2024-06-17T17:28:28,910 Created temporary directory: /tmp/pip-build-tracker-0ss4s881 2024-06-17T17:28:28,911 Initialized build tracking at /tmp/pip-build-tracker-0ss4s881 2024-06-17T17:28:28,911 Created build tracker: /tmp/pip-build-tracker-0ss4s881 2024-06-17T17:28:28,911 Entered build tracker: /tmp/pip-build-tracker-0ss4s881 2024-06-17T17:28:28,912 Created temporary directory: /tmp/pip-wheel-4vwej2ra 2024-06-17T17:28:28,916 Created temporary directory: /tmp/pip-ephem-wheel-cache-0bhbj2eh 2024-06-17T17:28:28,943 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-17T17:28:28,946 2 location(s) to search for versions of moleculekit: 2024-06-17T17:28:28,946 * https://pypi.org/simple/moleculekit/ 2024-06-17T17:28:28,946 * https://www.piwheels.org/simple/moleculekit/ 2024-06-17T17:28:28,947 Fetching project page and analyzing links: https://pypi.org/simple/moleculekit/ 2024-06-17T17:28:28,948 Getting page https://pypi.org/simple/moleculekit/ 2024-06-17T17:28:28,949 Found index url https://pypi.org/simple/ 2024-06-17T17:28:29,006 Fetched page https://pypi.org/simple/moleculekit/ as application/vnd.pypi.simple.v1+json 2024-06-17T17:28:29,049 Skipping link: No binaries permitted for moleculekit: https://files.pythonhosted.org/packages/91/e6/25b6853357dfef8a4026325e420d8213d34c17c078a2f13b60cbb6213ea3/moleculekit-0.1.4-py3-none-any.whl (from https://pypi.org/simple/moleculekit/) 2024-06-17T17:28:29,050 Found link https://files.pythonhosted.org/packages/13/0f/a200e8e7632d3a521cfc7c15fa4d0270802efce40f98ac5a5cae58385b7e/moleculekit-0.1.4.tar.gz (from https://pypi.org/simple/moleculekit/), version: 0.1.4 2024-06-17T17:28:29,050 Skipping link: No binaries permitted for moleculekit: https://files.pythonhosted.org/packages/9f/a5/eac32fcb2e9ff0d30298aa4cec8e152c95d675c4dd1a1a5d7676986d4d75/moleculekit-0.1.5-py3-none-any.whl (from https://pypi.org/simple/moleculekit/) 2024-06-17T17:28:29,050 Found link 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moleculekit: https://www.piwheels.org/simple/moleculekit/moleculekit-1.8.34-cp311-cp311-linux_armv7l.whl#sha256=942c98d7f1683d7846c9afa7242cfc6ce8754a90853a7129c5eae6f1081d1d0c (from https://www.piwheels.org/simple/moleculekit/) (requires-python:>=3.8) 2024-06-17T17:28:29,306 Skipping link: No binaries permitted for moleculekit: https://www.piwheels.org/simple/moleculekit/moleculekit-1.8.33-cp39-cp39-linux_armv6l.whl#sha256=3d6bb5aa26d1b0395385d5f79f151e71fc73ec74703c4bcd649823311c63a46d (from https://www.piwheels.org/simple/moleculekit/) (requires-python:>=3.8) 2024-06-17T17:28:29,306 Skipping link: No binaries permitted for moleculekit: https://www.piwheels.org/simple/moleculekit/moleculekit-1.8.33-cp39-cp39-linux_armv7l.whl#sha256=3d6bb5aa26d1b0395385d5f79f151e71fc73ec74703c4bcd649823311c63a46d (from https://www.piwheels.org/simple/moleculekit/) (requires-python:>=3.8) 2024-06-17T17:28:29,307 Skipping link: No binaries permitted for moleculekit: 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https://www.piwheels.org/simple/moleculekit/moleculekit-0.1.5-py3-none-any.whl#sha256=2f111e31b3f90e63ca0154c528585208b8bd41a065aa0078325683f4b36eacec (from https://www.piwheels.org/simple/moleculekit/) 2024-06-17T17:28:29,375 Skipping link: No binaries permitted for moleculekit: https://www.piwheels.org/simple/moleculekit/moleculekit-0.1.4-py3-none-any.whl#sha256=5784491ff294e145a00311f8239aaa0b92c12605db0508ee3e10469b80d4cadd (from https://www.piwheels.org/simple/moleculekit/) 2024-06-17T17:28:29,375 Skipping link: not a file: https://www.piwheels.org/simple/moleculekit/ 2024-06-17T17:28:29,375 Skipping link: not a file: https://pypi.org/simple/moleculekit/ 2024-06-17T17:28:29,417 Given no hashes to check 1 links for project 'moleculekit': discarding no candidates 2024-06-17T17:28:29,434 Collecting moleculekit==1.8.34 2024-06-17T17:28:29,436 Created temporary directory: /tmp/pip-unpack-_u1gtwrc 2024-06-17T17:28:29,485 Downloading moleculekit-1.8.34.tar.gz (6.8 MB) 2024-06-17T17:28:31,796 Added moleculekit==1.8.34 from https://files.pythonhosted.org/packages/d4/0f/1b1f0d41c3ff855afca374140213f1c43b3a9659eebc4460899fead843ff/moleculekit-1.8.34.tar.gz to build tracker '/tmp/pip-build-tracker-0ss4s881' 2024-06-17T17:28:31,804 Created temporary directory: /tmp/pip-build-env-3we63uhk 2024-06-17T17:28:31,816 Installing build dependencies: started 2024-06-17T17:28:31,817 Running command pip subprocess to install build dependencies 2024-06-17T17:28:32,979 Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2024-06-17T17:28:33,503 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-17T17:28:34,966 Collecting setuptools 2024-06-17T17:28:34,985 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.0.0-py3-none-any.whl (863 kB) 2024-06-17T17:28:36,068 Collecting numpy>=1.18.5 2024-06-17T17:28:36,086 Using cached https://www.piwheels.org/simple/numpy/numpy-2.0.0-cp39-cp39-linux_armv7l.whl (5.8 MB) 2024-06-17T17:28:37,750 Collecting Cython>=0.29.21 2024-06-17T17:28:37,766 Using cached https://www.piwheels.org/simple/cython/Cython-3.0.10-cp39-cp39-linux_armv7l.whl (10.7 MB) 2024-06-17T17:28:38,142 Collecting toml 2024-06-17T17:28:38,153 Downloading https://www.piwheels.org/simple/toml/toml-0.10.2-py2.py3-none-any.whl (16 kB) 2024-06-17T17:28:38,261 Collecting versioneer==0.28 (from versioneer[toml]==0.28) 2024-06-17T17:28:38,273 Downloading https://www.piwheels.org/simple/versioneer/versioneer-0.28-py3-none-any.whl (45 kB) 2024-06-17T17:28:38,294 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.3/45.3 kB 3.3 MB/s eta 0:00:00 2024-06-17T17:28:38,425 Collecting tomli (from versioneer[toml]==0.28) 2024-06-17T17:28:38,442 Using cached https://www.piwheels.org/simple/tomli/tomli-2.0.1-py3-none-any.whl (12 kB) 2024-06-17T17:28:40,275 Installing collected packages: versioneer, tomli, toml, setuptools, numpy, Cython 2024-06-17T17:28:40,310 Creating /tmp/pip-build-env-3we63uhk/overlay/bin 2024-06-17T17:28:40,312 changing mode of /tmp/pip-build-env-3we63uhk/overlay/bin/versioneer to 755 2024-06-17T17:28:50,591 changing mode of /tmp/pip-build-env-3we63uhk/overlay/bin/f2py to 755 2024-06-17T17:28:50,593 changing mode of /tmp/pip-build-env-3we63uhk/overlay/bin/numpy-config to 755 2024-06-17T17:28:54,046 changing mode of /tmp/pip-build-env-3we63uhk/overlay/bin/cygdb to 755 2024-06-17T17:28:54,048 changing mode of /tmp/pip-build-env-3we63uhk/overlay/bin/cython to 755 2024-06-17T17:28:54,050 changing mode of /tmp/pip-build-env-3we63uhk/overlay/bin/cythonize to 755 2024-06-17T17:28:54,076 Successfully installed Cython-3.0.10 numpy-2.0.0 setuptools-70.0.0 toml-0.10.2 tomli-2.0.1 versioneer-0.28 2024-06-17T17:28:54,772 Installing build dependencies: finished with status 'done' 2024-06-17T17:28:54,777 Getting requirements to build wheel: started 2024-06-17T17:28:54,778 Running command Getting requirements to build wheel 2024-06-17T17:29:33,979 warning: moleculekit/wrapping/wrapping.pyx:47:4: Unreachable code 2024-06-17T17:29:43,531 Compiling moleculekit/interactions/hbonds/hbonds.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,531 Compiling moleculekit/interactions/pipi/pipi.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,531 Compiling moleculekit/interactions/cationpi/cationpi.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,531 Compiling moleculekit/interactions/sigmahole/sigmahole.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,531 Compiling moleculekit/wrapping/wrapping.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,532 Compiling moleculekit/bondguesser_utils/bondguesser_utils.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,532 Compiling moleculekit/atomselect_utils/atomselect_utils.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,532 Compiling moleculekit/distance_utils/distance_utils.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,532 Compiling moleculekit/occupancy_utils/occupancy_utils.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,532 Compiling moleculekit/cython_utils/cython_utils.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,532 Compiling moleculekit/fileformats/xtc/xtc.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2024-06-17T17:29:43,532 Compiling moleculekit/fileformats/xtc/trr.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2024-06-17T17:29:43,533 Compiling moleculekit/fileformats/dcd/dcd.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2024-06-17T17:29:43,533 Compiling moleculekit/fileformats/binpos/binpos.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2024-06-17T17:29:43,533 Compiling moleculekit/tmalign/tmalign_util.pyx because it depends on /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-17T17:29:43,533 [ 1/15] Cythonizing moleculekit/atomselect_utils/atomselect_utils.pyx 2024-06-17T17:29:43,533 [ 2/15] Cythonizing moleculekit/bondguesser_utils/bondguesser_utils.pyx 2024-06-17T17:29:43,533 [ 3/15] Cythonizing moleculekit/cython_utils/cython_utils.pyx 2024-06-17T17:29:43,533 [ 4/15] Cythonizing moleculekit/distance_utils/distance_utils.pyx 2024-06-17T17:29:43,533 [ 5/15] Cythonizing moleculekit/fileformats/dcd/dcd.pyx 2024-06-17T17:29:43,534 [ 6/15] Cythonizing moleculekit/interactions/cationpi/cationpi.pyx 2024-06-17T17:29:43,534 [ 7/15] Cythonizing moleculekit/interactions/hbonds/hbonds.pyx 2024-06-17T17:29:43,534 [ 8/15] Cythonizing moleculekit/interactions/pipi/pipi.pyx 2024-06-17T17:29:43,534 [ 9/15] Cythonizing moleculekit/interactions/sigmahole/sigmahole.pyx 2024-06-17T17:29:43,534 [10/15] Cythonizing moleculekit/occupancy_utils/occupancy_utils.pyx 2024-06-17T17:29:43,534 [11/15] Cythonizing moleculekit/tmalign/tmalign_util.pyx 2024-06-17T17:29:43,534 [12/15] Cythonizing moleculekit/wrapping/wrapping.pyx 2024-06-17T17:29:43,535 [13/15] Cythonizing moleculekit/fileformats/binpos/binpos.pyx 2024-06-17T17:29:43,535 [14/15] Cythonizing moleculekit/fileformats/xtc/trr.pyx 2024-06-17T17:29:43,535 [15/15] Cythonizing moleculekit/fileformats/xtc/xtc.pyx 2024-06-17T17:29:43,839 running egg_info 2024-06-17T17:29:43,846 writing moleculekit.egg-info/PKG-INFO 2024-06-17T17:29:43,849 writing dependency_links to moleculekit.egg-info/dependency_links.txt 2024-06-17T17:29:43,851 writing requirements to moleculekit.egg-info/requires.txt 2024-06-17T17:29:43,852 writing top-level names to moleculekit.egg-info/top_level.txt 2024-06-17T17:29:43,884 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the 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the manifest: the path must be relative 2024-06-17T17:29:43,888 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,888 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,888 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,888 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,888 dependency 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the manifest: the path must be relative 2024-06-17T17:29:43,889 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,889 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,889 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,889 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,889 dependency 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the manifest: the path must be relative 2024-06-17T17:29:43,890 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,890 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,890 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,890 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,891 dependency 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the manifest: the path must be relative 2024-06-17T17:29:43,892 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,892 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,892 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,892 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,892 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,894 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,894 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,894 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,894 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,894 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,895 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,896 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,896 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,896 dependency 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the manifest: the path must be relative 2024-06-17T17:29:43,897 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,898 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:43,908 reading manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-06-17T17:29:43,945 reading manifest template 'MANIFEST.in' 2024-06-17T17:29:44,212 no previously-included directories found matching 'moleculekit/test-data' 2024-06-17T17:29:44,213 no previously-included directories found matching 'moleculekit/tests' 2024-06-17T17:29:44,214 no previously-included directories found matching 'package' 2024-06-17T17:29:44,214 adding license file 'LICENSE' 2024-06-17T17:29:44,233 writing manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-06-17T17:29:45,898 Getting requirements to build wheel: finished with status 'done' 2024-06-17T17:29:45,913 Installing backend dependencies: started 2024-06-17T17:29:45,914 Running command pip subprocess to install backend dependencies 2024-06-17T17:29:47,187 Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2024-06-17T17:29:47,758 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-17T17:29:48,149 Collecting wheel 2024-06-17T17:29:48,166 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-06-17T17:29:49,622 Installing collected packages: wheel 2024-06-17T17:29:49,852 Creating /tmp/pip-build-env-3we63uhk/normal/bin 2024-06-17T17:29:49,854 changing mode of /tmp/pip-build-env-3we63uhk/normal/bin/wheel to 755 2024-06-17T17:29:49,867 Successfully installed wheel-0.43.0 2024-06-17T17:29:50,259 Installing backend dependencies: finished with status 'done' 2024-06-17T17:29:50,261 Created temporary directory: /tmp/pip-modern-metadata-9shkle11 2024-06-17T17:29:50,264 Preparing metadata (pyproject.toml): started 2024-06-17T17:29:50,265 Running command Preparing metadata (pyproject.toml) 2024-06-17T17:29:52,757 running dist_info 2024-06-17T17:29:52,759 creating /tmp/pip-modern-metadata-9shkle11/moleculekit.egg-info 2024-06-17T17:29:52,765 writing /tmp/pip-modern-metadata-9shkle11/moleculekit.egg-info/PKG-INFO 2024-06-17T17:29:52,769 writing dependency_links to /tmp/pip-modern-metadata-9shkle11/moleculekit.egg-info/dependency_links.txt 2024-06-17T17:29:52,771 writing requirements to /tmp/pip-modern-metadata-9shkle11/moleculekit.egg-info/requires.txt 2024-06-17T17:29:52,772 writing top-level names to /tmp/pip-modern-metadata-9shkle11/moleculekit.egg-info/top_level.txt 2024-06-17T17:29:52,774 writing manifest file '/tmp/pip-modern-metadata-9shkle11/moleculekit.egg-info/SOURCES.txt' 2024-06-17T17:29:52,808 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,808 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,808 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,808 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,808 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,809 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,809 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,809 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,809 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,809 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,809 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,810 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,810 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,810 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in 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/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,812 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,812 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,812 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,812 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,812 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,813 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,813 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,813 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,813 dependency 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/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,814 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,814 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,815 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,815 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,815 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,815 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,815 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,815 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,815 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,816 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,816 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,816 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,816 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,816 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,818 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,818 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,818 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,818 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,818 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,819 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,819 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,819 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,819 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,820 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,820 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,820 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,821 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,821 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,821 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:52,828 reading manifest file '/tmp/pip-modern-metadata-9shkle11/moleculekit.egg-info/SOURCES.txt' 2024-06-17T17:29:52,830 reading manifest template 'MANIFEST.in' 2024-06-17T17:29:53,111 no previously-included directories found matching 'moleculekit/test-data' 2024-06-17T17:29:53,112 no previously-included directories found matching 'moleculekit/tests' 2024-06-17T17:29:53,113 no previously-included directories found matching 'package' 2024-06-17T17:29:53,113 adding license file 'LICENSE' 2024-06-17T17:29:53,127 writing manifest file '/tmp/pip-modern-metadata-9shkle11/moleculekit.egg-info/SOURCES.txt' 2024-06-17T17:29:53,136 creating '/tmp/pip-modern-metadata-9shkle11/moleculekit-1.8.34.dist-info' 2024-06-17T17:29:53,336 Preparing metadata (pyproject.toml): finished with status 'done' 2024-06-17T17:29:53,343 Source in /tmp/pip-wheel-4vwej2ra/moleculekit_b12b876714e04656837f804772c14289 has version 1.8.34, which satisfies requirement moleculekit==1.8.34 from https://files.pythonhosted.org/packages/d4/0f/1b1f0d41c3ff855afca374140213f1c43b3a9659eebc4460899fead843ff/moleculekit-1.8.34.tar.gz 2024-06-17T17:29:53,344 Removed moleculekit==1.8.34 from https://files.pythonhosted.org/packages/d4/0f/1b1f0d41c3ff855afca374140213f1c43b3a9659eebc4460899fead843ff/moleculekit-1.8.34.tar.gz from build tracker '/tmp/pip-build-tracker-0ss4s881' 2024-06-17T17:29:53,350 Created temporary directory: /tmp/pip-unpack-ahpp_cf4 2024-06-17T17:29:53,351 Created temporary directory: /tmp/pip-unpack-w_4qlnjt 2024-06-17T17:29:53,359 Building wheels for collected packages: moleculekit 2024-06-17T17:29:53,363 Created temporary directory: /tmp/pip-wheel-0wfwgm3u 2024-06-17T17:29:53,363 Destination directory: /tmp/pip-wheel-0wfwgm3u 2024-06-17T17:29:53,365 Building wheel for moleculekit (pyproject.toml): started 2024-06-17T17:29:53,366 Running command Building wheel for moleculekit (pyproject.toml) 2024-06-17T17:29:55,632 running bdist_wheel 2024-06-17T17:29:55,648 running build 2024-06-17T17:29:55,648 running build_py 2024-06-17T17:29:55,656 creating build 2024-06-17T17:29:55,656 creating build/lib.linux-armv7l-cpython-39 2024-06-17T17:29:55,657 creating build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,658 copying moleculekit/bondguesser.