-07-11T12:11:54,734 creating build/temp.linux-armv7l-cpython-311/moleculekit/atomselect_utils 2024-07-11T12:11:54,735 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-kqb5ac4z/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 2024-07-11T12:11:55,042 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:11:55,043 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:11:55,044 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:11:55,044 from moleculekit/atomselect_utils/atomselect_utils.cpp:1282: 2024-07-11T12:11:55,045 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:11:55,046 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:11:55,046 | ^~~~~~~ 2024-07-11T12:11:55,923 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:11:55,924 from moleculekit/atomselect_utils/atomselect_utils.cpp:1286: 2024-07-11T12:11:55,924 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:11:55,925 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:11:55,926 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:11:55,927 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:11:57,550 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 >&)’: 2024-07-11T12:11:57,551 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] 2024-07-11T12:11:57,551 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); 2024-07-11T12:11:57,552 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-07-11T12:11:57,558 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 >&)’: 2024-07-11T12:11:57,558 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] 2024-07-11T12:11:57,559 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); 2024-07-11T12:11:57,560 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-11T12:11:57,565 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 >&)’: 2024-07-11T12:11:57,566 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] 2024-07-11T12:11:57,567 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); 2024-07-11T12:11:57,568 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-11T12:12:31,827 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 2024-07-11T12:12:32,120 building 'moleculekit.distance_utils' extension 2024-07-11T12:12:32,120 creating build/temp.linux-armv7l-cpython-311/moleculekit/distance_utils 2024-07-11T12:12:32,121 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-kqb5ac4z/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 2024-07-11T12:12:32,446 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:12:32,447 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:12:32,447 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:12:32,448 from moleculekit/distance_utils/distance_utils.cpp:1265: 2024-07-11T12:12:32,448 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:12:32,449 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:12:32,449 | ^~~~~~~ 2024-07-11T12:12:33,330 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:12:33,331 from moleculekit/distance_utils/distance_utils.cpp:1269: 2024-07-11T12:12:33,331 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:12:33,332 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:12:33,333 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:12:33,334 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:12:34,850 moleculekit/distance_utils/distance_utils.cpp: In function ‘PyObject* __pyx_pf_11moleculekit_14distance_utils_2get_collisions(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, float)’: 2024-07-11T12:12:34,851 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] 2024-07-11T12:12:34,851 21813 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2024-07-11T12:12:34,852 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-11T12:12:34,853 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] 2024-07-11T12:12:34,853 21825 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2024-07-11T12:12:34,854 | ~~~~~~~~~~^~~~~~~~~~~ 2024-07-11T12:13:12,157 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 2024-07-11T12:13:12,452 building 'moleculekit.occupancy_utils' extension 2024-07-11T12:13:12,453 creating build/temp.linux-armv7l-cpython-311/moleculekit/occupancy_utils 2024-07-11T12:13:12,453 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-kqb5ac4z/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 2024-07-11T12:13:12,760 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:13:12,761 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:13:12,761 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:13:12,762 from moleculekit/occupancy_utils/occupancy_utils.cpp:1265: 2024-07-11T12:13:12,762 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:13:12,763 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:13:12,763 | ^~~~~~~ 2024-07-11T12:13:13,613 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:13:13,613 from moleculekit/occupancy_utils/occupancy_utils.cpp:1269: 2024-07-11T12:13:13,614 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:13:13,614 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:13:13,615 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:13:13,616 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:13:39,961 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 2024-07-11T12:13:40,150 building 'moleculekit.cython_utils' extension 2024-07-11T12:13:40,151 creating build/temp.linux-armv7l-cpython-311/moleculekit/cython_utils 2024-07-11T12:13:40,153 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-kqb5ac4z/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 2024-07-11T12:13:40,462 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:13:40,462 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:13:40,463 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:13:40,464 from moleculekit/cython_utils/cython_utils.cpp:1265: 2024-07-11T12:13:40,464 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:13:40,465 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:13:40,466 | ^~~~~~~ 2024-07-11T12:13:41,318 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-07-11T12:13:41,319 from moleculekit/cython_utils/cython_utils.cpp:1269: 2024-07-11T12:13:41,320 /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-07-11T12:13:41,321 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:13:41,322 405 | return ((longdouble_t *) &z)[0]; 2024-07-11T12:13:41,322 | ~^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:14:10,365 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 2024-07-11T12:14:10,641 building 'moleculekit.xtc' extension 2024-07-11T12:14:10,641 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats 2024-07-11T12:14:10,642 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc 2024-07-11T12:14:10,643 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src 2024-07-11T12:14:10,644 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-kqb5ac4z/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 2024-07-11T12:14:11,292 moleculekit/fileformats/xtc/src/xdrfile.cpp:66:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,292 66 | "OK", 2024-07-11T12:14:11,293 | ^~~~ 2024-07-11T12:14:11,294 moleculekit/fileformats/xtc/src/xdrfile.cpp:67:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,295 67 | "Header", 2024-07-11T12:14:11,295 | ^~~~~~~~ 2024-07-11T12:14:11,296 moleculekit/fileformats/xtc/src/xdrfile.cpp:68:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,296 68 | "String", 2024-07-11T12:14:11,297 | ^~~~~~~~ 2024-07-11T12:14:11,298 moleculekit/fileformats/xtc/src/xdrfile.cpp:69:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,299 69 | "Double", 2024-07-11T12:14:11,300 | ^~~~~~~~ 2024-07-11T12:14:11,300 moleculekit/fileformats/xtc/src/xdrfile.cpp:70:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,301 70 | "Integer", 2024-07-11T12:14:11,302 | ^~~~~~~~~ 2024-07-11T12:14:11,302 moleculekit/fileformats/xtc/src/xdrfile.cpp:71:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,303 71 | "Float", 2024-07-11T12:14:11,304 | ^~~~~~~ 2024-07-11T12:14:11,304 moleculekit/fileformats/xtc/src/xdrfile.cpp:72:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,305 72 | "Unsigned integer", 2024-07-11T12:14:11,306 | ^~~~~~~~~~~~~~~~~~ 2024-07-11T12:14:11,307 moleculekit/fileformats/xtc/src/xdrfile.cpp:73:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,307 73 | "Compressed 3D coordinate", 2024-07-11T12:14:11,308 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:14:11,309 moleculekit/fileformats/xtc/src/xdrfile.cpp:74:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,310 74 | "Closing file", 2024-07-11T12:14:11,310 | ^~~~~~~~~~~~~~ 2024-07-11T12:14:11,311 moleculekit/fileformats/xtc/src/xdrfile.cpp:75:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,311 75 | "Magic number", 2024-07-11T12:14:11,312 | ^~~~~~~~~~~~~~ 2024-07-11T12:14:11,312 moleculekit/fileformats/xtc/src/xdrfile.cpp:76:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,313 76 | "Not enough memory", 2024-07-11T12:14:11,313 | ^~~~~~~~~~~~~~~~~~~ 2024-07-11T12:14:11,314 moleculekit/fileformats/xtc/src/xdrfile.cpp:77:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,314 77 | "End of file", 2024-07-11T12:14:11,315 | ^~~~~~~~~~~~~ 2024-07-11T12:14:11,315 moleculekit/fileformats/xtc/src/xdrfile.cpp:78:9: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-07-11T12:14:11,316 78 | "File not found" 2024-07-11T12:14:11,316 | ^~~~~~~~~~~~~~~~ 2024-07-11T12:14:11,317 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofint(int)’: 2024-07-11T12:14:11,318 moleculekit/fileformats/xtc/src/xdrfile.cpp:459:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,318 459 | while (size >= num && num_of_bits < 32) 2024-07-11T12:14:11,319 | ~~~~~^~~~~~ 2024-07-11T12:14:11,319 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofints(int, unsigned int*)’: 2024-07-11T12:14:11,320 moleculekit/fileformats/xtc/src/xdrfile.cpp:505:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:11,320 505 | while (bytes[num_of_bytes] >= num) 2024-07-11T12:14:11,321 | ~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-07-11T12:14:11,322 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘void encodeints(int*, int, int, unsigned int*, unsigned int*)’: 2024-07-11T12:14:11,322 moleculekit/fileformats/xtc/src/xdrfile.cpp:614:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,323 614 | if (num_of_bits >= num_of_bytes * 8) 2024-07-11T12:14:11,324 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-07-11T12:14:11,325 moleculekit/fileformats/xtc/src/xdrfile.cpp:616:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,325 616 | for (i = 0; i < num_of_bytes; i++) 2024-07-11T12:14:11,326 | ~~^~~~~~~~~~~~~~ 2024-07-11T12:14:11,326 moleculekit/fileformats/xtc/src/xdrfile.cpp:624:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,327 624 | for (i = 0; i < num_of_bytes-1; i++) 2024-07-11T12:14:11,328 | ~~^~~~~~~~~~~~~~~~ 2024-07-11T12:14:11,328 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int decodebits(int*, int)’: 2024-07-11T12:14:11,329 moleculekit/fileformats/xtc/src/xdrfile.cpp:664:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:11,330 664 | if (lastbits < num_of_bits) 2024-07-11T12:14:11,330 | ~~~~~~~~~^~~~~~~~~~~~~ 2024-07-11T12:14:11,331 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_decompress_coord_float(float*, int*, float*, XDRFILE*)’: 2024-07-11T12:14:11,332 moleculekit/fileformats/xtc/src/xdrfile.cpp:785:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:11,333 785 | if(size3>xfp->buf1size) 2024-07-11T12:14:11,333 | ~~~~~^~~~~~~~~~~~~~ 2024-07-11T12:14:11,334 moleculekit/fileformats/xtc/src/xdrfile.cpp:842:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:11,334 842 | maxidx = (LASTIDX= size3 ) { return -1; } 2024-07-11T12:14:11,336 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:11,337 moleculekit/fileformats/xtc/src/xdrfile.cpp:935:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,337 935 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:11,338 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:11,339 moleculekit/fileformats/xtc/src/xdrfile.cpp:938:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,339 938 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:11,340 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:11,341 moleculekit/fileformats/xtc/src/xdrfile.cpp:945:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,341 945 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:11,342 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:11,342 moleculekit/fileformats/xtc/src/xdrfile.cpp:948:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,343 948 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:11,344 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:11,344 moleculekit/fileformats/xtc/src/xdrfile.cpp:951:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,345 951 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:11,346 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:11,346 moleculekit/fileformats/xtc/src/xdrfile.cpp:756:24: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-07-11T12:14:11,347 756 | int smallidx, minidx, maxidx; 2024-07-11T12:14:11,348 | ^~~~~~ 2024-07-11T12:14:11,348 moleculekit/fileformats/xtc/src/xdrfile.cpp:759:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-07-11T12:14:11,349 759 | int smallnum, smaller, larger, i, is_smaller, run; 2024-07-11T12:14:11,350 | ^~~~~~ 2024-07-11T12:14:11,350 moleculekit/fileformats/xtc/src/xdrfile.cpp:763:13: warning: unused variable ‘errval’ [-Wunused-variable] 2024-07-11T12:14:11,351 763 | int errval=1; 2024-07-11T12:14:11,352 | ^~~~~~ 2024-07-11T12:14:11,352 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_compress_coord_float(float*, int, float, XDRFILE*)’: 2024-07-11T12:14:11,353 moleculekit/fileformats/xtc/src/xdrfile.cpp:1011:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:11,354 1011 | if(size3>xfp->buf1size) 2024-07-11T12:14:11,354 | ~~~~~^~~~~~~~~~~~~~ 2024-07-11T12:14:11,355 moleculekit/fileformats/xtc/src/xdrfile.cpp:1068:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,356 1068 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-11T12:14:11,356 | ~~~~~~~~^~~~~~~ 2024-07-11T12:14:11,357 moleculekit/fileformats/xtc/src/xdrfile.cpp:1084:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,357 1084 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-11T12:14:11,358 | ~~~~~~~~^~~~~~~ 2024-07-11T12:14:11,358 moleculekit/fileformats/xtc/src/xdrfile.cpp:1098:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,359 1098 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-11T12:14:11,359 | ~~~~~~~~^~~~~~~ 2024-07-11T12:14:11,360 moleculekit/fileformats/xtc/src/xdrfile.cpp:1137:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,360 1137 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2024-07-11T12:14:11,361 | ^ 2024-07-11T12:14:11,362 moleculekit/fileformats/xtc/src/xdrfile.cpp:1143:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:11,362 1143 | maxidx = (LASTIDXxfp->buf1size) 2024-07-11T12:14:11,370 | ~~~~~^~~~~~~~~~~~~~ 2024-07-11T12:14:11,370 moleculekit/fileformats/xtc/src/xdrfile.cpp:1377:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:11,371 1377 | maxidx = (LASTIDXxfp->buf1size) { 2024-07-11T12:14:11,380 | ~~~~~^~~~~~~~~~~~~~ 2024-07-11T12:14:11,381 moleculekit/fileformats/xtc/src/xdrfile.cpp:1628:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:11,382 1628 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2024-07-11T12:14:11,382 | ^ 2024-07-11T12:14:11,383 moleculekit/fileformats/xtc/src/xdrfile.cpp:1633:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:11,383 1633 | maxidx = (LASTIDX= num && num_of_bits < 32) 2024-07-11T12:14:41,691 | ~~~~~^~~~~~ 2024-07-11T12:14:41,692 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofints(int, unsigned int*)’: 2024-07-11T12:14:41,692 moleculekit/fileformats/xtc/src/xdrfile.cpp:505:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:41,693 505 | while (bytes[num_of_bytes] >= num) 2024-07-11T12:14:41,694 | ~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-07-11T12:14:41,694 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘void encodeints(int*, int, int, unsigned int*, unsigned int*)’: 2024-07-11T12:14:41,695 moleculekit/fileformats/xtc/src/xdrfile.cpp:614:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,696 614 | if (num_of_bits >= num_of_bytes * 8) 2024-07-11T12:14:41,696 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-07-11T12:14:41,697 moleculekit/fileformats/xtc/src/xdrfile.cpp:616:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,698 616 | for (i = 0; i < num_of_bytes; i++) 2024-07-11T12:14:41,698 | ~~^~~~~~~~~~~~~~ 2024-07-11T12:14:41,699 moleculekit/fileformats/xtc/src/xdrfile.cpp:624:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,700 624 | for (i = 0; i < num_of_bytes-1; i++) 2024-07-11T12:14:41,701 | ~~^~~~~~~~~~~~~~~~ 2024-07-11T12:14:41,701 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int decodebits(int*, int)’: 2024-07-11T12:14:41,702 moleculekit/fileformats/xtc/src/xdrfile.cpp:664:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:41,703 664 | if (lastbits < num_of_bits) 2024-07-11T12:14:41,703 | ~~~~~~~~~^~~~~~~~~~~~~ 2024-07-11T12:14:41,704 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_decompress_coord_float(float*, int*, float*, XDRFILE*)’: 2024-07-11T12:14:41,705 moleculekit/fileformats/xtc/src/xdrfile.cpp:785:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:41,705 785 | if(size3>xfp->buf1size) 2024-07-11T12:14:41,706 | ~~~~~^~~~~~~~~~~~~~ 2024-07-11T12:14:41,708 moleculekit/fileformats/xtc/src/xdrfile.cpp:842:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:41,708 842 | maxidx = (LASTIDX= size3 ) { return -1; } 2024-07-11T12:14:41,713 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:41,714 moleculekit/fileformats/xtc/src/xdrfile.cpp:935:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,714 935 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:41,715 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:41,715 moleculekit/fileformats/xtc/src/xdrfile.cpp:938:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,716 938 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:41,716 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:41,717 moleculekit/fileformats/xtc/src/xdrfile.cpp:945:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,717 945 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:41,718 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:41,719 moleculekit/fileformats/xtc/src/xdrfile.cpp:948:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,719 948 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:41,720 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:41,721 moleculekit/fileformats/xtc/src/xdrfile.cpp:951:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,722 951 | if(countmjh >= size3 ) { return -1; } 2024-07-11T12:14:41,722 | ~~~~~~~~~^~~~~~~~ 2024-07-11T12:14:41,723 moleculekit/fileformats/xtc/src/xdrfile.cpp:756:24: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-07-11T12:14:41,724 756 | int smallidx, minidx, maxidx; 2024-07-11T12:14:41,724 | ^~~~~~ 2024-07-11T12:14:41,725 moleculekit/fileformats/xtc/src/xdrfile.cpp:759:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-07-11T12:14:41,726 759 | int smallnum, smaller, larger, i, is_smaller, run; 2024-07-11T12:14:41,727 | ^~~~~~ 2024-07-11T12:14:41,727 moleculekit/fileformats/xtc/src/xdrfile.cpp:763:13: warning: unused variable ‘errval’ [-Wunused-variable] 2024-07-11T12:14:41,728 763 | int errval=1; 2024-07-11T12:14:41,728 | ^~~~~~ 2024-07-11T12:14:41,729 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_compress_coord_float(float*, int, float, XDRFILE*)’: 2024-07-11T12:14:41,730 moleculekit/fileformats/xtc/src/xdrfile.cpp:1011:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:41,730 1011 | if(size3>xfp->buf1size) 2024-07-11T12:14:41,731 | ~~~~~^~~~~~~~~~~~~~ 2024-07-11T12:14:41,731 moleculekit/fileformats/xtc/src/xdrfile.cpp:1068:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,732 1068 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-11T12:14:41,733 | ~~~~~~~~^~~~~~~ 2024-07-11T12:14:41,734 moleculekit/fileformats/xtc/src/xdrfile.cpp:1084:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,734 1084 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-11T12:14:41,735 | ~~~~~~~~^~~~~~~ 2024-07-11T12:14:41,736 moleculekit/fileformats/xtc/src/xdrfile.cpp:1098:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,736 1098 | countmjh++; if( countmjh> size3) { return -1; } 2024-07-11T12:14:41,737 | ~~~~~~~~^~~~~~~ 2024-07-11T12:14:41,737 moleculekit/fileformats/xtc/src/xdrfile.cpp:1137:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,738 1137 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2024-07-11T12:14:41,738 | ^ 2024-07-11T12:14:41,739 moleculekit/fileformats/xtc/src/xdrfile.cpp:1143:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:41,739 1143 | maxidx = (LASTIDXxfp->buf1size) 2024-07-11T12:14:41,746 | ~~~~~^~~~~~~~~~~~~~ 2024-07-11T12:14:41,747 moleculekit/fileformats/xtc/src/xdrfile.cpp:1377:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:41,748 1377 | maxidx = (LASTIDXxfp->buf1size) { 2024-07-11T12:14:41,758 | ~~~~~^~~~~~~~~~~~~~ 2024-07-11T12:14:41,758 moleculekit/fileformats/xtc/src/xdrfile.cpp:1628:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:14:41,759 1628 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2024-07-11T12:14:41,759 | ^ 2024-07-11T12:14:41,760 moleculekit/fileformats/xtc/src/xdrfile.cpp:1633:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:14:41,760 1633 | maxidx = (LASTIDX= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; 2024-07-11T12:15:21,868 | ^ 2024-07-11T12:15:21,877 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2024-07-11T12:15:21,878 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-07-11T12:15:21,879 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:21,889 moleculekit/fileformats/xtc/trr.c:12009:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:21,890 12009 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-11T12:15:21,890 | ^ 2024-07-11T12:15:21,899 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2024-07-11T12:15:21,900 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-07-11T12:15:21,901 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:21,901 moleculekit/fileformats/xtc/trr.c:2485:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:21,902 2485 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-07-11T12:15:21,902 | ^ 2024-07-11T12:15:21,911 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-07-11T12:15:21,912 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-07-11T12:15:21,913 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:21,923 moleculekit/fileformats/xtc/trr.c:12003:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:21,923 12003 | __pyx_t_28 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-07-11T12:15:21,925 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-07-11T12:15:21,933 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2024-07-11T12:15:21,934 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-07-11T12:15:21,934 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:21,944 moleculekit/fileformats/xtc/trr.c:11956:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:21,945 11956 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; 2024-07-11T12:15:21,945 | ^ 2024-07-11T12:15:21,954 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2024-07-11T12:15:21,955 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-07-11T12:15:21,955 | ^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:21,965 moleculekit/fileformats/xtc/trr.c:11952:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:21,966 11952 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-11T12:15:21,966 | ^ 2024-07-11T12:15:21,976 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2024-07-11T12:15:21,976 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-07-11T12:15:21,977 | ^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:21,978 moleculekit/fileformats/xtc/trr.c:2485:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:21,978 2485 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-07-11T12:15:21,979 | ^ 2024-07-11T12:15:21,988 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-07-11T12:15:21,988 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-07-11T12:15:21,989 | ^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:21,999 moleculekit/fileformats/xtc/trr.c:11946:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:21,999 11946 | __pyx_t_28 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-07-11T12:15:22,000 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-07-11T12:15:22,009 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2024-07-11T12:15:22,010 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-07-11T12:15:22,010 | ^~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:22,021 moleculekit/fileformats/xtc/trr.c:12345:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:22,021 12345 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-11T12:15:22,022 | ^ 2024-07-11T12:15:22,031 moleculekit/fileformats/xtc/trr.c:10567:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2024-07-11T12:15:22,032 10567 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-07-11T12:15:22,032 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:22,043 moleculekit/fileformats/xtc/trr.c:12341:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:22,043 12341 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-07-11T12:15:22,044 | ^ 2024-07-11T12:15:22,053 moleculekit/fileformats/xtc/trr.c:10567:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2024-07-11T12:15:22,054 10567 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-07-11T12:15:22,055 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:22,064 moleculekit/fileformats/xtc/trr.c:12186:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:22,065 12186 | } else if (unlikely(__pyx_t_35 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-11T12:15:22,065 | ^ 2024-07-11T12:15:22,074 moleculekit/fileformats/xtc/trr.c:10563:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2024-07-11T12:15:22,075 10563 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-07-11T12:15:22,075 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:22,085 moleculekit/fileformats/xtc/trr.c:12182:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:22,086 12182 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-07-11T12:15:22,086 | ^ 2024-07-11T12:15:22,096 moleculekit/fileformats/xtc/trr.c:10563:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2024-07-11T12:15:22,096 10563 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-07-11T12:15:22,097 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:22,107 moleculekit/fileformats/xtc/trr.c:12238:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:22,107 12238 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-07-11T12:15:22,108 | ^ 2024-07-11T12:15:22,117 moleculekit/fileformats/xtc/trr.c:10547:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2024-07-11T12:15:22,117 10547 