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,660 copying moleculekit/viewer.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,662 copying moleculekit/distance.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,664 copying moleculekit/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,665 copying moleculekit/vmdgraphics.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,667 copying moleculekit/config.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,669 copying moleculekit/writers.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,673 copying moleculekit/periodictable.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,675 copying moleculekit/readers.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,679 copying moleculekit/align.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,682 copying moleculekit/home.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,683 copying moleculekit/pymolgraphics.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,685 copying moleculekit/opm.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,687 copying moleculekit/vmdviewer.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,689 copying moleculekit/_version.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,691 copying moleculekit/version.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,692 copying moleculekit/rcsb.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,694 copying moleculekit/dihedral.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,696 copying moleculekit/molecule.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,700 copying moleculekit/rdkitintegration.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,702 copying moleculekit/util.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:55,705 creating build/lib.linux-armv7l-cpython-39/moleculekit/ply 2024-06-17T17:29:55,706 copying moleculekit/ply/yacc.py -> build/lib.linux-armv7l-cpython-39/moleculekit/ply 2024-06-17T17:29:55,710 copying moleculekit/ply/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/ply 2024-06-17T17:29:55,712 copying moleculekit/ply/lex.py -> build/lib.linux-armv7l-cpython-39/moleculekit/ply 2024-06-17T17:29:55,715 creating build/lib.linux-armv7l-cpython-39/moleculekit/pdbx 2024-06-17T17:29:55,716 copying moleculekit/pdbx/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx 2024-06-17T17:29:55,718 creating build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,719 copying moleculekit/tools/detect.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,721 copying moleculekit/tools/hhblitsprofile.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,723 copying moleculekit/tools/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,725 copying moleculekit/tools/autosegment.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,727 copying moleculekit/tools/sequencestructuralalignment.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,730 copying moleculekit/tools/preparation.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,733 copying moleculekit/tools/preparation_customres.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,736 copying moleculekit/tools/modelling.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,738 copying moleculekit/tools/graphalignment.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,741 copying moleculekit/tools/docking.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,743 copying moleculekit/tools/atomtyper.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,745 copying moleculekit/tools/moleculechecks.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,747 copying moleculekit/tools/voxeldescriptors.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,750 copying moleculekit/tools/crystalpacking.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-17T17:29:55,753 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions 2024-06-17T17:29:55,754 copying moleculekit/interactions/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions 2024-06-17T17:29:55,756 copying moleculekit/interactions/interactions.py -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions 2024-06-17T17:29:55,760 creating build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-17T17:29:55,761 copying moleculekit/smallmol/test_smallmol.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-17T17:29:55,763 copying moleculekit/smallmol/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-17T17:29:55,765 copying moleculekit/smallmol/test_smallmollib.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-17T17:29:55,767 copying moleculekit/smallmol/smallmol.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-17T17:29:55,770 copying moleculekit/smallmol/smallmollib.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-17T17:29:55,772 copying moleculekit/smallmol/smallmolcdp.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-17T17:29:55,775 copying moleculekit/smallmol/util.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-17T17:29:55,778 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-17T17:29:55,779 copying moleculekit/fileformats/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-17T17:29:55,780 copying moleculekit/fileformats/utils.py -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-17T17:29:55,782 copying moleculekit/fileformats/netcdf.py -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-17T17:29:55,786 creating build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,787 copying moleculekit/projections/metricfluctuation.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,789 copying moleculekit/projections/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,791 copying moleculekit/projections/metricshell.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,793 copying moleculekit/projections/metricrmsd.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,795 copying moleculekit/projections/metricdihedral.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,798 copying moleculekit/projections/metriccoordinate.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,800 copying moleculekit/projections/metrictmscore.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,802 copying moleculekit/projections/metricsphericalcoordinate.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,804 copying moleculekit/projections/metricsecondarystructure.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,806 copying moleculekit/projections/metricgyration.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,808 copying moleculekit/projections/metricplumed2.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,811 copying moleculekit/projections/metricsasa.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,813 copying moleculekit/projections/projection.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,815 copying moleculekit/projections/util.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,817 copying moleculekit/projections/metricdistance.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-17T17:29:55,820 creating build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-17T17:29:55,821 copying moleculekit/atomselect/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-17T17:29:55,822 copying moleculekit/atomselect/analyze.py -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-17T17:29:55,824 copying moleculekit/atomselect/languageparser.py -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-17T17:29:55,826 copying moleculekit/atomselect/atomselect.py -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-17T17:29:55,829 creating build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-17T17:29:55,830 copying moleculekit/pdbx/tests/PdbxReadWriteTests.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-17T17:29:55,832 copying moleculekit/pdbx/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-17T17:29:55,834 copying moleculekit/pdbx/tests/PdbxReaderTests.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-17T17:29:55,836 copying moleculekit/pdbx/tests/PdbxWriterTests.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-17T17:29:55,838 creating build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-17T17:29:55,839 copying moleculekit/pdbx/reader/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-17T17:29:55,841 copying moleculekit/pdbx/reader/PdbxContainers.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-17T17:29:55,843 copying moleculekit/pdbx/reader/PdbxParser.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-17T17:29:55,846 copying moleculekit/pdbx/reader/PdbxReader.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-17T17:29:55,849 creating build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer 2024-06-17T17:29:55,850 copying moleculekit/pdbx/writer/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer 2024-06-17T17:29:55,851 copying moleculekit/pdbx/writer/PdbxWriter.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer 2024-06-17T17:29:55,854 creating build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools 2024-06-17T17:29:55,855 copying moleculekit/tools/obabel_tools/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools 2024-06-17T17:29:55,856 copying moleculekit/tools/obabel_tools/obabel_cli.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools 2024-06-17T17:29:55,859 creating build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-17T17:29:55,860 copying moleculekit/smallmol/tools/restrainedembed.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-17T17:29:55,861 copying moleculekit/smallmol/tools/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-17T17:29:55,863 copying moleculekit/smallmol/tools/clustering.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-17T17:29:55,865 copying moleculekit/smallmol/tools/test_tools.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-17T17:29:55,868 running egg_info 2024-06-17T17:29:55,873 writing moleculekit.egg-info/PKG-INFO 2024-06-17T17:29:55,877 writing dependency_links to moleculekit.egg-info/dependency_links.txt 2024-06-17T17:29:55,878 writing requirements to moleculekit.egg-info/requires.txt 2024-06-17T17:29:55,879 writing top-level names to moleculekit.egg-info/top_level.txt 2024-06-17T17:29:55,898 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,898 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,898 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,898 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,898 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,898 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,899 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,899 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,899 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,899 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,899 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,899 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,899 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,900 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,900 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,900 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,900 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,900 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,900 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,900 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,901 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,901 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,901 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,901 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,901 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,901 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,901 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,901 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,902 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,902 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,902 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,902 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,902 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,902 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,902 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,903 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,903 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,903 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,903 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,903 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,903 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,903 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,903 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,904 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,904 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,904 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,904 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,904 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,904 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,904 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,905 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,905 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,905 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,905 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,905 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,905 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,905 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,905 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,906 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,906 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,907 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,907 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,907 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,908 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,908 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,908 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,909 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,909 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,909 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,909 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,910 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,910 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,910 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,910 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,910 dependency /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-06-17T17:29:55,917 reading manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-06-17T17:29:55,927 reading manifest template 'MANIFEST.in' 2024-06-17T17:29:56,182 no previously-included directories found matching 'moleculekit/test-data' 2024-06-17T17:29:56,183 no previously-included directories found matching 'moleculekit/tests' 2024-06-17T17:29:56,184 no previously-included directories found matching 'package' 2024-06-17T17:29:56,184 adding license file 'LICENSE' 2024-06-17T17:29:56,202 writing manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-06-17T17:29:56,213 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.atomselect_utils' is absent from the `packages` configuration. 2024-06-17T17:29:56,213 !! 2024-06-17T17:29:56,213 ******************************************************************************** 2024-06-17T17:29:56,214 ############################ 2024-06-17T17:29:56,214 # Package would be ignored # 2024-06-17T17:29:56,214 ############################ 2024-06-17T17:29:56,214 Python recognizes 'moleculekit.atomselect_utils' as an importable package[^1], 2024-06-17T17:29:56,214 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,214 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,214 package, please make sure that 'moleculekit.atomselect_utils' is explicitly added 2024-06-17T17:29:56,215 to the `packages` configuration field. 