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-07-11T12:15:22,118 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:22,128 moleculekit/fileformats/xtc/trr.c:12234:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:22,129 12234 | } else if (unlikely(__pyx_t_35 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-07-11T12:15:22,129 | ^ 2024-07-11T12:15:22,138 moleculekit/fileformats/xtc/trr.c:10547:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2024-07-11T12:15:22,139 10547 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-07-11T12:15:22,140 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T12:15:28,688 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 2024-07-11T12:15:28,842 building 'moleculekit.dcd' extension 2024-07-11T12:15:28,843 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/dcd 2024-07-11T12:15:28,844 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src 2024-07-11T12:15:28,845 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-kqb5ac4z/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 2024-07-11T12:15:29,258 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:15:29,259 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:15:29,260 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:15:29,260 from moleculekit/fileformats/dcd/dcd.c:1256: 2024-07-11T12:15:29,261 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:15:29,261 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:15:29,262 | ^~~~~~~ 2024-07-11T12:15:30,540 In file included from moleculekit/fileformats/dcd/include/dcdplugin.h:1, 2024-07-11T12:15:30,540 from moleculekit/fileformats/dcd/dcd.c:1262: 2024-07-11T12:15:30,541 moleculekit/fileformats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2024-07-11T12:15:30,542 474 | static int fio_write_str(fio_fd fd, const char *str) { 2024-07-11T12:15:30,542 | ^~~~~~~~~~~~~ 2024-07-11T12:15:30,543 moleculekit/fileformats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2024-07-11T12:15:30,543 470 | static int fio_read_int32(fio_fd fd, int *i) { 2024-07-11T12:15:30,544 | ^~~~~~~~~~~~~~ 2024-07-11T12:15:30,545 moleculekit/fileformats/dcd/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 2024-07-11T12:15:30,546 466 | static int fio_write_int32(fio_fd fd, int i) { 2024-07-11T12:15:30,546 | ^~~~~~~~~~~~~~~ 2024-07-11T12:15:30,547 moleculekit/fileformats/dcd/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2024-07-11T12:15:30,548 457 | static fio_size_t fio_ftell(fio_fd fd) { 2024-07-11T12:15:30,549 | ^~~~~~~~~ 2024-07-11T12:15:30,549 moleculekit/fileformats/dcd/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 2024-07-11T12:15:30,550 450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { 2024-07-11T12:15:30,551 | ^~~~~~~~~ 2024-07-11T12:15:30,553 moleculekit/fileformats/dcd/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 2024-07-11T12:15:30,553 415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { 2024-07-11T12:15:30,554 | ^~~~~~~~~ 2024-07-11T12:15:30,555 moleculekit/fileformats/dcd/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2024-07-11T12:15:30,555 394 | static int fio_fclose(fio_fd fd) { 2024-07-11T12:15:30,556 | ^~~~~~~~~~ 2024-07-11T12:15:30,557 moleculekit/fileformats/dcd/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2024-07-11T12:15:30,557 366 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2024-07-11T12:15:30,558 | ^~~~~~~~ 2024-07-11T12:15:45,013 moleculekit/fileformats/dcd/dcd.c: In function ‘__pyx_pf_11moleculekit_3dcd_17DCDTrajectoryFile_18read’: 2024-07-11T12:15:45,014 moleculekit/fileformats/dcd/dcd.c:1158:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:15:45,015 1158 | #define PyInt_FromLong PyLong_FromLong 2024-07-11T12:15:45,015 | ^~~~~~~~~~~~~~~ 2024-07-11T12:15:45,022 moleculekit/fileformats/dcd/dcd.c:8476:7: note: ‘__pyx_v_i’ was declared here 2024-07-11T12:15:45,023 8476 | int __pyx_v_i; 2024-07-11T12:15:45,023 | ^~~~~~~~~ 2024-07-11T12:15:48,403 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-kqb5ac4z/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 2024-07-11T12:15:48,624 moleculekit/fileformats/dcd/src/dcdplugin.c: In function ‘read_dcdheader’: 2024-07-11T12:15:48,625 moleculekit/fileformats/dcd/src/dcdplugin.c:150:55: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:15:48,625 150 | else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) 2024-07-11T12:15:48,626 | ^~ 2024-07-11T12:15:48,626 moleculekit/fileformats/dcd/src/dcdplugin.c:173:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:15:48,627 173 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) 2024-07-11T12:15:48,627 | ^~ 2024-07-11T12:15:48,628 moleculekit/fileformats/dcd/src/dcdplugin.c:194:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:15:48,629 194 | if (input_integer[0] != dcdcordmagic) 2024-07-11T12:15:48,629 | ^~ 2024-07-11T12:15:48,630 moleculekit/fileformats/dcd/src/dcdplugin.c:409:47: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:15:48,631 409 | if ((input_integer[0] + input_integer[1]) != ((*N) - (*NAMNF)) * 4) 2024-07-11T12:15:48,632 | ^~ 2024-07-11T12:15:48,633 moleculekit/fileformats/dcd/src/dcdplugin.c:428:47: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T12:15:48,633 428 | if ((input_integer[0] + input_integer[1]) != ((*N) - (*NAMNF)) * 4) 2024-07-11T12:15:48,634 | ^~ 2024-07-11T12:15:48,637 moleculekit/fileformats/dcd/src/dcdplugin.c: In function ‘read_dcdstep’: 2024-07-11T12:15:48,637 moleculekit/fileformats/dcd/src/dcdplugin.c:651:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:15:48,638 651 | if (tmpbuf[i] != sizeof(float) * N) 2024-07-11T12:15:48,638 | ^~ 2024-07-11T12:15:48,639 moleculekit/fileformats/dcd/src/dcdplugin.c:659:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T12:15:48,640 659 | if ((tmpbuf[2 * i] + tmpbuf[2 * i + 1]) != sizeof(float) * N) 2024-07-11T12:15:48,640 | ^~ 2024-07-11T12:15:48,666 In file included from moleculekit/fileformats/dcd/src/dcdplugin.c:55: 2024-07-11T12:15:48,667 moleculekit/fileformats/dcd/include/endianswap.h: At top level: 2024-07-11T12:15:48,668 moleculekit/fileformats/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2024-07-11T12:15:48,669 96 | static void swap2_aligned(void *v, long ndata) { 2024-07-11T12:15:48,669 | ^~~~~~~~~~~~~ 2024-07-11T12:15:48,670 moleculekit/fileformats/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2024-07-11T12:15:48,671 32 | static void swap2_unaligned(void *v, long ndata) { 2024-07-11T12:15:48,671 | ^~~~~~~~~~~~~~~ 2024-07-11T12:15:48,672 In file included from moleculekit/fileformats/dcd/src/dcdplugin.c:46: 2024-07-11T12:15:48,672 moleculekit/fileformats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2024-07-11T12:15:48,673 474 | static int fio_write_str(fio_fd fd, const char *str) { 2024-07-11T12:15:48,673 | ^~~~~~~~~~~~~ 2024-07-11T12:15:48,674 moleculekit/fileformats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2024-07-11T12:15:48,675 470 | static int fio_read_int32(fio_fd fd, int *i) { 2024-07-11T12:15:48,675 | ^~~~~~~~~~~~~~ 2024-07-11T12:15:49,954 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 2024-07-11T12:15:50,088 building 'moleculekit.binpos' extension 2024-07-11T12:15:50,089 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/binpos 2024-07-11T12:15:50,090 creating build/temp.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src 2024-07-11T12:15:50,091 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-kqb5ac4z/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 2024-07-11T12:15:50,500 In file included from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-07-11T12:15:50,501 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-07-11T12:15:50,501 from /tmp/pip-build-env-kqb5ac4z/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-07-11T12:15:50,502 from moleculekit/fileformats/binpos/binpos.c:1256: 2024-07-11T12:15:50,503 /tmp/pip-build-env-kqb5ac4z/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] 2024-07-11T12:15:50,504 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-07-11T12:15:50,504 | ^~~~~~~ 2024-07-11T12:16:05,058 In function ‘__pyx_pf_11moleculekit_6binpos_20BINPOSTrajectoryFile_6_read’, 2024-07-11T12:16:05,059 inlined from ‘__pyx_pw_11moleculekit_6binpos_20BINPOSTrajectoryFile_7_read’ at moleculekit/fileformats/binpos/binpos.c:7958:13: 2024-07-11T12:16:05,066 moleculekit/fileformats/binpos/binpos.c:8499:6: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:16:05,067 8499 | if (__pyx_t_1) { 2024-07-11T12:16:05,068 | ^ 2024-07-11T12:16:05,068 moleculekit/fileformats/binpos/binpos.c: In function ‘__pyx_pw_11moleculekit_6binpos_20BINPOSTrajectoryFile_7_read’: 2024-07-11T12:16:05,074 moleculekit/fileformats/binpos/binpos.c:7976:7: note: ‘__pyx_v_status’ was declared here 2024-07-11T12:16:05,074 7976 | int __pyx_v_status; 2024-07-11T12:16:05,075 | ^~~~~~~~~~~~~~ 2024-07-11T12:16:05,076 moleculekit/fileformats/binpos/binpos.c:1158:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T12:16:05,077 1158 | #define PyInt_FromLong PyLong_FromLong 2024-07-11T12:16:05,077 | ^~~~~~~~~~~~~~~ 2024-07-11T12:16:05,084 moleculekit/fileformats/binpos/binpos.c:7973:7: note: ‘__pyx_v_i’ was declared here 2024-07-11T12:16:05,084 7973 | int __pyx_v_i; 2024-07-11T12:16:05,085 | ^~~~~~~~~ 2024-07-11T12:16:08,562 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-kqb5ac4z/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 2024-07-11T12:16:08,901 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 2024-07-11T12:16:09,028 building 'moleculekit.tmalign' extension 2024-07-11T12:16:09,029 creating build/temp.linux-armv7l-cpython-311/moleculekit/tmalign 2024-07-11T12:16:09,029 creating build/temp.linux-armv7l-cpython-311/moleculekit/tmalign/src 2024-07-11T12:16:09,031 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-kqb5ac4z/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 2024-07-11T12:16:43,016 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-kqb5ac4z/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 2024-07-11T12:17:05,642 In file included from /usr/include/c++/12/vector:70, 2024-07-11T12:17:05,642 from moleculekit/tmalign/tmalign_util.cpp:1280: 2024-07-11T12:17:05,643 /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]’: 2024-07-11T12:17:05,644 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-07-11T12:17:05,645 439 | vector<_Tp, _Alloc>:: 2024-07-11T12:17:05,645 | ^~~~~~~~~~~~~~~~~~~ 2024-07-11T12:17:06,452 In file included from /usr/include/c++/12/vector:64: 2024-07-11T12:17:06,453 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-07-11T12:17:06,454 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, 2024-07-11T12:17:06,455 inlined from ‘PyObject* __pyx_pw_11moleculekit_7tmalign_1tmalign(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at moleculekit/tmalign/tmalign_util.cpp:20718:52: 2024-07-11T12:17:06,455 /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 2024-07-11T12:17:06,456 1287 | _M_realloc_insert(end(), __x); 2024-07-11T12:17:06,457 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-11T12:17:06,458 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-07-11T12:17:06,458 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, 2024-07-11T12:17:06,459 inlined from ‘PyObject* __pyx_pw_11moleculekit_7tmalign_1tmalign(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at moleculekit/tmalign/tmalign_util.cpp:20718:52: 2024-07-11T12:17:06,459 /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 2024-07-11T12:17:06,460 1287 | _M_realloc_insert(end(), __x); 2024-07-11T12:17:06,460 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-11T12:17:06,461 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2024-07-11T12:17:06,461 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, 2024-07-11T12:17:06,462 inlined from ‘PyObject* __pyx_pw_11moleculekit_7tmalign_1tmalign(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at moleculekit/tmalign/tmalign_util.cpp:20718:52: 2024-07-11T12:17:06,463 /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 2024-07-11T12:17:06,463 1287 | _M_realloc_insert(end(), __x); 2024-07-11T12:17:06,464 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-07-11T12:17:08,850 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 2024-07-11T12:17:09,236 UPDATING build/lib.linux-armv7l-cpython-311/moleculekit/_version.py 2024-07-11T12:17:09,237 set build/lib.linux-armv7l-cpython-311/moleculekit/_version.py to '1.9.0' 2024-07-11T12:17:09,237 installing to build/bdist.linux-armv7l/wheel 2024-07-11T12:17:09,238 running install 2024-07-11T12:17:09,262 running install_lib 2024-07-11T12:17:09,267 creating build/bdist.linux-armv7l 2024-07-11T12:17:09,268 creating build/bdist.linux-armv7l/wheel 2024-07-11T12:17:09,271 creating build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,272 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,323 copying build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,348 copying build/lib.linux-armv7l-cpython-311/moleculekit/vmd_wrapper -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,350 copying build/lib.linux-armv7l-cpython-311/moleculekit/_version.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,352 creating build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-07-11T12:17:09,353 copying build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils/bondguesser_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-07-11T12:17:09,372 copying build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils/bondguesser_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-07-11T12:17:09,374 copying build/lib.linux-armv7l-cpython-311/moleculekit/logging.ini -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,376 copying build/lib.linux-armv7l-cpython-311/moleculekit/distance.