2024-06-17T17:29:56,215 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,215 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,215 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,215 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,216 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,216 If you don't want 'moleculekit.atomselect_utils' to be distributed and are 2024-06-17T17:29:56,216 already explicitly excluding 'moleculekit.atomselect_utils' via 2024-06-17T17:29:56,216 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,216 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,216 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,217 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,217 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,217 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,217 even if it does not contain any `.py` files. 2024-06-17T17:29:56,217 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,217 directory, all directories are treated like packages. 2024-06-17T17:29:56,218 ******************************************************************************** 2024-06-17T17:29:56,218 !! 2024-06-17T17:29:56,218 check.warn(importable) 2024-06-17T17:29:56,218 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.bondguesser_utils' is absent from the `packages` configuration. 2024-06-17T17:29:56,218 !! 2024-06-17T17:29:56,219 ******************************************************************************** 2024-06-17T17:29:56,219 ############################ 2024-06-17T17:29:56,219 # Package would be ignored # 2024-06-17T17:29:56,219 ############################ 2024-06-17T17:29:56,219 Python recognizes 'moleculekit.bondguesser_utils' as an importable package[^1], 2024-06-17T17:29:56,219 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,219 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,219 package, please make sure that 'moleculekit.bondguesser_utils' is explicitly added 2024-06-17T17:29:56,220 to the `packages` configuration field. 2024-06-17T17:29:56,220 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,220 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,220 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,220 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,221 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,221 If you don't want 'moleculekit.bondguesser_utils' to be distributed and are 2024-06-17T17:29:56,221 already explicitly excluding 'moleculekit.bondguesser_utils' via 2024-06-17T17:29:56,221 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,221 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,221 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,221 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,222 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,222 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,222 even if it does not contain any `.py` files. 2024-06-17T17:29:56,222 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,222 directory, all directories are treated like packages. 2024-06-17T17:29:56,223 ******************************************************************************** 2024-06-17T17:29:56,223 !! 2024-06-17T17:29:56,223 check.warn(importable) 2024-06-17T17:29:56,223 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.cython_utils' is absent from the `packages` configuration. 2024-06-17T17:29:56,223 !! 2024-06-17T17:29:56,223 ******************************************************************************** 2024-06-17T17:29:56,223 ############################ 2024-06-17T17:29:56,224 # Package would be ignored # 2024-06-17T17:29:56,224 ############################ 2024-06-17T17:29:56,224 Python recognizes 'moleculekit.cython_utils' as an importable package[^1], 2024-06-17T17:29:56,224 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,224 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,224 package, please make sure that 'moleculekit.cython_utils' is explicitly added 2024-06-17T17:29:56,225 to the `packages` configuration field. 2024-06-17T17:29:56,225 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,225 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,225 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,225 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,225 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,226 If you don't want 'moleculekit.cython_utils' to be distributed and are 2024-06-17T17:29:56,226 already explicitly excluding 'moleculekit.cython_utils' via 2024-06-17T17:29:56,226 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,226 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,226 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,226 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,226 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,227 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,227 even if it does not contain any `.py` files. 2024-06-17T17:29:56,227 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,227 directory, all directories are treated like packages. 2024-06-17T17:29:56,227 ******************************************************************************** 2024-06-17T17:29:56,227 !! 2024-06-17T17:29:56,228 check.warn(importable) 2024-06-17T17:29:56,228 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.distance_utils' is absent from the `packages` configuration. 2024-06-17T17:29:56,228 !! 2024-06-17T17:29:56,228 ******************************************************************************** 2024-06-17T17:29:56,228 ############################ 2024-06-17T17:29:56,228 # Package would be ignored # 2024-06-17T17:29:56,228 ############################ 2024-06-17T17:29:56,228 Python recognizes 'moleculekit.distance_utils' as an importable package[^1], 2024-06-17T17:29:56,228 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,229 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,229 package, please make sure that 'moleculekit.distance_utils' is explicitly added 2024-06-17T17:29:56,229 to the `packages` configuration field. 2024-06-17T17:29:56,229 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,229 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,229 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,230 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,230 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,230 If you don't want 'moleculekit.distance_utils' to be distributed and are 2024-06-17T17:29:56,230 already explicitly excluding 'moleculekit.distance_utils' via 2024-06-17T17:29:56,230 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,230 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,230 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,231 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,231 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,231 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,231 even if it does not contain any `.py` files. 2024-06-17T17:29:56,231 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,231 directory, all directories are treated like packages. 2024-06-17T17:29:56,232 ******************************************************************************** 2024-06-17T17:29:56,232 !! 2024-06-17T17:29:56,232 check.warn(importable) 2024-06-17T17:29:56,232 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.binpos' is absent from the `packages` configuration. 2024-06-17T17:29:56,232 !! 2024-06-17T17:29:56,232 ******************************************************************************** 2024-06-17T17:29:56,232 ############################ 2024-06-17T17:29:56,233 # Package would be ignored # 2024-06-17T17:29:56,233 ############################ 2024-06-17T17:29:56,233 Python recognizes 'moleculekit.fileformats.binpos' as an importable package[^1], 2024-06-17T17:29:56,233 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,233 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,233 package, please make sure that 'moleculekit.fileformats.binpos' is explicitly added 2024-06-17T17:29:56,233 to the `packages` configuration field. 2024-06-17T17:29:56,234 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,234 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,234 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,234 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,234 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,234 If you don't want 'moleculekit.fileformats.binpos' to be distributed and are 2024-06-17T17:29:56,235 already explicitly excluding 'moleculekit.fileformats.binpos' via 2024-06-17T17:29:56,235 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,235 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,235 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,235 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,235 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,236 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,236 even if it does not contain any `.py` files. 2024-06-17T17:29:56,236 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,236 directory, all directories are treated like packages. 2024-06-17T17:29:56,236 ******************************************************************************** 2024-06-17T17:29:56,236 !! 2024-06-17T17:29:56,236 check.warn(importable) 2024-06-17T17:29:56,237 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.binpos.include' is absent from the `packages` configuration. 2024-06-17T17:29:56,237 !! 2024-06-17T17:29:56,237 ******************************************************************************** 2024-06-17T17:29:56,237 ############################ 2024-06-17T17:29:56,237 # Package would be ignored # 2024-06-17T17:29:56,237 ############################ 2024-06-17T17:29:56,238 Python recognizes 'moleculekit.fileformats.binpos.include' as an importable package[^1], 2024-06-17T17:29:56,238 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,238 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,238 package, please make sure that 'moleculekit.fileformats.binpos.include' is explicitly added 2024-06-17T17:29:56,238 to the `packages` configuration field. 2024-06-17T17:29:56,239 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,239 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,239 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,239 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,239 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,240 If you don't want 'moleculekit.fileformats.binpos.include' to be distributed and are 2024-06-17T17:29:56,240 already explicitly excluding 'moleculekit.fileformats.binpos.include' via 2024-06-17T17:29:56,240 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,240 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,240 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,240 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,240 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,241 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,241 even if it does not contain any `.py` files. 2024-06-17T17:29:56,241 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,241 directory, all directories are treated like packages. 2024-06-17T17:29:56,241 ******************************************************************************** 2024-06-17T17:29:56,242 !! 2024-06-17T17:29:56,242 check.warn(importable) 2024-06-17T17:29:56,242 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.binpos.src' is absent from the `packages` configuration. 2024-06-17T17:29:56,242 !! 2024-06-17T17:29:56,242 ******************************************************************************** 2024-06-17T17:29:56,242 ############################ 2024-06-17T17:29:56,243 # Package would be ignored # 2024-06-17T17:29:56,243 ############################ 2024-06-17T17:29:56,243 Python recognizes 'moleculekit.fileformats.binpos.src' as an importable package[^1], 2024-06-17T17:29:56,243 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,243 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,243 package, please make sure that 'moleculekit.fileformats.binpos.src' is explicitly added 2024-06-17T17:29:56,243 to the `packages` configuration field. 2024-06-17T17:29:56,244 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,244 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,244 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,244 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,245 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,245 If you don't want 'moleculekit.fileformats.binpos.src' to be distributed and are 2024-06-17T17:29:56,245 already explicitly excluding 'moleculekit.fileformats.binpos.src' via 2024-06-17T17:29:56,245 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,245 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,245 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,246 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,246 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,246 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,246 even if it does not contain any `.py` files. 2024-06-17T17:29:56,247 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,247 directory, all directories are treated like packages. 2024-06-17T17:29:56,247 ******************************************************************************** 2024-06-17T17:29:56,247 !! 2024-06-17T17:29:56,247 check.warn(importable) 2024-06-17T17:29:56,248 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.dcd' is absent from the `packages` configuration. 2024-06-17T17:29:56,248 !! 2024-06-17T17:29:56,248 ******************************************************************************** 2024-06-17T17:29:56,248 ############################ 2024-06-17T17:29:56,248 # Package would be ignored # 2024-06-17T17:29:56,248 ############################ 2024-06-17T17:29:56,249 Python recognizes 'moleculekit.fileformats.dcd' as an importable package[^1], 2024-06-17T17:29:56,249 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,249 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,249 package, please make sure that 'moleculekit.fileformats.dcd' is explicitly added 2024-06-17T17:29:56,249 to the `packages` configuration field. 2024-06-17T17:29:56,250 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,250 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,250 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,250 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,250 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,250 If you don't want 'moleculekit.fileformats.dcd' to be distributed and are 2024-06-17T17:29:56,251 already explicitly excluding 'moleculekit.fileformats.dcd' via 2024-06-17T17:29:56,251 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,251 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,251 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,251 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,251 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,252 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,252 even if it does not contain any `.py` files. 2024-06-17T17:29:56,252 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,252 directory, all directories are treated like packages. 2024-06-17T17:29:56,252 ******************************************************************************** 2024-06-17T17:29:56,252 !! 2024-06-17T17:29:56,253 check.warn(importable) 2024-06-17T17:29:56,253 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.dcd.include' is absent from the `packages` configuration. 2024-06-17T17:29:56,253 !! 2024-06-17T17:29:56,253 ******************************************************************************** 2024-06-17T17:29:56,253 ############################ 2024-06-17T17:29:56,253 # Package would be ignored # 2024-06-17T17:29:56,253 ############################ 2024-06-17T17:29:56,253 Python recognizes 'moleculekit.fileformats.dcd.include' as an importable package[^1], 2024-06-17T17:29:56,254 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,254 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,254 package, please make sure that 'moleculekit.fileformats.dcd.include' is explicitly added 2024-06-17T17:29:56,254 to the `packages` configuration field. 2024-06-17T17:29:56,254 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,254 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,254 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,255 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,255 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,255 If you don't want 'moleculekit.fileformats.dcd.include' to be distributed and are 2024-06-17T17:29:56,255 already explicitly excluding 'moleculekit.fileformats.dcd.include' via 2024-06-17T17:29:56,255 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,256 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,256 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,256 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,256 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,257 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,257 even if it does not contain any `.py` files. 2024-06-17T17:29:56,257 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,257 directory, all directories are treated like packages. 2024-06-17T17:29:56,257 ******************************************************************************** 2024-06-17T17:29:56,257 !! 2024-06-17T17:29:56,257 check.warn(importable) 2024-06-17T17:29:56,257 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.dcd.src' is absent from the `packages` configuration. 2024-06-17T17:29:56,258 !! 2024-06-17T17:29:56,258 ******************************************************************************** 2024-06-17T17:29:56,258 ############################ 2024-06-17T17:29:56,258 # Package would be ignored # 2024-06-17T17:29:56,258 ############################ 2024-06-17T17:29:56,258 Python recognizes 'moleculekit.fileformats.dcd.src' as an importable package[^1], 2024-06-17T17:29:56,258 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,259 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,259 package, please make sure that 'moleculekit.fileformats.dcd.src' is explicitly added 2024-06-17T17:29:56,259 to the `packages` configuration field. 2024-06-17T17:29:56,259 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,259 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,259 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,259 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,260 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,260 If you don't want 'moleculekit.fileformats.dcd.src' to be distributed and are 2024-06-17T17:29:56,260 already explicitly excluding 'moleculekit.fileformats.dcd.src' via 2024-06-17T17:29:56,260 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,260 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,260 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,261 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,261 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,261 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,261 even if it does not contain any `.py` files. 2024-06-17T17:29:56,261 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,261 directory, all directories are treated like packages. 2024-06-17T17:29:56,262 ******************************************************************************** 2024-06-17T17:29:56,262 !! 2024-06-17T17:29:56,262 check.warn(importable) 2024-06-17T17:29:56,262 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.xtc' is absent from the `packages` configuration. 2024-06-17T17:29:56,262 !! 2024-06-17T17:29:56,262 ******************************************************************************** 2024-06-17T17:29:56,262 ############################ 2024-06-17T17:29:56,263 # Package would be ignored # 2024-06-17T17:29:56,263 ############################ 2024-06-17T17:29:56,263 Python recognizes 'moleculekit.fileformats.xtc' as an importable package[^1], 2024-06-17T17:29:56,263 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,263 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,263 package, please make sure that 'moleculekit.fileformats.xtc' is explicitly added 2024-06-17T17:29:56,263 to the `packages` configuration field. 2024-06-17T17:29:56,264 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,264 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,264 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,264 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,264 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,265 If you don't want 'moleculekit.fileformats.xtc' to be distributed and are 2024-06-17T17:29:56,265 already explicitly excluding 'moleculekit.fileformats.xtc' via 2024-06-17T17:29:56,265 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,265 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,265 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,265 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,265 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,266 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,266 even if it does not contain any `.py` files. 2024-06-17T17:29:56,266 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,266 directory, all directories are treated like packages. 2024-06-17T17:29:56,266 ******************************************************************************** 2024-06-17T17:29:56,266 !! 2024-06-17T17:29:56,266 check.warn(importable) 2024-06-17T17:29:56,267 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.xtc.include' is absent from the `packages` configuration. 2024-06-17T17:29:56,267 !! 2024-06-17T17:29:56,267 ******************************************************************************** 2024-06-17T17:29:56,267 ############################ 2024-06-17T17:29:56,267 # Package would be ignored # 2024-06-17T17:29:56,267 ############################ 2024-06-17T17:29:56,267 Python recognizes 'moleculekit.fileformats.xtc.include' as an importable package[^1], 2024-06-17T17:29:56,268 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,268 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,268 package, please make sure that 'moleculekit.fileformats.xtc.include' is explicitly added 2024-06-17T17:29:56,268 to the `packages` configuration field. 2024-06-17T17:29:56,268 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,268 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,268 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,269 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,269 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,269 If you don't want 'moleculekit.fileformats.xtc.include' to be distributed and are 2024-06-17T17:29:56,269 already explicitly excluding 'moleculekit.fileformats.xtc.include' via 2024-06-17T17:29:56,269 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,269 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,270 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,270 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,270 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,270 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,270 even if it does not contain any `.py` files. 2024-06-17T17:29:56,271 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,271 directory, all directories are treated like packages. 2024-06-17T17:29:56,271 ******************************************************************************** 2024-06-17T17:29:56,271 !! 2024-06-17T17:29:56,271 check.warn(importable) 2024-06-17T17:29:56,271 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.fileformats.xtc.src' is absent from the `packages` configuration. 2024-06-17T17:29:56,272 !! 2024-06-17T17:29:56,272 ******************************************************************************** 2024-06-17T17:29:56,272 ############################ 2024-06-17T17:29:56,272 # Package would be ignored # 2024-06-17T17:29:56,272 ############################ 2024-06-17T17:29:56,272 Python recognizes 'moleculekit.fileformats.xtc.src' as an importable package[^1], 2024-06-17T17:29:56,272 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,273 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,273 package, please make sure that 'moleculekit.fileformats.xtc.src' is explicitly added 2024-06-17T17:29:56,273 to the `packages` configuration field. 2024-06-17T17:29:56,273 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,273 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,273 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,274 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,274 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,274 If you don't want 'moleculekit.fileformats.xtc.src' to be distributed and are 2024-06-17T17:29:56,274 already explicitly excluding 'moleculekit.fileformats.xtc.src' via 2024-06-17T17:29:56,275 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,275 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,275 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,275 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,275 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,275 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,276 even if it does not contain any `.py` files. 2024-06-17T17:29:56,276 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,276 directory, all directories are treated like packages. 2024-06-17T17:29:56,276 ******************************************************************************** 2024-06-17T17:29:56,276 !! 2024-06-17T17:29:56,276 check.warn(importable) 2024-06-17T17:29:56,276 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.interactions.cationpi' is absent from the `packages` configuration. 2024-06-17T17:29:56,277 !! 2024-06-17T17:29:56,277 ******************************************************************************** 2024-06-17T17:29:56,277 ############################ 2024-06-17T17:29:56,277 # Package would be ignored # 2024-06-17T17:29:56,277 ############################ 2024-06-17T17:29:56,277 Python recognizes 'moleculekit.interactions.cationpi' as an importable package[^1], 2024-06-17T17:29:56,277 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,278 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,278 package, please make sure that 'moleculekit.interactions.cationpi' is explicitly added 2024-06-17T17:29:56,278 to the `packages` configuration field. 2024-06-17T17:29:56,278 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,278 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,278 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,279 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,279 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,279 If you don't want 'moleculekit.interactions.cationpi' to be distributed and are 2024-06-17T17:29:56,279 already explicitly excluding 'moleculekit.interactions.cationpi' via 2024-06-17T17:29:56,279 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,280 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,280 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,280 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,280 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,281 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,281 even if it does not contain any `.py` files. 2024-06-17T17:29:56,281 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,281 directory, all directories are treated like packages. 2024-06-17T17:29:56,281 ******************************************************************************** 2024-06-17T17:29:56,282 !! 2024-06-17T17:29:56,282 check.warn(importable) 2024-06-17T17:29:56,282 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.interactions.hbonds' is absent from the `packages` configuration. 2024-06-17T17:29:56,282 !! 2024-06-17T17:29:56,283 ******************************************************************************** 2024-06-17T17:29:56,283 ############################ 2024-06-17T17:29:56,283 # Package would be ignored # 2024-06-17T17:29:56,283 ############################ 2024-06-17T17:29:56,283 Python recognizes 'moleculekit.interactions.hbonds' as an importable package[^1], 2024-06-17T17:29:56,283 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,284 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,284 package, please make sure that 'moleculekit.interactions.hbonds' is explicitly added 2024-06-17T17:29:56,284 to the `packages` configuration field. 2024-06-17T17:29:56,284 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,284 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,284 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,285 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,285 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,285 If you don't want 'moleculekit.interactions.hbonds' to be distributed and are 2024-06-17T17:29:56,286 already explicitly excluding 'moleculekit.interactions.hbonds' via 2024-06-17T17:29:56,286 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,286 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,286 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,286 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,287 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,287 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,287 even if it does not contain any `.py` files. 2024-06-17T17:29:56,287 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,288 directory, all directories are treated like packages. 2024-06-17T17:29:56,288 ******************************************************************************** 2024-06-17T17:29:56,288 !! 2024-06-17T17:29:56,288 check.warn(importable) 2024-06-17T17:29:56,288 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.interactions.pipi' is absent from the `packages` configuration. 2024-06-17T17:29:56,288 !! 2024-06-17T17:29:56,289 ******************************************************************************** 2024-06-17T17:29:56,289 ############################ 2024-06-17T17:29:56,289 # Package would be ignored # 2024-06-17T17:29:56,289 ############################ 2024-06-17T17:29:56,289 Python recognizes 'moleculekit.interactions.pipi' as an importable package[^1], 2024-06-17T17:29:56,289 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,290 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,290 package, please make sure that 'moleculekit.interactions.pipi' is explicitly added 2024-06-17T17:29:56,290 to the `packages` configuration field. 2024-06-17T17:29:56,290 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,290 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,290 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,291 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,291 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,291 If you don't want 'moleculekit.interactions.pipi' to be distributed and are 2024-06-17T17:29:56,291 already explicitly excluding 'moleculekit.interactions.pipi' via 2024-06-17T17:29:56,292 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,292 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,292 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,292 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,292 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,293 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,293 even if it does not contain any `.py` files. 2024-06-17T17:29:56,294 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,294 directory, all directories are treated like packages. 2024-06-17T17:29:56,294 ******************************************************************************** 2024-06-17T17:29:56,295 !! 2024-06-17T17:29:56,295 check.warn(importable) 2024-06-17T17:29:56,295 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.interactions.sigmahole' is absent from the `packages` configuration. 2024-06-17T17:29:56,295 !! 2024-06-17T17:29:56,295 ******************************************************************************** 2024-06-17T17:29:56,295 ############################ 2024-06-17T17:29:56,296 # Package would be ignored # 2024-06-17T17:29:56,296 ############################ 2024-06-17T17:29:56,296 Python recognizes 'moleculekit.interactions.sigmahole' as an importable package[^1], 2024-06-17T17:29:56,296 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,296 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,297 package, please make sure that 'moleculekit.interactions.sigmahole' is explicitly added 2024-06-17T17:29:56,298 to the `packages` configuration field. 2024-06-17T17:29:56,299 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,300 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,300 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,300 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,301 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,301 If you don't want 'moleculekit.interactions.sigmahole' to be distributed and are 2024-06-17T17:29:56,301 already explicitly excluding 'moleculekit.interactions.sigmahole' via 2024-06-17T17:29:56,301 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,302 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,302 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,302 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,302 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,303 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,303 even if it does not contain any `.py` files. 2024-06-17T17:29:56,303 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,304 directory, all directories are treated like packages. 2024-06-17T17:29:56,304 ******************************************************************************** 2024-06-17T17:29:56,305 !! 2024-06-17T17:29:56,305 check.warn(importable) 2024-06-17T17:29:56,305 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.occupancy_utils' is absent from the `packages` configuration. 2024-06-17T17:29:56,306 !! 2024-06-17T17:29:56,306 ******************************************************************************** 2024-06-17T17:29:56,306 ############################ 2024-06-17T17:29:56,307 # Package would be ignored # 2024-06-17T17:29:56,307 ############################ 2024-06-17T17:29:56,307 Python recognizes 'moleculekit.occupancy_utils' as an importable package[^1], 2024-06-17T17:29:56,307 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,307 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,307 package, please make sure that 'moleculekit.occupancy_utils' is explicitly added 2024-06-17T17:29:56,307 to the `packages` configuration field. 2024-06-17T17:29:56,308 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,308 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,308 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,308 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,308 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,309 If you don't want 'moleculekit.occupancy_utils' to be distributed and are 2024-06-17T17:29:56,309 already explicitly excluding 'moleculekit.occupancy_utils' via 2024-06-17T17:29:56,309 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,309 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,309 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,309 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,310 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,310 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,310 even if it does not contain any `.py` files. 2024-06-17T17:29:56,310 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,310 directory, all directories are treated like packages. 2024-06-17T17:29:56,311 ******************************************************************************** 2024-06-17T17:29:56,311 !! 2024-06-17T17:29:56,311 check.warn(importable) 2024-06-17T17:29:56,311 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.share' is absent from the `packages` configuration. 2024-06-17T17:29:56,311 !! 2024-06-17T17:29:56,311 ******************************************************************************** 2024-06-17T17:29:56,312 ############################ 2024-06-17T17:29:56,312 # Package would be ignored # 2024-06-17T17:29:56,312 ############################ 2024-06-17T17:29:56,312 Python recognizes 'moleculekit.share' as an importable package[^1], 2024-06-17T17:29:56,312 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,312 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,312 package, please make sure that 'moleculekit.share' is explicitly added 2024-06-17T17:29:56,313 to the `packages` configuration field. 