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,378 creating build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,379 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/autosegment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,381 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/sequencestructuralalignment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,384 creating build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-07-11T12:17:09,385 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools/obabel_cli.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-07-11T12:17:09,386 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/obabel_tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-07-11T12:17:09,388 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/detect.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,391 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/hhblitsprofile.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,393 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/modelling.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,395 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,396 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/graphalignment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,399 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/docking.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,401 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/preparation.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,404 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/crystalpacking.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,406 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/atomtyper.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,408 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/voxeldescriptors.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,411 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/preparation_customres.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,413 copying build/lib.linux-armv7l-cpython-311/moleculekit/tools/moleculechecks.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-07-11T12:17:09,416 creating build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-11T12:17:09,417 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect/languageparser.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-11T12:17:09,419 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect/analyze.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-11T12:17:09,421 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect/atomselect.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-11T12:17:09,424 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-07-11T12:17:09,426 creating build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-07-11T12:17:09,427 copying build/lib.linux-armv7l-cpython-311/moleculekit/wrapping/wrapping.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-07-11T12:17:09,429 copying build/lib.linux-armv7l-cpython-311/moleculekit/wrapping/wrapping.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-07-11T12:17:09,450 creating build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,451 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricrmsd.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,454 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/projection.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,456 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricsecondarystructure.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,458 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metriccoordinate.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,460 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/util.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,462 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricplumed2.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,465 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricgyration.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,467 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,468 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricshell.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,471 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metrictmscore.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,473 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricsasa.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,475 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricfluctuation.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,477 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricdihedral.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,479 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricdistance.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,482 copying build/lib.linux-armv7l-cpython-311/moleculekit/projections/metricsphericalcoordinate.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-07-11T12:17:09,484 copying build/lib.linux-armv7l-cpython-311/moleculekit/binpos.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,497 copying build/lib.linux-armv7l-cpython-311/moleculekit/molecule.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,501 copying build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,525 copying build/lib.linux-armv7l-cpython-311/moleculekit/readers.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,531 copying build/lib.linux-armv7l-cpython-311/moleculekit/config.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,533 copying build/lib.linux-armv7l-cpython-311/moleculekit/align.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,536 copying build/lib.linux-armv7l-cpython-311/moleculekit/writers.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:09,540 creating build/bdist.linux-armv7l/wheel/moleculekit/share 2024-07-11T12:17:09,541 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/opm_sequences.json -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-07-11T12:17:09,765 creating build/bdist.linux-armv7l/wheel/moleculekit/share/atomselect 2024-07-11T12:17:09,766 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/atomselect/atomselect.json -> build/bdist.linux-armv7l/wheel/moleculekit/share/atomselect 2024-07-11T12:17:09,768 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/backbone.cif -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-07-11T12:17:09,770 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/ALA.cif -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-07-11T12:17:09,772 creating build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr 2024-07-11T12:17:09,776 creating build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,777 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PTR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,779 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,780 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/YCM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,782 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DPP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,784 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/OCY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,785 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4IN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,787 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,789 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,791 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NLE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,797 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ORM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,799 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/FGL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,801 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,802 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DA2.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,805 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NAL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,807 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/YNM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,808 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HHK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,810 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,812 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NZC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,814 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,816 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/APD.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,818 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NVA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,820 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,821 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MMO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,823 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0BN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,825 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MVA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,827 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HPE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,829 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/AHP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,831 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/YNM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,832 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HLX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,834 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ME0.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,836 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GHG.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,838 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PRK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,840 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ORM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,842 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,844 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HLU.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,846 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ABA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,848 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2AS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,849 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BTK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,852 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PCA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,854 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0A1.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,856 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GHG.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,858 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/I2M.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,859 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/03Y.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,861 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MMO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,863 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GNC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,865 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,866 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,868 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/D4P.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,870 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,871 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BTK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,873 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/SEP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,874 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ME0.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,876 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,878 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/.gitkeep -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,880 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/FGL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,882 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PRK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,883 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2GX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,886 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/M3L.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,887 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BCS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,889 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,891 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NLE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,893 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,895 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NCY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,897 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PTR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,899 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HYP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,901 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/P1L.