2024-06-17T17:29:56,313 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,313 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,313 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,313 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,313 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,314 If you don't want 'moleculekit.share' to be distributed and are 2024-06-17T17:29:56,314 already explicitly excluding 'moleculekit.share' via 2024-06-17T17:29:56,314 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,314 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,314 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,314 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,315 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,315 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,315 even if it does not contain any `.py` files. 2024-06-17T17:29:56,315 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,315 directory, all directories are treated like packages. 2024-06-17T17:29:56,315 ******************************************************************************** 2024-06-17T17:29:56,316 !! 2024-06-17T17:29:56,316 check.warn(importable) 2024-06-17T17:29:56,316 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.share.atomselect' is absent from the `packages` configuration. 2024-06-17T17:29:56,316 !! 2024-06-17T17:29:56,316 ******************************************************************************** 2024-06-17T17:29:56,316 ############################ 2024-06-17T17:29:56,316 # Package would be ignored # 2024-06-17T17:29:56,317 ############################ 2024-06-17T17:29:56,317 Python recognizes 'moleculekit.share.atomselect' as an importable package[^1], 2024-06-17T17:29:56,317 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,317 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,317 package, please make sure that 'moleculekit.share.atomselect' is explicitly added 2024-06-17T17:29:56,317 to the `packages` configuration field. 2024-06-17T17:29:56,317 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,318 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,318 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,318 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,318 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,318 If you don't want 'moleculekit.share.atomselect' to be distributed and are 2024-06-17T17:29:56,319 already explicitly excluding 'moleculekit.share.atomselect' via 2024-06-17T17:29:56,319 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,319 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,319 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,319 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,319 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,320 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,320 even if it does not contain any `.py` files. 2024-06-17T17:29:56,320 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,320 directory, all directories are treated like packages. 2024-06-17T17:29:56,320 ******************************************************************************** 2024-06-17T17:29:56,320 !! 2024-06-17T17:29:56,320 check.warn(importable) 2024-06-17T17:29:56,320 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.share.pdb2pqr.residues' is absent from the `packages` configuration. 2024-06-17T17:29:56,321 !! 2024-06-17T17:29:56,321 ******************************************************************************** 2024-06-17T17:29:56,321 ############################ 2024-06-17T17:29:56,321 # Package would be ignored # 2024-06-17T17:29:56,321 ############################ 2024-06-17T17:29:56,321 Python recognizes 'moleculekit.share.pdb2pqr.residues' as an importable package[^1], 2024-06-17T17:29:56,321 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,322 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,322 package, please make sure that 'moleculekit.share.pdb2pqr.residues' is explicitly added 2024-06-17T17:29:56,322 to the `packages` configuration field. 2024-06-17T17:29:56,322 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,322 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,322 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,323 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,323 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,323 If you don't want 'moleculekit.share.pdb2pqr.residues' to be distributed and are 2024-06-17T17:29:56,323 already explicitly excluding 'moleculekit.share.pdb2pqr.residues' via 2024-06-17T17:29:56,323 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,323 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,324 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,324 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,324 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,325 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,325 even if it does not contain any `.py` files. 2024-06-17T17:29:56,325 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,325 directory, all directories are treated like packages. 2024-06-17T17:29:56,325 ******************************************************************************** 2024-06-17T17:29:56,325 !! 2024-06-17T17:29:56,325 check.warn(importable) 2024-06-17T17:29:56,326 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.tmalign' is absent from the `packages` configuration. 2024-06-17T17:29:56,326 !! 2024-06-17T17:29:56,326 ******************************************************************************** 2024-06-17T17:29:56,326 ############################ 2024-06-17T17:29:56,326 # Package would be ignored # 2024-06-17T17:29:56,326 ############################ 2024-06-17T17:29:56,326 Python recognizes 'moleculekit.tmalign' as an importable package[^1], 2024-06-17T17:29:56,327 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,327 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,327 package, please make sure that 'moleculekit.tmalign' is explicitly added 2024-06-17T17:29:56,327 to the `packages` configuration field. 2024-06-17T17:29:56,327 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,327 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,328 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,328 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,328 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,328 If you don't want 'moleculekit.tmalign' to be distributed and are 2024-06-17T17:29:56,328 already explicitly excluding 'moleculekit.tmalign' via 2024-06-17T17:29:56,329 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,329 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,329 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,329 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,329 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,330 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,330 even if it does not contain any `.py` files. 2024-06-17T17:29:56,330 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,330 directory, all directories are treated like packages. 2024-06-17T17:29:56,330 ******************************************************************************** 2024-06-17T17:29:56,330 !! 2024-06-17T17:29:56,330 check.warn(importable) 2024-06-17T17:29:56,331 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.tmalign.include' is absent from the `packages` configuration. 2024-06-17T17:29:56,331 !! 2024-06-17T17:29:56,331 ******************************************************************************** 2024-06-17T17:29:56,331 ############################ 2024-06-17T17:29:56,331 # Package would be ignored # 2024-06-17T17:29:56,331 ############################ 2024-06-17T17:29:56,331 Python recognizes 'moleculekit.tmalign.include' as an importable package[^1], 2024-06-17T17:29:56,332 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,332 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,332 package, please make sure that 'moleculekit.tmalign.include' is explicitly added 2024-06-17T17:29:56,332 to the `packages` configuration field. 2024-06-17T17:29:56,332 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,332 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,332 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,333 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,333 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,333 If you don't want 'moleculekit.tmalign.include' to be distributed and are 2024-06-17T17:29:56,333 already explicitly excluding 'moleculekit.tmalign.include' via 2024-06-17T17:29:56,333 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,334 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,334 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,334 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,334 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,335 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,335 even if it does not contain any `.py` files. 2024-06-17T17:29:56,335 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,335 directory, all directories are treated like packages. 2024-06-17T17:29:56,335 ******************************************************************************** 2024-06-17T17:29:56,336 !! 2024-06-17T17:29:56,336 check.warn(importable) 2024-06-17T17:29:56,336 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.tmalign.src' is absent from the `packages` configuration. 2024-06-17T17:29:56,336 !! 2024-06-17T17:29:56,336 ******************************************************************************** 2024-06-17T17:29:56,336 ############################ 2024-06-17T17:29:56,336 # Package would be ignored # 2024-06-17T17:29:56,337 ############################ 2024-06-17T17:29:56,337 Python recognizes 'moleculekit.tmalign.src' as an importable package[^1], 2024-06-17T17:29:56,337 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,337 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,337 package, please make sure that 'moleculekit.tmalign.src' is explicitly added 2024-06-17T17:29:56,337 to the `packages` configuration field. 2024-06-17T17:29:56,337 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,338 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,338 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,338 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,338 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,338 If you don't want 'moleculekit.tmalign.src' to be distributed and are 2024-06-17T17:29:56,339 already explicitly excluding 'moleculekit.tmalign.src' via 2024-06-17T17:29:56,339 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,339 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,339 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,339 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,339 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,340 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,340 even if it does not contain any `.py` files. 2024-06-17T17:29:56,340 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,340 directory, all directories are treated like packages. 2024-06-17T17:29:56,340 ******************************************************************************** 2024-06-17T17:29:56,340 !! 2024-06-17T17:29:56,341 check.warn(importable) 2024-06-17T17:29:56,341 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'moleculekit.wrapping' is absent from the `packages` configuration. 2024-06-17T17:29:56,341 !! 2024-06-17T17:29:56,341 ******************************************************************************** 2024-06-17T17:29:56,341 ############################ 2024-06-17T17:29:56,341 # Package would be ignored # 2024-06-17T17:29:56,342 ############################ 2024-06-17T17:29:56,342 Python recognizes 'moleculekit.wrapping' as an importable package[^1], 2024-06-17T17:29:56,342 but it is absent from setuptools' `packages` configuration. 2024-06-17T17:29:56,342 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-17T17:29:56,342 package, please make sure that 'moleculekit.wrapping' is explicitly added 2024-06-17T17:29:56,342 to the `packages` configuration field. 2024-06-17T17:29:56,342 Alternatively, you can also rely on setuptools' discovery methods 2024-06-17T17:29:56,343 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-17T17:29:56,343 instead of `find_packages(...)`/`find:`). 2024-06-17T17:29:56,343 You can read more about "package discovery" on setuptools documentation page: 2024-06-17T17:29:56,343 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-17T17:29:56,343 If you don't want 'moleculekit.wrapping' to be distributed and are 2024-06-17T17:29:56,344 already explicitly excluding 'moleculekit.wrapping' via 2024-06-17T17:29:56,344 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-17T17:29:56,344 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-17T17:29:56,344 combination with a more fine grained `package-data` configuration. 2024-06-17T17:29:56,345 You can read more about "package data files" on setuptools documentation page: 2024-06-17T17:29:56,347 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-17T17:29:56,348 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-17T17:29:56,348 even if it does not contain any `.py` files. 2024-06-17T17:29:56,348 On the other hand, currently there is no concept of package data 2024-06-17T17:29:56,349 directory, all directories are treated like packages. 2024-06-17T17:29:56,349 ******************************************************************************** 2024-06-17T17:29:56,349 !! 2024-06-17T17:29:56,349 check.warn(importable) 2024-06-17T17:29:56,350 copying moleculekit/logging.ini -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:56,350 copying moleculekit/vmd_wrapper -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:56,350 creating build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils 2024-06-17T17:29:56,350 copying moleculekit/atomselect_utils/atomselect_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils 2024-06-17T17:29:56,350 copying moleculekit/atomselect_utils/atomselect_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils 2024-06-17T17:29:56,350 creating build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils 2024-06-17T17:29:56,350 copying moleculekit/bondguesser_utils/bondguesser_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils 2024-06-17T17:29:56,358 copying moleculekit/bondguesser_utils/bondguesser_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils 2024-06-17T17:29:56,360 creating build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils 2024-06-17T17:29:56,361 copying moleculekit/cython_utils/cython_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils 2024-06-17T17:29:56,390 copying moleculekit/cython_utils/cython_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils 2024-06-17T17:29:56,392 creating build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils 2024-06-17T17:29:56,393 copying moleculekit/distance_utils/distance_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils 2024-06-17T17:29:56,424 copying moleculekit/distance_utils/distance_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils 2024-06-17T17:29:56,427 creating build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils 2024-06-17T17:29:56,428 copying moleculekit/occupancy_utils/occupancy_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils 2024-06-17T17:29:56,453 copying moleculekit/occupancy_utils/occupancy_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils 2024-06-17T17:29:56,455 creating build/lib.linux-armv7l-cpython-39/moleculekit/share 2024-06-17T17:29:56,456 copying moleculekit/share/ALA.cif -> build/lib.linux-armv7l-cpython-39/moleculekit/share 2024-06-17T17:29:56,460 copying moleculekit/share/backbone.cif -> build/lib.linux-armv7l-cpython-39/moleculekit/share 2024-06-17T17:29:56,463 copying moleculekit/share/opm_sequences.json -> build/lib.linux-armv7l-cpython-39/moleculekit/share 2024-06-17T17:29:56,785 creating build/lib.linux-armv7l-cpython-39/moleculekit/share/atomselect 2024-06-17T17:29:56,786 copying moleculekit/share/atomselect/atomselect.json -> build/lib.linux-armv7l-cpython-39/moleculekit/share/atomselect 2024-06-17T17:29:56,788 creating build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr 2024-06-17T17:29:56,789 creating build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,790 copying moleculekit/share/pdb2pqr/residues/.gitkeep -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,792 copying moleculekit/share/pdb2pqr/residues/004.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,795 copying moleculekit/share/pdb2pqr/residues/004.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,797 copying moleculekit/share/pdb2pqr/residues/03Y.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,800 copying moleculekit/share/pdb2pqr/residues/03Y.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,802 copying moleculekit/share/pdb2pqr/residues/0A1.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,804 copying moleculekit/share/pdb2pqr/residues/0A1.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,807 copying moleculekit/share/pdb2pqr/residues/0AF.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,809 copying moleculekit/share/pdb2pqr/residues/0AF.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,811 copying moleculekit/share/pdb2pqr/residues/0BN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,813 copying moleculekit/share/pdb2pqr/residues/0BN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,815 copying moleculekit/share/pdb2pqr/residues/1MH.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,816 copying moleculekit/share/pdb2pqr/residues/1MH.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,818 copying moleculekit/share/pdb2pqr/residues/2AS.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,820 copying moleculekit/share/pdb2pqr/residues/2AS.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,822 copying moleculekit/share/pdb2pqr/residues/2GX.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,824 copying moleculekit/share/pdb2pqr/residues/2GX.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,827 copying moleculekit/share/pdb2pqr/residues/2ML.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,829 copying moleculekit/share/pdb2pqr/residues/2ML.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,831 copying moleculekit/share/pdb2pqr/residues/2MR.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,833 copying moleculekit/share/pdb2pqr/residues/2MR.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,835 copying moleculekit/share/pdb2pqr/residues/4IN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,837 copying moleculekit/share/pdb2pqr/residues/4IN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,839 copying moleculekit/share/pdb2pqr/residues/4PH.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,841 copying moleculekit/share/pdb2pqr/residues/4PH.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,843 copying moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,845 copying moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,847 copying moleculekit/share/pdb2pqr/residues/5JP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,849 copying moleculekit/share/pdb2pqr/residues/5JP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,851 copying moleculekit/share/pdb2pqr/residues/AA4.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,853 copying moleculekit/share/pdb2pqr/residues/AA4.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,855 copying moleculekit/share/pdb2pqr/residues/ABA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,856 copying moleculekit/share/pdb2pqr/residues/ABA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,859 copying moleculekit/share/pdb2pqr/residues/AHP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,861 copying moleculekit/share/pdb2pqr/residues/AHP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,862 copying moleculekit/share/pdb2pqr/residues/ALC.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,864 copying moleculekit/share/pdb2pqr/residues/ALC.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,866 copying moleculekit/share/pdb2pqr/residues/ALN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,868 copying moleculekit/share/pdb2pqr/residues/ALN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,870 copying moleculekit/share/pdb2pqr/residues/ALY.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,872 copying moleculekit/share/pdb2pqr/residues/ALY.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,874 copying moleculekit/share/pdb2pqr/residues/APD.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,876 copying moleculekit/share/pdb2pqr/residues/APD.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,878 copying moleculekit/share/pdb2pqr/residues/BB8.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,880 copying moleculekit/share/pdb2pqr/residues/BB8.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,882 copying moleculekit/share/pdb2pqr/residues/BCS.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,884 copying moleculekit/share/pdb2pqr/residues/BCS.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,886 copying moleculekit/share/pdb2pqr/residues/BTK.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,888 copying moleculekit/share/pdb2pqr/residues/BTK.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,890 copying moleculekit/share/pdb2pqr/residues/CCS.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,892 copying moleculekit/share/pdb2pqr/residues/CCS.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,894 copying moleculekit/share/pdb2pqr/residues/CGU.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,896 copying moleculekit/share/pdb2pqr/residues/CGU.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,898 copying moleculekit/share/pdb2pqr/residues/CSA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,900 copying moleculekit/share/pdb2pqr/residues/CSA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,902 copying moleculekit/share/pdb2pqr/residues/CSO.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,903 copying moleculekit/share/pdb2pqr/residues/CSO.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,906 copying moleculekit/share/pdb2pqr/residues/CSP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,907 copying moleculekit/share/pdb2pqr/residues/CSP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,909 copying moleculekit/share/pdb2pqr/residues/CSS.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,911 copying moleculekit/share/pdb2pqr/residues/CSS.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,913 copying moleculekit/share/pdb2pqr/residues/D4P.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,915 copying moleculekit/share/pdb2pqr/residues/D4P.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,917 copying moleculekit/share/pdb2pqr/residues/DA2.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,919 copying moleculekit/share/pdb2pqr/residues/DA2.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,921 copying moleculekit/share/pdb2pqr/residues/DAB.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,923 copying moleculekit/share/pdb2pqr/residues/DAB.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,925 copying moleculekit/share/pdb2pqr/residues/DAH.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,927 copying moleculekit/share/pdb2pqr/residues/DAH.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,929 copying moleculekit/share/pdb2pqr/residues/DPP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,931 copying moleculekit/share/pdb2pqr/residues/DPP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,933 copying moleculekit/share/pdb2pqr/residues/ESC.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,935 copying moleculekit/share/pdb2pqr/residues/ESC.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,937 copying moleculekit/share/pdb2pqr/residues/FGL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,939 copying moleculekit/share/pdb2pqr/residues/FGL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,941 copying moleculekit/share/pdb2pqr/residues/GHG.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,943 copying moleculekit/share/pdb2pqr/residues/GHG.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,945 copying moleculekit/share/pdb2pqr/residues/GME.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,947 copying moleculekit/share/pdb2pqr/residues/GME.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,949 copying moleculekit/share/pdb2pqr/residues/GNC.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,951 copying moleculekit/share/pdb2pqr/residues/GNC.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,953 copying moleculekit/share/pdb2pqr/residues/HHK.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,955 copying moleculekit/share/pdb2pqr/residues/HHK.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,957 copying moleculekit/share/pdb2pqr/residues/HLU.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,959 copying moleculekit/share/pdb2pqr/residues/HLU.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,961 copying moleculekit/share/pdb2pqr/residues/HLX.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,963 copying moleculekit/share/pdb2pqr/residues/HLX.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,965 copying moleculekit/share/pdb2pqr/residues/HOX.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,967 copying moleculekit/share/pdb2pqr/residues/HOX.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,968 copying moleculekit/share/pdb2pqr/residues/HPE.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,970 copying moleculekit/share/pdb2pqr/residues/HPE.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,972 copying moleculekit/share/pdb2pqr/residues/HQA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,974 copying moleculekit/share/pdb2pqr/residues/HQA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,976 copying moleculekit/share/pdb2pqr/residues/HTR.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,978 copying moleculekit/share/pdb2pqr/residues/HTR.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,980 copying moleculekit/share/pdb2pqr/residues/HYP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,982 copying moleculekit/share/pdb2pqr/residues/HYP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,984 copying moleculekit/share/pdb2pqr/residues/I2M.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,986 copying moleculekit/share/pdb2pqr/residues/I2M.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,989 copying moleculekit/share/pdb2pqr/residues/IGL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,990 copying moleculekit/share/pdb2pqr/residues/IGL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,992 copying moleculekit/share/pdb2pqr/residues/IIL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,995 copying moleculekit/share/pdb2pqr/residues/IIL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,997 copying moleculekit/share/pdb2pqr/residues/IML.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:56,998 copying moleculekit/share/pdb2pqr/residues/IML.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,000 copying moleculekit/share/pdb2pqr/residues/KYN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,002 copying moleculekit/share/pdb2pqr/residues/KYN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,004 copying moleculekit/share/pdb2pqr/residues/LME.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,006 copying moleculekit/share/pdb2pqr/residues/LME.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,008 copying moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,010 copying moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,012 copying moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,015 copying moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,016 copying moleculekit/share/pdb2pqr/residues/M3L.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,019 copying moleculekit/share/pdb2pqr/residues/M3L.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,021 copying moleculekit/share/pdb2pqr/residues/ME0.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,023 copying moleculekit/share/pdb2pqr/residues/ME0.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,025 copying moleculekit/share/pdb2pqr/residues/MEA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,027 copying moleculekit/share/pdb2pqr/residues/MEA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,029 copying moleculekit/share/pdb2pqr/residues/MEN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,030 copying moleculekit/share/pdb2pqr/residues/MEN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,032 copying moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,034 copying moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,036 copying moleculekit/share/pdb2pqr/residues/MLE.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,038 copying moleculekit/share/pdb2pqr/residues/MLE.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,040 copying moleculekit/share/pdb2pqr/residues/MLY.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,042 copying moleculekit/share/pdb2pqr/residues/MLY.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,044 copying moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,046 copying moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,048 copying moleculekit/share/pdb2pqr/residues/MME.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,050 copying moleculekit/share/pdb2pqr/residues/MME.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,052 copying moleculekit/share/pdb2pqr/residues/MMO.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,054 copying moleculekit/share/pdb2pqr/residues/MMO.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,056 copying moleculekit/share/pdb2pqr/residues/MVA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,058 copying moleculekit/share/pdb2pqr/residues/MVA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,060 copying moleculekit/share/pdb2pqr/residues/NAL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,061 copying moleculekit/share/pdb2pqr/residues/NAL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,063 copying moleculekit/share/pdb2pqr/residues/NCY.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,065 copying moleculekit/share/pdb2pqr/residues/NCY.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,067 copying moleculekit/share/pdb2pqr/residues/NLE.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,069 copying moleculekit/share/pdb2pqr/residues/NLE.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,071 copying moleculekit/share/pdb2pqr/residues/NVA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,073 copying moleculekit/share/pdb2pqr/residues/NVA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,075 copying moleculekit/share/pdb2pqr/residues/NZC.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,077 copying moleculekit/share/pdb2pqr/residues/NZC.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,079 copying moleculekit/share/pdb2pqr/residues/OCY.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,081 copying moleculekit/share/pdb2pqr/residues/OCY.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,083 copying moleculekit/share/pdb2pqr/residues/OMX.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,085 copying moleculekit/share/pdb2pqr/residues/OMX.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,087 copying moleculekit/share/pdb2pqr/residues/ONL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,089 copying moleculekit/share/pdb2pqr/residues/ONL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,091 copying moleculekit/share/pdb2pqr/residues/ORM.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,093 copying moleculekit/share/pdb2pqr/residues/ORM.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,095 copying moleculekit/share/pdb2pqr/residues/P1L.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,096 copying moleculekit/share/pdb2pqr/residues/P1L.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,099 copying moleculekit/share/pdb2pqr/residues/PCA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,101 copying moleculekit/share/pdb2pqr/residues/PCA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,103 copying moleculekit/share/pdb2pqr/residues/PRK.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,105 copying moleculekit/share/pdb2pqr/residues/PRK.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,107 copying moleculekit/share/pdb2pqr/residues/PTR.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,109 copying moleculekit/share/pdb2pqr/residues/PTR.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,111 copying moleculekit/share/pdb2pqr/residues/SEP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,113 copying moleculekit/share/pdb2pqr/residues/SEP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,115 copying moleculekit/share/pdb2pqr/residues/TPO.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,117 copying moleculekit/share/pdb2pqr/residues/TPO.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,119 copying moleculekit/share/pdb2pqr/residues/TRO.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,121 copying moleculekit/share/pdb2pqr/residues/TRO.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,123 copying moleculekit/share/pdb2pqr/residues/TY2.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,125 copying moleculekit/share/pdb2pqr/residues/TY2.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,127 copying moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,129 copying moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,131 copying moleculekit/share/pdb2pqr/residues/YCM.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,133 copying moleculekit/share/pdb2pqr/residues/YCM.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,135 copying moleculekit/share/pdb2pqr/residues/YNM.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,137 copying moleculekit/share/pdb2pqr/residues/YNM.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-17T17:29:57,139 creating build/lib.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-17T17:29:57,140 copying moleculekit/tmalign/tmalign_util.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-17T17:29:57,166 copying moleculekit/tmalign/tmalign_util.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-17T17:29:57,169 copying moleculekit/tmalign/tmalignlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-17T17:29:57,171 creating build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/include 2024-06-17T17:29:57,171 copying moleculekit/tmalign/include/TMAlign.h -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/include 2024-06-17T17:29:57,174 creating build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/src 2024-06-17T17:29:57,175 copying moleculekit/tmalign/src/TMAlign.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/src 2024-06-17T17:29:57,181 creating build/lib.linux-armv7l-cpython-39/moleculekit/wrapping 2024-06-17T17:29:57,182 copying moleculekit/wrapping/wrapping.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/wrapping 2024-06-17T17:29:57,206 copying moleculekit/wrapping/wrapping.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/wrapping 2024-06-17T17:29:57,209 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi 2024-06-17T17:29:57,210 copying moleculekit/interactions/cationpi/cationpi.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi 2024-06-17T17:29:57,234 copying moleculekit/interactions/cationpi/cationpi.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi 2024-06-17T17:29:57,236 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds 2024-06-17T17:29:57,237 copying moleculekit/interactions/hbonds/hbonds.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds 2024-06-17T17:29:57,270 copying moleculekit/interactions/hbonds/hbonds.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds 2024-06-17T17:29:57,273 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi 2024-06-17T17:29:57,274 copying moleculekit/interactions/pipi/pipi.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi 2024-06-17T17:29:57,308 copying moleculekit/interactions/pipi/pipi.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi 2024-06-17T17:29:57,312 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole 2024-06-17T17:29:57,313 copying moleculekit/interactions/sigmahole/sigmahole.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole 2024-06-17T17:29:57,356 copying moleculekit/interactions/sigmahole/sigmahole.