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,904 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,905 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/OCY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,907 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/AA4.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,909 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IGL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,911 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IGL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,913 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HTR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,914 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HTR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,916 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/004.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,918 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ESC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,920 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,922 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,923 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,925 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DPP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,927 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/5JP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,929 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,931 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NAL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,932 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/M3L.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,935 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,937 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,939 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2MR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,941 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/AA4.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,942 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/OMX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,944 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HYP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,946 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,948 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TPO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,950 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0A1.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,951 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,953 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,954 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/AHP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,956 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0AF.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,958 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ESC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,960 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DAH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,962 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CGU.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,963 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/SEP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,965 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CCS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,967 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,969 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IIL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,971 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ONL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,973 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/OMX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,974 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NZC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,976 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0BN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,978 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4PH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,980 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NVA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,982 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BCS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,984 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TY2.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,985 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HPE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,987 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TY2.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,989 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2MR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,991 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DAB.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,992 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/004.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,994 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,996 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/YCM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,997 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ABA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:09,999 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HOX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,001 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,003 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,005 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,007 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/03Y.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,008 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HOX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,010 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/P1L.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,012 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IML.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,013 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2AS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,015 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4PH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,017 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IIL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,019 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/1MH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,021 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DA2.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,022 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2ML.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,024 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ONL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,026 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TRO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,028 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DAB.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,030 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,031 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,033 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TRO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,035 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/PCA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,037 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/D4P.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,039 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MEA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,041 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,042 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/I2M.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,044 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,046 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BB8.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,048 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CCS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,050 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MVA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,052 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,054 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HLX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,055 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/IML.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,057 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CGU.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,059 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,061 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/CSS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,063 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/KYN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,065 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HLU.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,066 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2GX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,068 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TPO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,070 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HQA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,071 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/APD.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,073 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/MLY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,075 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/NCY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,077 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/KYN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,079 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/DAH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,081 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/0AF.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,083 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/4IN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,085 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/ALC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,086 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HHK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,089 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/BB8.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,090 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/5JP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,092 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/1MH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,094 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/2ML.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,096 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,098 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/HQA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,100 copying build/lib.linux-armv7l-cpython-311/moleculekit/share/pdb2pqr/residues/GNC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-07-11T12:17:10,102 copying build/lib.linux-armv7l-cpython-311/moleculekit/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,115 copying build/lib.linux-armv7l-cpython-311/moleculekit/vmdgraphics.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,118 copying build/lib.linux-armv7l-cpython-311/moleculekit/vmdviewer.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,120 copying build/lib.linux-armv7l-cpython-311/moleculekit/util.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,123 creating build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-07-11T12:17:10,124 copying build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils/cython_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-07-11T12:17:10,143 copying build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils/cython_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-07-11T12:17:10,145 copying build/lib.linux-armv7l-cpython-311/moleculekit/opm.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,147 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-07-11T12:17:10,148 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-07-11T12:17:10,150 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/src 2024-07-11T12:17:10,151 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/src/dcdplugin.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/src 2024-07-11T12:17:10,153 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/dcd.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-07-11T12:17:10,156 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/dcd.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-07-11T12:17:10,172 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-11T12:17:10,173 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/molfile_plugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-11T12:17:10,176 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/endianswap.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-11T12:17:10,179 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/fastio.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-11T12:17:10,181 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/largefiles.