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole 2024-06-17T17:29:57,358 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-17T17:29:57,359 copying moleculekit/fileformats/binpos/binpos.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-17T17:29:57,386 copying moleculekit/fileformats/binpos/binpos.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-17T17:29:57,389 copying moleculekit/fileformats/binpos/binposlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-17T17:29:57,391 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include 2024-06-17T17:29:57,393 copying moleculekit/fileformats/binpos/include/binposplugin.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include 2024-06-17T17:29:57,396 copying moleculekit/fileformats/binpos/include/largefiles.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include 2024-06-17T17:29:57,398 copying moleculekit/fileformats/binpos/include/molfile_plugin.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include 2024-06-17T17:29:57,402 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src 2024-06-17T17:29:57,404 copying moleculekit/fileformats/binpos/src/binposplugin.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src 2024-06-17T17:29:57,407 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-17T17:29:57,408 copying moleculekit/fileformats/dcd/dcd.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-17T17:29:57,433 copying moleculekit/fileformats/dcd/dcd.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-17T17:29:57,436 copying moleculekit/fileformats/dcd/dcdlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-17T17:29:57,438 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-17T17:29:57,439 copying moleculekit/fileformats/dcd/include/dcdplugin.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-17T17:29:57,441 copying moleculekit/fileformats/dcd/include/endianswap.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-17T17:29:57,445 copying moleculekit/fileformats/dcd/include/fastio.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-17T17:29:57,449 copying moleculekit/fileformats/dcd/include/largefiles.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-17T17:29:57,454 copying moleculekit/fileformats/dcd/include/molfile_plugin.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-17T17:29:57,461 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src 2024-06-17T17:29:57,463 copying moleculekit/fileformats/dcd/src/dcdplugin.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src 2024-06-17T17:29:57,466 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:29:57,467 copying moleculekit/fileformats/xtc/trr.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:29:57,504 copying moleculekit/fileformats/xtc/trr.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:29:57,508 copying moleculekit/fileformats/xtc/trrlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:29:57,509 copying moleculekit/fileformats/xtc/xdrlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:29:57,512 copying moleculekit/fileformats/xtc/xtc.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:29:57,543 copying moleculekit/fileformats/xtc/xtc.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:29:57,545 copying moleculekit/fileformats/xtc/xtclib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:29:57,547 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-17T17:29:57,548 copying moleculekit/fileformats/xtc/include/trr_header.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-17T17:29:57,550 copying moleculekit/fileformats/xtc/include/xdr_seek.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-17T17:29:57,552 copying moleculekit/fileformats/xtc/include/xdrfile.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-17T17:29:57,557 copying moleculekit/fileformats/xtc/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-17T17:29:57,561 copying moleculekit/fileformats/xtc/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-17T17:29:57,563 copying moleculekit/fileformats/xtc/include/xtc.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-17T17:29:57,565 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-17T17:29:57,566 copying moleculekit/fileformats/xtc/src/xdr_seek.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-17T17:29:57,568 copying moleculekit/fileformats/xtc/src/xdrfile.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-17T17:29:57,571 copying moleculekit/fileformats/xtc/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-17T17:29:57,574 copying moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-17T17:29:57,576 copying moleculekit/fileformats/xtc/src/xtc.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-17T17:29:57,589 UPDATING build/lib.linux-armv7l-cpython-39/moleculekit/_version.py 2024-06-17T17:29:57,589 set build/lib.linux-armv7l-cpython-39/moleculekit/_version.py to '1.8.34' 2024-06-17T17:29:57,589 running build_ext 2024-06-17T17:29:57,603 building 'moleculekit.interactions.hbonds' extension 2024-06-17T17:29:57,604 creating build/temp.linux-armv7l-cpython-39 2024-06-17T17:29:57,604 creating build/temp.linux-armv7l-cpython-39/moleculekit 2024-06-17T17:29:57,605 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions 2024-06-17T17:29:57,606 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions/hbonds 2024-06-17T17:29:57,607 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/interactions/hbonds/hbonds.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/interactions/hbonds/hbonds.o -O3 2024-06-17T17:29:57,868 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:29:57,868 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:29:57,868 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:29:57,869 from moleculekit/interactions/hbonds/hbonds.cpp:1265: 2024-06-17T17:29:57,869 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:29:57,869 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:29:57,869 | ^~~~~~~ 2024-06-17T17:29:58,323 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:29:58,323 from moleculekit/interactions/hbonds/hbonds.cpp:1269: 2024-06-17T17:29:58,323 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:29:58,323 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:29:58,323 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:29:58,323 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:30:21,060 moleculekit/interactions/hbonds/hbonds.cpp: In function ‘PyObject* __pyx_pw_11moleculekit_12interactions_6hbonds_1calculate(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’: 2024-06-17T17:30:21,060 moleculekit/interactions/hbonds/hbonds.cpp:21469:52: warning: ‘__pyx_v_d_idx_h’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:30:21,060 21469 | (__pyx_v_results[__pyx_v_f]).push_back(__pyx_v_d_idx_h); 2024-06-17T17:30:21,060 | ^~~~~~~~~~~~~~~ 2024-06-17T17:30:21,061 moleculekit/interactions/hbonds/hbonds.cpp:20486:57: note: ‘__pyx_v_d_idx_h’ was declared here 2024-06-17T17:30:21,061 20486 | __pyx_t_11moleculekit_12interactions_6hbonds_UINT32_t __pyx_v_d_idx_h; 2024-06-17T17:30:21,061 | ^~~~~~~~~~~~~~~ 2024-06-17T17:30:24,263 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/interactions/hbonds/hbonds.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:30:24,587 building 'moleculekit.interactions.pipi' extension 2024-06-17T17:30:24,588 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions/pipi 2024-06-17T17:30:24,588 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/interactions/pipi/pipi.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/interactions/pipi/pipi.o -O3 2024-06-17T17:30:24,849 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:30:24,849 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:30:24,849 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:30:24,850 from moleculekit/interactions/pipi/pipi.cpp:1265: 2024-06-17T17:30:24,850 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:30:24,850 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:30:24,850 | ^~~~~~~ 2024-06-17T17:30:25,290 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:30:25,290 from moleculekit/interactions/pipi/pipi.cpp:1269: 2024-06-17T17:30:25,291 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:30:25,291 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:30:25,291 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:30:25,291 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:30:53,102 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/interactions/pipi/pipi.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:30:53,429 building 'moleculekit.interactions.cationpi' extension 2024-06-17T17:30:53,430 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions/cationpi 2024-06-17T17:30:53,430 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/interactions/cationpi/cationpi.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/interactions/cationpi/cationpi.o -O3 2024-06-17T17:30:53,707 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:30:53,707 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:30:53,707 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:30:53,707 from moleculekit/interactions/cationpi/cationpi.cpp:1265: 2024-06-17T17:30:53,707 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:30:53,708 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:30:53,708 | ^~~~~~~ 2024-06-17T17:30:54,155 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:30:54,155 from moleculekit/interactions/cationpi/cationpi.cpp:1269: 2024-06-17T17:30:54,155 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:30:54,155 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:30:54,156 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:30:54,156 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:31:21,791 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/interactions/cationpi/cationpi.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:31:22,147 building 'moleculekit.interactions.sigmahole' extension 2024-06-17T17:31:22,148 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole 2024-06-17T17:31:22,150 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/interactions/sigmahole/sigmahole.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole/sigmahole.o -O3 2024-06-17T17:31:22,389 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:31:22,389 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:31:22,390 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:31:22,390 from moleculekit/interactions/sigmahole/sigmahole.cpp:1265: 2024-06-17T17:31:22,390 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:31:22,390 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:31:22,390 | ^~~~~~~ 2024-06-17T17:31:22,836 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:31:22,836 from moleculekit/interactions/sigmahole/sigmahole.cpp:1269: 2024-06-17T17:31:22,837 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:31:22,837 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:31:22,837 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:31:22,837 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:31:49,953 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole/sigmahole.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:31:50,275 building 'moleculekit.wrapping' extension 2024-06-17T17:31:50,275 creating build/temp.linux-armv7l-cpython-39/moleculekit/wrapping 2024-06-17T17:31:50,276 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/wrapping/wrapping.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/wrapping/wrapping.o -O3 2024-06-17T17:31:50,528 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:31:50,528 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:31:50,528 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:31:50,528 from moleculekit/wrapping/wrapping.cpp:1265: 2024-06-17T17:31:50,529 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:31:50,529 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:31:50,529 | ^~~~~~~ 2024-06-17T17:31:50,967 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:31:50,967 from moleculekit/wrapping/wrapping.cpp:1269: 2024-06-17T17:31:50,967 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:31:50,968 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:31:50,968 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:31:50,968 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:16,494 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/wrapping/wrapping.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/wrapping.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:32:16,711 building 'moleculekit.bondguesser_utils' extension 2024-06-17T17:32:16,712 creating build/temp.linux-armv7l-cpython-39/moleculekit/bondguesser_utils 2024-06-17T17:32:16,712 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/bondguesser_utils/bondguesser_utils.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/bondguesser_utils/bondguesser_utils.o -O3 2024-06-17T17:32:16,942 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:32:16,942 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:32:16,942 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:32:16,942 from moleculekit/bondguesser_utils/bondguesser_utils.cpp:1265: 2024-06-17T17:32:16,943 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:32:16,943 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:32:16,943 | ^~~~~~~ 2024-06-17T17:32:17,373 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:32:17,373 from moleculekit/bondguesser_utils/bondguesser_utils.cpp:1269: 2024-06-17T17:32:17,373 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:32:17,373 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:32:17,373 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:32:17,374 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,485 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)’: 2024-06-17T17:32:18,485 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] 2024-06-17T17:32:18,485 20255 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2024-06-17T17:32:18,485 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-17T17:32:18,485 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] 2024-06-17T17:32:18,486 20267 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2024-06-17T17:32:18,486 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-17T17:32:18,486 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] 2024-06-17T17:32:18,486 20279 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2024-06-17T17:32:18,486 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-17T17:32:18,486 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20318:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,487 20318 | __pyx_t_12 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-17T17:32:18,487 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,487 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20357:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,487 20357 | __pyx_t_12 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-17T17:32:18,487 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,487 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20396:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,487 20396 | __pyx_t_12 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,488 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,488 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20435:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,488 20435 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-17T17:32:18,488 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,488 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20441:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,488 20441 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-17T17:32:18,488 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,489 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20482:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,489 20482 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-17T17:32:18,489 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,489 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20488:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,489 20488 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,489 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,489 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20529:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,490 20529 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-17T17:32:18,490 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,490 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20535:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,490 20535 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,490 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,490 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20576:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,490 20576 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-17T17:32:18,491 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,491 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20629:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,491 20629 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,491 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,491 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20676:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,491 20676 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,491 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,492 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20717:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,492 20717 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-17T17:32:18,492 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,492 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20723:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,492 20723 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-17T17:32:18,492 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,492 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20729:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,493 20729 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,493 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,493 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20776:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,493 20776 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-17T17:32:18,493 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,493 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20782:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,493 20782 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,494 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,494 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20823:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,494 20823 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-17T17:32:18,494 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,494 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20835:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,494 20835 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,494 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,495 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20888:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-17T17:32:18,495 20888 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-17T17:32:18,495 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,514 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)’: 2024-06-17T17:32:18,514 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] 2024-06-17T17:32:18,514 21510 | __pyx_t_6 = (__pyx_v_boxneigh == __pyx_v_n_boxes); 2024-06-17T17:32:18,514 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:18,514 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] 2024-06-17T17:32:18,515 21547 | __pyx_t_6 = (__pyx_v_boxneigh == __pyx_v_boxidx); 2024-06-17T17:32:18,515 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-06-17T17:32:41,635 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/bondguesser_utils/bondguesser_utils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:32:41,937 building 'moleculekit.atomselect_utils' extension 2024-06-17T17:32:41,938 creating build/temp.linux-armv7l-cpython-39/moleculekit/atomselect_utils 2024-06-17T17:32:41,939 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/atomselect_utils/atomselect_utils.