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-11T12:17:10,183 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/include/dcdplugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-07-11T12:17:10,184 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/dcd/dcdlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-07-11T12:17:10,187 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-07-11T12:17:10,188 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/src 2024-07-11T12:17:10,189 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/src/binposplugin.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/src 2024-07-11T12:17:10,191 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/binpos.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-07-11T12:17:10,211 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-07-11T12:17:10,212 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include/molfile_plugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-07-11T12:17:10,215 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include/binposplugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-07-11T12:17:10,217 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/include/largefiles.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-07-11T12:17:10,219 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/binpos.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-07-11T12:17:10,222 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/binpos/binposlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-07-11T12:17:10,223 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/netcdf.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-07-11T12:17:10,226 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/utils.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-07-11T12:17:10,228 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-07-11T12:17:10,230 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-11T12:17:10,231 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-11T12:17:10,232 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-11T12:17:10,236 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-11T12:17:10,238 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-11T12:17:10,240 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdr_seek.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-11T12:17:10,242 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-07-11T12:17:10,245 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/trrlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-11T12:17:10,247 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/xtclib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-11T12:17:10,249 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-11T12:17:10,269 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-11T12:17:10,270 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-11T12:17:10,272 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xdr_seek.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-11T12:17:10,274 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-11T12:17:10,276 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-11T12:17:10,278 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/xtc.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-11T12:17:10,280 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/include/trr_header.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-07-11T12:17:10,282 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/trr.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-11T12:17:10,285 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/trr.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-11T12:17:10,314 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/xdrlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-11T12:17:10,316 copying build/lib.linux-armv7l-cpython-311/moleculekit/fileformats/xtc/xtc.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-07-11T12:17:10,318 copying build/lib.linux-armv7l-cpython-311/moleculekit/wrapping.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,343 copying build/lib.linux-armv7l-cpython-311/moleculekit/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,345 copying build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,370 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-07-11T12:17:10,371 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/tmalign_util.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-07-11T12:17:10,373 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign/src 2024-07-11T12:17:10,374 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/src/TMAlign.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign/src 2024-07-11T12:17:10,381 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/tmalignlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-07-11T12:17:10,383 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign/include 2024-07-11T12:17:10,384 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/include/TMAlign.h -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign/include 2024-07-11T12:17:10,386 copying build/lib.linux-armv7l-cpython-311/moleculekit/tmalign/tmalign_util.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-07-11T12:17:10,414 creating build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-07-11T12:17:10,415 copying build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils/occupancy_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-07-11T12:17:10,439 copying build/lib.linux-armv7l-cpython-311/moleculekit/occupancy_utils/occupancy_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-07-11T12:17:10,441 copying build/lib.linux-armv7l-cpython-311/moleculekit/viewer.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,444 creating build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-07-11T12:17:10,445 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils/atomselect_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-07-11T12:17:10,448 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils/atomselect_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-07-11T12:17:10,472 creating build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-11T12:17:10,473 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/smallmol.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-11T12:17:10,476 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/smallmollib.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-11T12:17:10,479 creating build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-11T12:17:10,480 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools/clustering.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-11T12:17:10,482 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools/restrainedembed.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-11T12:17:10,484 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-11T12:17:10,486 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/tools/test_tools.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-07-11T12:17:10,489 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/smallmolcdp.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-11T12:17:10,491 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/util.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-11T12:17:10,494 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-11T12:17:10,495 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/test_smallmollib.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-11T12:17:10,498 copying build/lib.linux-armv7l-cpython-311/moleculekit/smallmol/test_smallmol.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-07-11T12:17:10,500 copying build/lib.linux-armv7l-cpython-311/moleculekit/rdkitintegration.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,502 copying build/lib.linux-armv7l-cpython-311/moleculekit/home.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,503 copying build/lib.linux-armv7l-cpython-311/moleculekit/dihedral.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,505 copying build/lib.linux-armv7l-cpython-311/moleculekit/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,526 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx 2024-07-11T12:17:10,527 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-11T12:17:10,528 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/PdbxReader.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-11T12:17:10,531 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/PdbxContainers.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-11T12:17:10,534 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/PdbxParser.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-11T12:17:10,537 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-11T12:17:10,539 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/reader/BinaryCifReader.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-07-11T12:17:10,542 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx 2024-07-11T12:17:10,544 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-11T12:17:10,545 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests/PdbxReadWriteTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-11T12:17:10,548 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-11T12:17:10,550 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests/PdbxReaderTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-11T12:17:10,552 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/tests/PdbxWriterTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-07-11T12:17:10,555 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-07-11T12:17:10,557 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer/PdbxWriter.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-07-11T12:17:10,559 copying build/lib.linux-armv7l-cpython-311/moleculekit/pdbx/writer/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-07-11T12:17:10,561 copying build/lib.linux-armv7l-cpython-311/moleculekit/periodictable.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,564 copying build/lib.linux-armv7l-cpython-311/moleculekit/pymolgraphics.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,566 copying build/lib.linux-armv7l-cpython-311/moleculekit/rcsb.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,569 creating build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-07-11T12:17:10,570 copying build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils/distance_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-07-11T12:17:10,595 copying build/lib.linux-armv7l-cpython-311/moleculekit/distance_utils/distance_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-07-11T12:17:10,597 creating build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-07-11T12:17:10,598 copying build/lib.linux-armv7l-cpython-311/moleculekit/ply/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-07-11T12:17:10,600 copying build/lib.linux-armv7l-cpython-311/moleculekit/ply/lex.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-07-11T12:17:10,603 copying build/lib.linux-armv7l-cpython-311/moleculekit/ply/yacc.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-07-11T12:17:10,607 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-11T12:17:10,608 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-07-11T12:17:10,609 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi/pipi.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-07-11T12:17:10,611 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi/pipi.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-07-11T12:17:10,640 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-11T12:17:10,642 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/pipi.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-11T12:17:10,672 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-11T12:17:10,692 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-07-11T12:17:10,693 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds/hbonds.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-07-11T12:17:10,715 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/hbonds/hbonds.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-07-11T12:17:10,717 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/interactions.py -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-11T12:17:10,720 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-07-11T12:17:10,721 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi/cationpi.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-07-11T12:17:10,742 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi/cationpi.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-07-11T12:17:10,745 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/cationpi.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-11T12:17:10,769 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-07-11T12:17:10,790 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-07-11T12:17:10,791 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole/sigmahole.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-07-11T12:17:10,811 copying build/lib.linux-armv7l-cpython-311/moleculekit/interactions/sigmahole/sigmahole.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-07-11T12:17:10,813 copying build/lib.linux-armv7l-cpython-311/moleculekit/cython_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,833 copying build/lib.linux-armv7l-cpython-311/moleculekit/bondguesser.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,836 copying build/lib.linux-armv7l-cpython-311/moleculekit/version.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,837 copying build/lib.linux-armv7l-cpython-311/moleculekit/atomselect_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,862 copying build/lib.linux-armv7l-cpython-311/moleculekit/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-07-11T12:17:10,884 running install_egg_info 2024-07-11T12:17:10,889 Copying moleculekit.egg-info to build/bdist.linux-armv7l/wheel/moleculekit-1.9.0-py3.11.egg-info 2024-07-11T12:17:10,901 running install_scripts 2024-07-11T12:17:10,949 creating build/bdist.linux-armv7l/wheel/moleculekit-1.9.0.dist-info/WHEEL 2024-07-11T12:17:10,951 creating '/tmp/pip-wheel-j63sbhe6/.tmp-dsg1yqne/moleculekit-1.9.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-11T12:17:10,954 adding 'moleculekit/__init__.py' 2024-07-11T12:17:10,956 adding 'moleculekit/_version.py' 2024-07-11T12:17:10,958 adding 'moleculekit/align.py' 2024-07-11T12:17:11,312 adding 'moleculekit/atomselect_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:11,471 adding 'moleculekit/binpos.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:11,478 adding 'moleculekit/bondguesser.py' 2024-07-11T12:17:11,722 adding 'moleculekit/bondguesser_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:11,731 adding 'moleculekit/config.py' 2024-07-11T12:17:11,990 adding 'moleculekit/cython_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:12,149 adding 'moleculekit/dcd.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:12,155 adding 'moleculekit/dihedral.py' 2024-07-11T12:17:12,156 adding 'moleculekit/distance.py' 2024-07-11T12:17:12,473 adding 'moleculekit/distance_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:12,484 adding 'moleculekit/home.py' 2024-07-11T12:17:12,485 adding 'moleculekit/logging.ini' 2024-07-11T12:17:12,500 adding 'moleculekit/molecule.py' 2024-07-11T12:17:12,728 adding 'moleculekit/occupancy_utils.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:12,736 adding 'moleculekit/opm.py' 2024-07-11T12:17:12,739 adding 'moleculekit/periodictable.py' 2024-07-11T12:17:12,740 adding 'moleculekit/pymolgraphics.py' 2024-07-11T12:17:12,741 adding 'moleculekit/rcsb.py' 2024-07-11T12:17:12,743 adding 'moleculekit/rdkitintegration.py' 2024-07-11T12:17:12,758 adding 'moleculekit/readers.py' 2024-07-11T12:17:13,354 adding 'moleculekit/tmalign.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:13,658 adding 'moleculekit/trr.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:13,669 adding 'moleculekit/util.py' 2024-07-11T12:17:13,671 adding 'moleculekit/version.py' 2024-07-11T12:17:13,672 adding 'moleculekit/viewer.py' 2024-07-11T12:17:13,674 adding 'moleculekit/vmd_wrapper' 2024-07-11T12:17:13,676 adding 'moleculekit/vmdgraphics.py' 2024-07-11T12:17:13,678 adding 'moleculekit/vmdviewer.py' 2024-07-11T12:17:13,930 adding 'moleculekit/wrapping.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:13,944 adding 'moleculekit/writers.py' 2024-07-11T12:17:14,203 adding 'moleculekit/xtc.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:14,213 adding 'moleculekit/atomselect/__init__.py' 2024-07-11T12:17:14,214 adding 'moleculekit/atomselect/analyze.py' 2024-07-11T12:17:14,216 adding 'moleculekit/atomselect/atomselect.py' 2024-07-11T12:17:14,218 adding 'moleculekit/atomselect/languageparser.py' 2024-07-11T12:17:14,323 adding 'moleculekit/atomselect_utils/atomselect_utils.cpp' 2024-07-11T12:17:14,334 adding 'moleculekit/atomselect_utils/atomselect_utils.pyx' 2024-07-11T12:17:14,426 adding 'moleculekit/bondguesser_utils/bondguesser_utils.cpp' 2024-07-11T12:17:14,435 adding 'moleculekit/bondguesser_utils/bondguesser_utils.pyx' 2024-07-11T12:17:14,525 adding 'moleculekit/cython_utils/cython_utils.cpp' 2024-07-11T12:17:14,534 adding 'moleculekit/cython_utils/cython_utils.pyx' 2024-07-11T12:17:14,637 adding 'moleculekit/distance_utils/distance_utils.cpp' 2024-07-11T12:17:14,648 adding 'moleculekit/distance_utils/distance_utils.pyx' 2024-07-11T12:17:14,650 adding 'moleculekit/fileformats/__init__.py' 2024-07-11T12:17:14,655 adding 'moleculekit/fileformats/netcdf.py' 2024-07-11T12:17:14,656 adding 'moleculekit/fileformats/utils.py' 2024-07-11T12:17:14,718 adding 'moleculekit/fileformats/binpos/binpos.c' 2024-07-11T12:17:14,725 adding 'moleculekit/fileformats/binpos/binpos.pyx' 2024-07-11T12:17:14,727 adding 'moleculekit/fileformats/binpos/binposlib.pxd' 2024-07-11T12:17:14,728 adding 'moleculekit/fileformats/binpos/include/binposplugin.h' 2024-07-11T12:17:14,729 adding 'moleculekit/fileformats/binpos/include/largefiles.h' 2024-07-11T12:17:14,735 adding 'moleculekit/fileformats/binpos/include/molfile_plugin.h' 2024-07-11T12:17:14,737 adding 'moleculekit/fileformats/binpos/src/binposplugin.c' 2024-07-11T12:17:14,801 adding 'moleculekit/fileformats/dcd/dcd.c' 2024-07-11T12:17:14,809 adding 'moleculekit/fileformats/dcd/dcd.pyx' 2024-07-11T12:17:14,810 adding 'moleculekit/fileformats/dcd/dcdlib.pxd' 2024-07-11T12:17:14,812 adding 'moleculekit/fileformats/dcd/include/dcdplugin.h' 2024-07-11T12:17:14,813 adding 'moleculekit/fileformats/dcd/include/endianswap.h' 2024-07-11T12:17:14,815 adding 'moleculekit/fileformats/dcd/include/fastio.h' 2024-07-11T12:17:14,816 adding 'moleculekit/fileformats/dcd/include/largefiles.h' 2024-07-11T12:17:14,821 adding 'moleculekit/fileformats/dcd/include/molfile_plugin.h' 2024-07-11T12:17:14,827 adding 'moleculekit/fileformats/dcd/src/dcdplugin.c' 2024-07-11T12:17:14,922 adding 'moleculekit/fileformats/xtc/trr.c' 2024-07-11T12:17:14,933 adding 'moleculekit/fileformats/xtc/trr.pyx' 2024-07-11T12:17:14,935 adding 'moleculekit/fileformats/xtc/trrlib.pxd' 2024-07-11T12:17:14,936 adding 'moleculekit/fileformats/xtc/xdrlib.pxd' 2024-07-11T12:17:15,026 adding 'moleculekit/fileformats/xtc/xtc.cpp' 2024-07-11T12:17:15,034 adding 'moleculekit/fileformats/xtc/xtc.pyx' 2024-07-11T12:17:15,035 adding 'moleculekit/fileformats/xtc/xtclib.pxd' 2024-07-11T12:17:15,037 adding 'moleculekit/fileformats/xtc/include/trr_header.h' 2024-07-11T12:17:15,038 adding 'moleculekit/fileformats/xtc/include/xdr_seek.h' 2024-07-11T12:17:15,041 adding 'moleculekit/fileformats/xtc/include/xdrfile.h' 2024-07-11T12:17:15,042 adding 'moleculekit/fileformats/xtc/include/xdrfile_trr.h' 2024-07-11T12:17:15,044 adding 'moleculekit/fileformats/xtc/include/xdrfile_xtc.h' 2024-07-11T12:17:15,045 adding 'moleculekit/fileformats/xtc/include/xtc.h' 2024-07-11T12:17:15,047 adding 'moleculekit/fileformats/xtc/src/xdr_seek.c' 2024-07-11T12:17:15,053 adding 'moleculekit/fileformats/xtc/src/xdrfile.cpp' 2024-07-11T12:17:15,055 adding 'moleculekit/fileformats/xtc/src/xdrfile_trr.c' 2024-07-11T12:17:15,057 adding 'moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp' 2024-07-11T12:17:15,059 adding 'moleculekit/fileformats/xtc/src/xtc.cpp' 2024-07-11T12:17:15,061 adding 'moleculekit/interactions/__init__.py' 2024-07-11T12:17:15,339 adding 'moleculekit/interactions/cationpi.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:15,603 adding 'moleculekit/interactions/hbonds.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:15,615 adding 'moleculekit/interactions/interactions.py' 2024-07-11T12:17:15,896 adding 'moleculekit/interactions/pipi.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:16,177 adding 'moleculekit/interactions/sigmahole.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T12:17:16,278 adding 'moleculekit/interactions/cationpi/cationpi.cpp' 2024-07-11T12:17:16,287 adding 'moleculekit/interactions/cationpi/cationpi.pyx' 2024-07-11T12:17:16,379 adding 'moleculekit/interactions/hbonds/hbonds.cpp' 2024-07-11T12:17:16,388 adding 'moleculekit/interactions/hbonds/hbonds.pyx' 2024-07-11T12:17:16,480 adding 'moleculekit/interactions/pipi/pipi.cpp' 2024-07-11T12:17:16,489 adding 'moleculekit/interactions/pipi/pipi.pyx' 2024-07-11T12:17:16,581 adding 'moleculekit/interactions/sigmahole/sigmahole.cpp' 2024-07-11T12:17:16,590 adding 'moleculekit/interactions/sigmahole/sigmahole.pyx' 2024-07-11T12:17:16,677 adding 'moleculekit/occupancy_utils/occupancy_utils.cpp' 2024-07-11T12:17:16,686 adding 'moleculekit/occupancy_utils/occupancy_utils.pyx' 2024-07-11T12:17:16,687 adding 'moleculekit/pdbx/__init__.py' 2024-07-11T12:17:16,690 adding 'moleculekit/pdbx/reader/BinaryCifReader.py' 2024-07-11T12:17:16,693 adding 'moleculekit/pdbx/reader/PdbxContainers.py' 2024-07-11T12:17:16,696 adding 'moleculekit/pdbx/reader/PdbxParser.py' 2024-07-11T12:17:16,698 adding 'moleculekit/pdbx/reader/PdbxReader.py' 2024-07-11T12:17:16,699 adding 'moleculekit/pdbx/reader/__init__.py' 2024-07-11T12:17:16,701 adding 'moleculekit/pdbx/tests/PdbxReadWriteTests.py' 2024-07-11T12:17:16,702 adding 'moleculekit/pdbx/tests/PdbxReaderTests.py' 2024-07-11T12:17:16,704 adding 'moleculekit/pdbx/tests/PdbxWriterTests.py' 2024-07-11T12:17:16,705 adding 'moleculekit/pdbx/tests/__init__.py' 2024-07-11T12:17:16,707 adding 'moleculekit/pdbx/writer/PdbxWriter.py' 2024-07-11T12:17:16,708 adding 'moleculekit/pdbx/writer/__init__.py' 2024-07-11T12:17:16,710 adding 'moleculekit/ply/__init__.py' 2024-07-11T12:17:16,714 adding 'moleculekit/ply/lex.py' 2024-07-11T12:17:16,725 adding 'moleculekit/ply/yacc.py' 2024-07-11T12:17:16,727 adding 'moleculekit/projections/__init__.py' 2024-07-11T12:17:16,729 adding 'moleculekit/projections/metriccoordinate.py' 2024-07-11T12:17:16,733 adding 'moleculekit/projections/metricdihedral.py' 2024-07-11T12:17:16,737 adding 'moleculekit/projections/metricdistance.py' 2024-07-11T12:17:16,739 adding 'moleculekit/projections/metricfluctuation.py' 2024-07-11T12:17:16,740 adding 'moleculekit/projections/metricgyration.py' 2024-07-11T12:17:16,744 adding 'moleculekit/projections/metricplumed2.py' 2024-07-11T12:17:16,746 adding 'moleculekit/projections/metricrmsd.py' 2024-07-11T12:17:16,748 adding 'moleculekit/projections/metricsasa.py' 2024-07-11T12:17:16,750 adding 'moleculekit/projections/metricsecondarystructure.py' 2024-07-11T12:17:16,751 adding 'moleculekit/projections/metricshell.py' 2024-07-11T12:17:16,753 adding 'moleculekit/projections/metricsphericalcoordinate.py' 2024-07-11T12:17:16,755 adding 'moleculekit/projections/metrictmscore.py' 2024-07-11T12:17:16,756 adding 'moleculekit/projections/projection.py' 2024-07-11T12:17:16,758 adding 'moleculekit/projections/util.py' 2024-07-11T12:17:16,760 adding 'moleculekit/share/ALA.cif' 2024-07-11T12:17:16,761 adding 'moleculekit/share/backbone.cif' 2024-07-11T12:17:18,059 adding 'moleculekit/share/opm_sequences.json' 2024-07-11T12:17:18,145 adding 'moleculekit/share/atomselect/atomselect.json' 2024-07-11T12:17:18,150 adding 'moleculekit/share/pdb2pqr/residues/.gitkeep' 2024-07-11T12:17:18,151 adding 'moleculekit/share/pdb2pqr/residues/004.dat' 2024-07-11T12:17:18,152 adding 'moleculekit/share/pdb2pqr/residues/004.xml' 2024-07-11T12:17:18,153 adding 'moleculekit/share/pdb2pqr/residues/03Y.dat' 2024-07-11T12:17:18,155 adding 'moleculekit/share/pdb2pqr/residues/03Y.xml' 2024-07-11T12:17:18,156 adding 'moleculekit/share/pdb2pqr/residues/0A1.dat' 2024-07-11T12:17:18,157 adding 'moleculekit/share/pdb2pqr/residues/0A1.xml' 2024-07-11T12:17:18,158 adding 'moleculekit/share/pdb2pqr/residues/0AF.dat' 2024-07-11T12:17:18,160 adding 'moleculekit/share/pdb2pqr/residues/0AF.xml' 2024-07-11T12:17:18,161 adding 'moleculekit/share/pdb2pqr/residues/0BN.dat' 2024-07-11T12:17:18,162 adding 'moleculekit/share/pdb2pqr/residues/0BN.xml' 2024-07-11T12:17:18,163 adding 'moleculekit/share/pdb2pqr/residues/1MH.dat' 2024-07-11T12:17:18,165 adding 'moleculekit/share/pdb2pqr/residues/1MH.xml' 2024-07-11T12:17:18,166 adding 'moleculekit/share/pdb2pqr/residues/2AS.dat' 2024-07-11T12:17:18,167 adding 'moleculekit/share/pdb2pqr/residues/2AS.xml' 2024-07-11T12:17:18,169 adding 'moleculekit/share/pdb2pqr/residues/2GX.dat' 2024-07-11T12:17:18,170 adding 'moleculekit/share/pdb2pqr/residues/2GX.xml' 2024-07-11T12:17:18,171 adding 'moleculekit/share/pdb2pqr/residues/2ML.dat' 2024-07-11T12:17:18,172 adding 'moleculekit/share/pdb2pqr/residues/2ML.xml' 2024-07-11T12:17:18,173 adding 'moleculekit/share/pdb2pqr/residues/2MR.dat' 2024-07-11T12:17:18,175 adding 'moleculekit/share/pdb2pqr/residues/2MR.xml' 2024-07-11T12:17:18,176 adding 'moleculekit/share/pdb2pqr/residues/4IN.dat' 2024-07-11T12:17:18,177 adding 'moleculekit/share/pdb2pqr/residues/4IN.xml' 2024-07-11T12:17:18,178 adding 'moleculekit/share/pdb2pqr/residues/4PH.dat' 2024-07-11T12:17:18,179 adding 'moleculekit/share/pdb2pqr/residues/4PH.xml' 2024-07-11T12:17:18,181 adding 'moleculekit/share/pdb2pqr/residues/4PQ.dat' 2024-07-11T12:17:18,182 adding 'moleculekit/share/pdb2pqr/residues/4PQ.xml' 2024-07-11T12:17:18,183 adding 'moleculekit/share/pdb2pqr/residues/5JP.dat' 2024-07-11T12:17:18,184 adding 'moleculekit/share/pdb2pqr/residues/5JP.xml' 2024-07-11T12:17:18,185 adding 'moleculekit/share/pdb2pqr/residues/AA4.dat' 2024-07-11T12:17:18,186 adding 'moleculekit/share/pdb2pqr/residues/AA4.xml' 2024-07-11T12:17:18,188 adding 'moleculekit/share/pdb2pqr/residues/ABA.dat' 2024-07-11T12:17:18,189 adding 'moleculekit/share/pdb2pqr/residues/ABA.xml' 2024-07-11T12:17:18,190 adding 'moleculekit/share/pdb2pqr/residues/AHP.dat' 2024-07-11T12:17:18,191 adding 'moleculekit/share/pdb2pqr/residues/AHP.xml' 2024-07-11T12:17:18,192 adding 'moleculekit/share/pdb2pqr/residues/ALC.dat' 2024-07-11T12:17:18,194 adding 'moleculekit/share/pdb2pqr/residues/ALC.xml' 2024-07-11T12:17:18,195 adding 'moleculekit/share/pdb2pqr/residues/ALN.dat' 2024-07-11T12:17:18,196 adding 'moleculekit/share/pdb2pqr/residues/ALN.xml' 2024-07-11T12:17:18,198 adding 'moleculekit/share/pdb2pqr/residues/ALY.dat' 2024-07-11T12:17:18,199 adding 'moleculekit/share/pdb2pqr/residues/ALY.xml' 2024-07-11T12:17:18,200 adding 'moleculekit/share/pdb2pqr/residues/APD.dat' 2024-07-11T12:17:18,202 adding 'moleculekit/share/pdb2pqr/residues/APD.xml' 2024-07-11T12:17:18,203 adding 'moleculekit/share/pdb2pqr/residues/BB8.dat' 2024-07-11T12:17:18,204 adding 'moleculekit/share/pdb2pqr/residues/BB8.xml' 2024-07-11T12:17:18,206 adding 'moleculekit/share/pdb2pqr/residues/BCS.dat' 2024-07-11T12:17:18,207 adding 'moleculekit/share/pdb2pqr/residues/BCS.xml' 2024-07-11T12:17:18,208 adding 'moleculekit/share/pdb2pqr/residues/BTK.dat' 2024-07-11T12:17:18,210 adding 'moleculekit/share/pdb2pqr/residues/BTK.xml' 2024-07-11T12:17:18,211 adding 'moleculekit/share/pdb2pqr/residues/CCS.dat' 2024-07-11T12:17:18,212 adding 'moleculekit/share/pdb2pqr/residues/CCS.xml' 2024-07-11T12:17:18,213 adding 'moleculekit/share/pdb2pqr/residues/CGU.dat' 2024-07-11T12:17:18,215 adding 'moleculekit/share/pdb2pqr/residues/CGU.xml' 2024-07-11T12:17:18,216 adding 'moleculekit/share/pdb2pqr/residues/CSA.dat' 2024-07-11T12:17:18,217 adding 'moleculekit/share/pdb2pqr/residues/CSA.xml' 2024-07-11T12:17:18,218 adding 'moleculekit/share/pdb2pqr/residues/CSO.dat' 2024-07-11T12:17:18,220 adding 'moleculekit/share/pdb2pqr/residues/CSO.xml' 2024-07-11T12:17:18,221 adding 'moleculekit/share/pdb2pqr/residues/CSP.dat' 2024-07-11T12:17:18,222 adding 'moleculekit/share/pdb2pqr/residues/CSP.xml' 2024-07-11T12:17:18,223 adding 'moleculekit/share/pdb2pqr/residues/CSS.dat' 2024-07-11T12:17:18,225 adding 'moleculekit/share/pdb2pqr/residues/CSS.xml' 2024-07-11T12:17:18,226 adding 'moleculekit/share/pdb2pqr/residues/D4P.dat' 2024-07-11T12:17:18,227 adding 'moleculekit/share/pdb2pqr/residues/D4P.xml' 2024-07-11T12:17:18,229 adding 'moleculekit/share/pdb2pqr/residues/DA2.dat' 2024-07-11T12:17:18,230 adding 'moleculekit/share/pdb2pqr/residues/DA2.xml' 2024-07-11T12:17:18,231 adding 'moleculekit/share/pdb2pqr/residues/DAB.dat' 2024-07-11T12:17:18,232 adding 'moleculekit/share/pdb2pqr/residues/DAB.xml' 2024-07-11T12:17:18,233 adding 'moleculekit/share/pdb2pqr/residues/DAH.dat' 2024-07-11T12:17:18,235 adding 'moleculekit/share/pdb2pqr/residues/DAH.xml' 2024-07-11T12:17:18,236 adding 'moleculekit/share/pdb2pqr/residues/DPP.dat' 2024-07-11T12:17:18,238 adding 'moleculekit/share/pdb2pqr/residues/DPP.xml' 2024-07-11T12:17:18,239 adding 'moleculekit/share/pdb2pqr/residues/ESC.dat' 2024-07-11T12:17:18,240 adding 'moleculekit/share/pdb2pqr/residues/ESC.xml' 2024-07-11T12:17:18,241 adding 'moleculekit/share/pdb2pqr/residues/FGL.dat' 2024-07-11T12:17:18,243 adding 'moleculekit/share/pdb2pqr/residues/FGL.xml' 2024-07-11T12:17:18,244 adding 'moleculekit/share/pdb2pqr/residues/GHG.dat' 2024-07-11T12:17:18,245 adding 'moleculekit/share/pdb2pqr/residues/GHG.xml' 2024-07-11T12:17:18,246 adding 'moleculekit/share/pdb2pqr/residues/GME.dat' 2024-07-11T12:17:18,248 adding 'moleculekit/share/pdb2pqr/residues/GME.xml' 2024-07-11T12:17:18,249 adding 'moleculekit/share/pdb2pqr/residues/GNC.dat' 2024-07-11T12:17:18,250 adding 'moleculekit/share/pdb2pqr/residues/GNC.xml' 2024-07-11T12:17:18,251 adding 'moleculekit/share/pdb2pqr/residues/HHK.dat' 2024-07-11T12:17:18,253 adding 'moleculekit/share/pdb2pqr/residues/HHK.xml' 2024-07-11T12:17:18,254 adding 'moleculekit/share/pdb2pqr/residues/HLU.dat' 2024-07-11T12:17:18,255 adding 'moleculekit/share/pdb2pqr/residues/HLU.xml' 2024-07-11T12:17:18,257 adding 'moleculekit/share/pdb2pqr/residues/HLX.dat' 2024-07-11T12:17:18,258 adding 'moleculekit/share/pdb2pqr/residues/HLX.xml' 2024-07-11T12:17:18,259 adding 'moleculekit/share/pdb2pqr/residues/HOX.dat' 2024-07-11T12:17:18,260 adding 'moleculekit/share/pdb2pqr/residues/HOX.xml' 2024-07-11T12:17:18,261 adding 'moleculekit/share/pdb2pqr/residues/HPE.dat' 2024-07-11T12:17:18,262 adding 'moleculekit/share/pdb2pqr/residues/HPE.xml' 2024-07-11T12:17:18,264 adding 'moleculekit/share/pdb2pqr/residues/HQA.dat' 2024-07-11T12:17:18,265 adding 'moleculekit/share/pdb2pqr/residues/HQA.xml' 2024-07-11T12:17:18,266 adding 'moleculekit/share/pdb2pqr/residues/HTR.dat' 2024-07-11T12:17:18,267 adding 'moleculekit/share/pdb2pqr/residues/HTR.xml' 2024-07-11T12:17:18,269 adding 'moleculekit/share/pdb2pqr/residues/HYP.dat' 2024-07-11T12:17:18,270 adding 'moleculekit/share/pdb2pqr/residues/HYP.xml' 2024-07-11T12:17:18,271 adding 'moleculekit/share/pdb2pqr/residues/I2M.dat' 2024-07-11T12:17:18,272 adding 'moleculekit/share/pdb2pqr/residues/I2M.xml' 2024-07-11T12:17:18,273 adding 'moleculekit/share/pdb2pqr/residues/IGL.dat' 2024-07-11T12:17:18,275 adding 'moleculekit/share/pdb2pqr/residues/IGL.xml' 2024-07-11T12:17:18,276 adding 'moleculekit/share/pdb2pqr/residues/IIL.dat' 2024-07-11T12:17:18,277 adding 'moleculekit/share/pdb2pqr/residues/IIL.xml' 2024-07-11T12:17:18,279 adding 'moleculekit/share/pdb2pqr/residues/IML.dat' 2024-07-11T12:17:18,280 adding 'moleculekit/share/pdb2pqr/residues/IML.xml' 2024-07-11T12:17:18,281 adding 'moleculekit/share/pdb2pqr/residues/KYN.dat' 2024-07-11T12:17:18,283 adding 'moleculekit/share/pdb2pqr/residues/KYN.xml' 2024-07-11T12:17:18,284 adding 'moleculekit/share/pdb2pqr/residues/LME.dat' 2024-07-11T12:17:18,285 adding 'moleculekit/share/pdb2pqr/residues/LME.xml' 2024-07-11T12:17:18,287 adding 'moleculekit/share/pdb2pqr/residues/LMQ.dat' 2024-07-11T12:17:18,288 adding 'moleculekit/share/pdb2pqr/residues/LMQ.xml' 2024-07-11T12:17:18,289 adding 'moleculekit/share/pdb2pqr/residues/LYZ.dat' 2024-07-11T12:17:18,291 adding 'moleculekit/share/pdb2pqr/residues/LYZ.xml' 2024-07-11T12:17:18,292 adding 'moleculekit/share/pdb2pqr/residues/M3L.dat' 2024-07-11T12:17:18,294 adding 'moleculekit/share/pdb2pqr/residues/M3L.xml' 2024-07-11T12:17:18,295 adding 'moleculekit/share/pdb2pqr/residues/ME0.dat' 2024-07-11T12:17:18,296 adding 'moleculekit/share/pdb2pqr/residues/ME0.xml' 2024-07-11T12:17:18,298 adding 'moleculekit/share/pdb2pqr/residues/MEA.dat' 2024-07-11T12:17:18,299 adding 'moleculekit/share/pdb2pqr/residues/MEA.xml' 2024-07-11T12:17:18,300 adding 'moleculekit/share/pdb2pqr/residues/MEN.dat' 2024-07-11T12:17:18,301 adding 'moleculekit/share/pdb2pqr/residues/MEN.xml' 2024-07-11T12:17:18,302 adding 'moleculekit/share/pdb2pqr/residues/MEQ.dat' 2024-07-11T12:17:18,304 adding 'moleculekit/share/pdb2pqr/residues/MEQ.xml' 2024-07-11T12:17:18,305 adding 'moleculekit/share/pdb2pqr/residues/MLE.dat' 2024-07-11T12:17:18,306 adding 'moleculekit/share/pdb2pqr/residues/MLE.xml' 2024-07-11T12:17:18,307 adding 'moleculekit/share/pdb2pqr/residues/MLY.dat' 2024-07-11T12:17:18,308 adding 'moleculekit/share/pdb2pqr/residues/MLY.xml' 2024-07-11T12:17:18,309 adding 'moleculekit/share/pdb2pqr/residues/MLZ.dat' 2024-07-11T12:17:18,311 adding 'moleculekit/share/pdb2pqr/residues/MLZ.xml' 2024-07-11T12:17:18,312 adding 'moleculekit/share/pdb2pqr/residues/MME.dat' 2024-07-11T12:17:18,313 adding 'moleculekit/share/pdb2pqr/residues/MME.xml' 2024-07-11T12:17:18,314 adding 'moleculekit/share/pdb2pqr/residues/MMO.dat' 2024-07-11T12:17:18,315 adding 'moleculekit/share/pdb2pqr/residues/MMO.xml' 2024-07-11T12:17:18,316 adding 'moleculekit/share/pdb2pqr/residues/MVA.dat' 2024-07-11T12:17:18,318 adding 'moleculekit/share/pdb2pqr/residues/MVA.xml' 2024-07-11T12:17:18,319 adding 'moleculekit/share/pdb2pqr/residues/NAL.dat' 2024-07-11T12:17:18,320 adding 'moleculekit/share/pdb2pqr/residues/NAL.xml' 2024-07-11T12:17:18,321 adding 'moleculekit/share/pdb2pqr/residues/NCY.dat' 2024-07-11T12:17:18,322 adding 'moleculekit/share/pdb2pqr/residues/NCY.xml' 2024-07-11T12:17:18,323 adding 'moleculekit/share/pdb2pqr/residues/NLE.dat' 2024-07-11T12:17:18,325 adding 'moleculekit/share/pdb2pqr/residues/NLE.xml' 2024-07-11T12:17:18,326 adding 'moleculekit/share/pdb2pqr/residues/NVA.dat' 2024-07-11T12:17:18,327 adding 'moleculekit/share/pdb2pqr/residues/NVA.xml' 2024-07-11T12:17:18,328 adding 'moleculekit/share/pdb2pqr/residues/NZC.dat' 2024-07-11T12:17:18,330 adding 'moleculekit/share/pdb2pqr/residues/NZC.xml' 2024-07-11T12:17:18,331 adding 'moleculekit/share/pdb2pqr/residues/OCY.dat' 2024-07-11T12:17:18,332 adding 'moleculekit/share/pdb2pqr/residues/OCY.xml' 2024-07-11T12:17:18,333 adding 'moleculekit/share/pdb2pqr/residues/OMX.dat' 2024-07-11T12:17:18,334 adding 'moleculekit/share/pdb2pqr/residues/OMX.xml' 2024-07-11T12:17:18,336 adding 'moleculekit/share/pdb2pqr/residues/ONL.dat' 2024-07-11T12:17:18,337 adding 'moleculekit/share/pdb2pqr/residues/ONL.xml' 2024-07-11T12:17:18,338 adding 'moleculekit/share/pdb2pqr/residues/ORM.dat' 2024-07-11T12:17:18,339 adding 'moleculekit/share/pdb2pqr/residues/ORM.xml' 2024-07-11T12:17:18,341 adding 'moleculekit/share/pdb2pqr/residues/P1L.dat' 2024-07-11T12:17:18,342 adding 'moleculekit/share/pdb2pqr/residues/P1L.xml' 2024-07-11T12:17:18,344 adding 'moleculekit/share/pdb2pqr/residues/PCA.dat' 2024-07-11T12:17:18,345 adding 'moleculekit/share/pdb2pqr/residues/PCA.xml' 2024-07-11T12:17:18,346 adding 'moleculekit/share/pdb2pqr/residues/PRK.dat' 2024-07-11T12:17:18,348 adding 'moleculekit/share/pdb2pqr/residues/PRK.xml' 2024-07-11T12:17:18,349 adding 'moleculekit/share/pdb2pqr/residues/PTR.dat' 2024-07-11T12:17:18,350 adding 'moleculekit/share/pdb2pqr/residues/PTR.xml' 2024-07-11T12:17:18,351 adding 'moleculekit/share/pdb2pqr/residues/SEP.dat' 2024-07-11T12:17:18,353 adding 'moleculekit/share/pdb2pqr/residues/SEP.xml' 2024-07-11T12:17:18,354 adding 'moleculekit/share/pdb2pqr/residues/TPO.dat' 2024-07-11T12:17:18,355 adding 'moleculekit/share/pdb2pqr/residues/TPO.xml' 2024-07-11T12:17:18,357 adding 'moleculekit/share/pdb2pqr/residues/TRO.dat' 2024-07-11T12:17:18,358 adding 'moleculekit/share/pdb2pqr/residues/TRO.xml' 2024-07-11T12:17:18,359 adding 'moleculekit/share/pdb2pqr/residues/TY2.dat' 2024-07-11T12:17:18,360 adding 'moleculekit/share/pdb2pqr/residues/TY2.xml' 2024-07-11T12:17:18,362 adding 'moleculekit/share/pdb2pqr/residues/TYQ.dat' 2024-07-11T12:17:18,363 adding 'moleculekit/share/pdb2pqr/residues/TYQ.xml' 2024-07-11T12:17:18,364 adding 'moleculekit/share/pdb2pqr/residues/YCM.dat' 2024-07-11T12:17:18,365 adding 'moleculekit/share/pdb2pqr/residues/YCM.xml' 2024-07-11T12:17:18,366 adding 'moleculekit/share/pdb2pqr/residues/YNM.dat' 2024-07-11T12:17:18,368 adding 'moleculekit/share/pdb2pqr/residues/YNM.xml' 2024-07-11T12:17:18,370 adding 'moleculekit/smallmol/__init__.py' 2024-07-11T12:17:18,375 adding 'moleculekit/smallmol/smallmol.py' 2024-07-11T12:17:18,376 adding 'moleculekit/smallmol/smallmolcdp.py' 2024-07-11T12:17:18,379 adding 'moleculekit/smallmol/smallmollib.py' 2024-07-11T12:17:18,380 adding 'moleculekit/smallmol/test_smallmol.py' 2024-07-11T12:17:18,382 adding 'moleculekit/smallmol/test_smallmollib.py' 2024-07-11T12:17:18,384 adding 'moleculekit/smallmol/util.py' 2024-07-11T12:17:18,385 adding 'moleculekit/smallmol/tools/__init__.py' 2024-07-11T12:17:18,387 adding 'moleculekit/smallmol/tools/clustering.py' 2024-07-11T12:17:18,388 adding 'moleculekit/smallmol/tools/restrainedembed.py' 2024-07-11T12:17:18,390 adding 'moleculekit/smallmol/tools/test_tools.py' 2024-07-11T12:17:18,480 adding 'moleculekit/tmalign/tmalign_util.cpp' 2024-07-11T12:17:18,489 adding 'moleculekit/tmalign/tmalign_util.pyx' 2024-07-11T12:17:18,490 adding 'moleculekit/tmalign/tmalignlib.pxd' 2024-07-11T12:17:18,492 adding 'moleculekit/tmalign/include/TMAlign.h' 2024-07-11T12:17:18,509 adding 'moleculekit/tmalign/src/TMAlign.cpp' 2024-07-11T12:17:18,513 adding 'moleculekit/tools/__init__.py' 2024-07-11T12:17:18,515 adding 'moleculekit/tools/atomtyper.py' 2024-07-11T12:17:18,517 adding 'moleculekit/tools/autosegment.py' 2024-07-11T12:17:18,519 adding 'moleculekit/tools/crystalpacking.py' 2024-07-11T12:17:18,522 adding 'moleculekit/tools/detect.py' 2024-07-11T12:17:18,524 adding 'moleculekit/tools/docking.py' 2024-07-11T12:17:18,526 adding 'moleculekit/tools/graphalignment.py' 2024-07-11T12:17:18,527 adding 'moleculekit/tools/hhblitsprofile.py' 2024-07-11T12:17:18,529 adding 'moleculekit/tools/modelling.py' 2024-07-11T12:17:18,530 adding 'moleculekit/tools/moleculechecks.py' 2024-07-11T12:17:18,537 adding 'moleculekit/tools/preparation.py' 2024-07-11T12:17:18,539 adding 'moleculekit/tools/preparation_customres.py' 2024-07-11T12:17:18,541 adding 'moleculekit/tools/sequencestructuralalignment.py' 2024-07-11T12:17:18,544 adding 'moleculekit/tools/voxeldescriptors.py' 2024-07-11T12:17:18,546 adding 'moleculekit/tools/obabel_tools/__init__.py' 2024-07-11T12:17:18,547 adding 'moleculekit/tools/obabel_tools/obabel_cli.py' 2024-07-11T12:17:18,639 adding 'moleculekit/wrapping/wrapping.cpp' 2024-07-11T12:17:18,648 adding 'moleculekit/wrapping/wrapping.pyx' 2024-07-11T12:17:18,651 adding 'moleculekit-1.9.0.dist-info/LICENSE' 2024-07-11T12:17:18,652 adding 'moleculekit-1.9.0.dist-info/METADATA' 2024-07-11T12:17:18,653 adding 'moleculekit-1.9.0.dist-info/WHEEL' 2024-07-11T12:17:18,654 adding 'moleculekit-1.9.0.dist-info/top_level.txt' 2024-07-11T12:17:18,659 adding 'moleculekit-1.9.0.dist-info/RECORD' 2024-07-11T12:17:18,823 removing build/bdist.linux-armv7l/wheel 2024-07-11T12:17:19,127 Building wheel for moleculekit (pyproject.toml): finished with status 'done' 2024-07-11T12:17:19,449 Created wheel for moleculekit: filename=moleculekit-1.9.0-cp311-cp311-linux_armv7l.whl size=15302345 sha256=d6035d34abe9a702dc48a7b6e979670c6e0eb97db1a3a940dbd9f96bfc42eb03 2024-07-11T12:17:19,450 Stored in directory: /tmp/pip-ephem-wheel-cache-3hu4ir25/wheels/45/86/8f/d8e2099d6ce0e9fcbe28928497fa312bc5ecf2f1da83faad05 2024-07-11T12:17:19,476 Successfully built moleculekit 2024-07-11T12:17:19,820 Removed build tracker: '/tmp/pip-build-tracker-r3t0f_85'