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/atomselect_utils/atomselect_utils.o -O3 2024-06-17T17:32:42,173 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:32:42,173 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:32:42,174 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:32:42,174 from moleculekit/atomselect_utils/atomselect_utils.cpp:1282: 2024-06-17T17:32:42,174 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:32:42,174 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:32:42,174 | ^~~~~~~ 2024-06-17T17:32:42,631 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:32:42,631 from moleculekit/atomselect_utils/atomselect_utils.cpp:1286: 2024-06-17T17:32:42,632 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:32:42,632 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:32:42,632 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:32:42,632 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:32:43,880 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 >&)’: 2024-06-17T17:32:43,880 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] 2024-06-17T17:32:43,880 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); 2024-06-17T17:32:43,880 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-06-17T17:32:43,885 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 >&)’: 2024-06-17T17:32:43,885 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] 2024-06-17T17:32:43,885 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); 2024-06-17T17:32:43,886 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-17T17:32:43,890 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 >&)’: 2024-06-17T17:32:43,891 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] 2024-06-17T17:32:43,891 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); 2024-06-17T17:32:43,891 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-17T17:33:14,079 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/atomselect_utils/atomselect_utils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:33:14,415 building 'moleculekit.distance_utils' extension 2024-06-17T17:33:14,416 creating build/temp.linux-armv7l-cpython-39/moleculekit/distance_utils 2024-06-17T17:33:14,417 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/distance_utils/distance_utils.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/distance_utils/distance_utils.o -O3 2024-06-17T17:33:14,649 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:33:14,650 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:33:14,650 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:33:14,650 from moleculekit/distance_utils/distance_utils.cpp:1265: 2024-06-17T17:33:14,650 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:33:14,650 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:33:14,650 | ^~~~~~~ 2024-06-17T17:33:15,098 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:33:15,098 from moleculekit/distance_utils/distance_utils.cpp:1269: 2024-06-17T17:33:15,098 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:33:15,099 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:33:15,099 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:33:15,099 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:33:16,282 moleculekit/distance_utils/distance_utils.cpp: In function ‘PyObject* __pyx_pf_11moleculekit_14distance_utils_2get_collisions(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, float)’: 2024-06-17T17:33:16,283 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] 2024-06-17T17:33:16,283 21813 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2024-06-17T17:33:16,283 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-17T17:33:16,283 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] 2024-06-17T17:33:16,283 21825 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2024-06-17T17:33:16,284 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-17T17:33:49,618 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/distance_utils/distance_utils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:33:49,959 building 'moleculekit.occupancy_utils' extension 2024-06-17T17:33:49,959 creating build/temp.linux-armv7l-cpython-39/moleculekit/occupancy_utils 2024-06-17T17:33:49,960 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/occupancy_utils/occupancy_utils.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/occupancy_utils/occupancy_utils.o -O3 2024-06-17T17:33:50,195 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:33:50,195 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:33:50,195 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:33:50,195 from moleculekit/occupancy_utils/occupancy_utils.cpp:1265: 2024-06-17T17:33:50,196 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:33:50,196 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:33:50,196 | ^~~~~~~ 2024-06-17T17:33:50,622 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:33:50,622 from moleculekit/occupancy_utils/occupancy_utils.cpp:1269: 2024-06-17T17:33:50,622 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:33:50,622 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:33:50,623 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:33:50,623 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:34:13,239 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/occupancy_utils/occupancy_utils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:34:13,451 building 'moleculekit.cython_utils' extension 2024-06-17T17:34:13,452 creating build/temp.linux-armv7l-cpython-39/moleculekit/cython_utils 2024-06-17T17:34:13,452 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/cython_utils/cython_utils.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/cython_utils/cython_utils.o -O3 2024-06-17T17:34:13,690 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:34:13,690 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:34:13,690 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:34:13,690 from moleculekit/cython_utils/cython_utils.cpp:1265: 2024-06-17T17:34:13,691 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:34:13,691 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:34:13,691 | ^~~~~~~ 2024-06-17T17:34:14,119 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-17T17:34:14,119 from moleculekit/cython_utils/cython_utils.cpp:1269: 2024-06-17T17:34:14,119 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-17T17:34:14,120 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h:405:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 2024-06-17T17:34:14,120 405 | return ((longdouble_t *) &z)[0]; 2024-06-17T17:34:14,120 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:34:39,209 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/cython_utils/cython_utils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:34:39,526 building 'moleculekit.xtc' extension 2024-06-17T17:34:39,527 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-17T17:34:39,528 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-17T17:34:39,529 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-17T17:34:39,530 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/xtc -Imoleculekit/fileformats/xtc/include/ -Imoleculekit/fileformats/xtc/ -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/fileformats/xtc/src/xdrfile.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile.o 2024-06-17T17:34:39,798 moleculekit/fileformats/xtc/src/xdrfile.cpp:66:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,798 66 | "OK", 2024-06-17T17:34:39,798 | ^~~~ 2024-06-17T17:34:39,799 moleculekit/fileformats/xtc/src/xdrfile.cpp:67:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,799 67 | "Header", 2024-06-17T17:34:39,799 | ^~~~~~~~ 2024-06-17T17:34:39,799 moleculekit/fileformats/xtc/src/xdrfile.cpp:68:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,799 68 | "String", 2024-06-17T17:34:39,799 | ^~~~~~~~ 2024-06-17T17:34:39,799 moleculekit/fileformats/xtc/src/xdrfile.cpp:69:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,800 69 | "Double", 2024-06-17T17:34:39,800 | ^~~~~~~~ 2024-06-17T17:34:39,800 moleculekit/fileformats/xtc/src/xdrfile.cpp:70:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,800 70 | "Integer", 2024-06-17T17:34:39,800 | ^~~~~~~~~ 2024-06-17T17:34:39,800 moleculekit/fileformats/xtc/src/xdrfile.cpp:71:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,800 71 | "Float", 2024-06-17T17:34:39,801 | ^~~~~~~ 2024-06-17T17:34:39,801 moleculekit/fileformats/xtc/src/xdrfile.cpp:72:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,801 72 | "Unsigned integer", 2024-06-17T17:34:39,801 | ^~~~~~~~~~~~~~~~~~ 2024-06-17T17:34:39,801 moleculekit/fileformats/xtc/src/xdrfile.cpp:73:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,801 73 | "Compressed 3D coordinate", 2024-06-17T17:34:39,801 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:34:39,802 moleculekit/fileformats/xtc/src/xdrfile.cpp:74:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,802 74 | "Closing file", 2024-06-17T17:34:39,802 | ^~~~~~~~~~~~~~ 2024-06-17T17:34:39,802 moleculekit/fileformats/xtc/src/xdrfile.cpp:75:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,802 75 | "Magic number", 2024-06-17T17:34:39,802 | ^~~~~~~~~~~~~~ 2024-06-17T17:34:39,802 moleculekit/fileformats/xtc/src/xdrfile.cpp:76:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,803 76 | "Not enough memory", 2024-06-17T17:34:39,803 | ^~~~~~~~~~~~~~~~~~~ 2024-06-17T17:34:39,803 moleculekit/fileformats/xtc/src/xdrfile.cpp:77:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,803 77 | "End of file", 2024-06-17T17:34:39,803 | ^~~~~~~~~~~~~ 2024-06-17T17:34:39,803 moleculekit/fileformats/xtc/src/xdrfile.cpp:78:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-17T17:34:39,803 78 | "File not found" 2024-06-17T17:34:39,804 | ^~~~~~~~~~~~~~~~ 2024-06-17T17:34:39,807 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofint(int)’: 2024-06-17T17:34:39,808 moleculekit/fileformats/xtc/src/xdrfile.cpp:459:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,808 459 | while (size >= num && num_of_bits < 32) 2024-06-17T17:34:39,808 | ~~~~~^~~~~~ 2024-06-17T17:34:39,808 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofints(int, unsigned int*)’: 2024-06-17T17:34:39,808 moleculekit/fileformats/xtc/src/xdrfile.cpp:505:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:34:39,809 505 | while (bytes[num_of_bytes] >= num) 2024-06-17T17:34:39,809 | ~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-06-17T17:34:39,811 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘void encodeints(int*, int, int, unsigned int*, unsigned int*)’: 2024-06-17T17:34:39,811 moleculekit/fileformats/xtc/src/xdrfile.cpp:614:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,811 614 | if (num_of_bits >= num_of_bytes * 8) 2024-06-17T17:34:39,811 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-06-17T17:34:39,811 moleculekit/fileformats/xtc/src/xdrfile.cpp:616:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,812 616 | for (i = 0; i < num_of_bytes; i++) 2024-06-17T17:34:39,812 | ~~^~~~~~~~~~~~~~ 2024-06-17T17:34:39,812 moleculekit/fileformats/xtc/src/xdrfile.cpp:624:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,812 624 | for (i = 0; i < num_of_bytes-1; i++) 2024-06-17T17:34:39,812 | ~~^~~~~~~~~~~~~~~~ 2024-06-17T17:34:39,812 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int decodebits(int*, int)’: 2024-06-17T17:34:39,812 moleculekit/fileformats/xtc/src/xdrfile.cpp:664:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:34:39,813 664 | if (lastbits < num_of_bits) 2024-06-17T17:34:39,813 | ~~~~~~~~~^~~~~~~~~~~~~ 2024-06-17T17:34:39,816 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_decompress_coord_float(float*, int*, float*, XDRFILE*)’: 2024-06-17T17:34:39,816 moleculekit/fileformats/xtc/src/xdrfile.cpp:785:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:34:39,816 785 | if(size3>xfp->buf1size) 2024-06-17T17:34:39,816 | ~~~~~^~~~~~~~~~~~~~ 2024-06-17T17:34:39,818 moleculekit/fileformats/xtc/src/xdrfile.cpp:842:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:34:39,818 842 | maxidx = (LASTIDX= size3 ) { return -1; } 2024-06-17T17:34:39,821 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:34:39,821 moleculekit/fileformats/xtc/src/xdrfile.cpp:935:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,821 935 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:34:39,821 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:34:39,821 moleculekit/fileformats/xtc/src/xdrfile.cpp:938:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,822 938 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:34:39,822 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:34:39,822 moleculekit/fileformats/xtc/src/xdrfile.cpp:945:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,822 945 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:34:39,822 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:34:39,822 moleculekit/fileformats/xtc/src/xdrfile.cpp:948:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,822 948 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:34:39,822 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:34:39,823 moleculekit/fileformats/xtc/src/xdrfile.cpp:951:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,823 951 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:34:39,823 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:34:39,823 moleculekit/fileformats/xtc/src/xdrfile.cpp:756:17: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-06-17T17:34:39,823 756 | int smallidx, minidx, maxidx; 2024-06-17T17:34:39,823 | ^~~~~~ 2024-06-17T17:34:39,823 moleculekit/fileformats/xtc/src/xdrfile.cpp:759:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-06-17T17:34:39,824 759 | int smallnum, smaller, larger, i, is_smaller, run; 2024-06-17T17:34:39,824 | ^~~~~~ 2024-06-17T17:34:39,824 moleculekit/fileformats/xtc/src/xdrfile.cpp:763:6: warning: unused variable ‘errval’ [-Wunused-variable] 2024-06-17T17:34:39,824 763 | int errval=1; 2024-06-17T17:34:39,824 | ^~~~~~ 2024-06-17T17:34:39,825 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_compress_coord_float(float*, int, float, XDRFILE*)’: 2024-06-17T17:34:39,825 moleculekit/fileformats/xtc/src/xdrfile.cpp:1011:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:34:39,825 1011 | if(size3>xfp->buf1size) 2024-06-17T17:34:39,825 | ~~~~~^~~~~~~~~~~~~~ 2024-06-17T17:34:39,827 moleculekit/fileformats/xtc/src/xdrfile.cpp:1068:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,827 1068 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-17T17:34:39,827 | ~~~~~~~~^~~~~~~ 2024-06-17T17:34:39,828 moleculekit/fileformats/xtc/src/xdrfile.cpp:1084:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,828 1084 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-17T17:34:39,828 | ~~~~~~~~^~~~~~~ 2024-06-17T17:34:39,828 moleculekit/fileformats/xtc/src/xdrfile.cpp:1098:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,828 1098 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-17T17:34:39,829 | ~~~~~~~~^~~~~~~ 2024-06-17T17:34:39,830 moleculekit/fileformats/xtc/src/xdrfile.cpp:1137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,830 1137 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2024-06-17T17:34:39,830 | ^ 2024-06-17T17:34:39,830 moleculekit/fileformats/xtc/src/xdrfile.cpp:1143:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:34:39,830 1143 | maxidx = (LASTIDXxfp->buf1size) 2024-06-17T17:34:39,838 | ~~~~~^~~~~~~~~~~~~~ 2024-06-17T17:34:39,839 moleculekit/fileformats/xtc/src/xdrfile.cpp:1377:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:34:39,840 1377 | maxidx = (LASTIDXxfp->buf1size) { 2024-06-17T17:34:39,845 | ~~~~~^~~~~~~~~~~~~~ 2024-06-17T17:34:39,849 moleculekit/fileformats/xtc/src/xdrfile.cpp:1628:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:34:39,849 1628 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2024-06-17T17:34:39,849 | ^ 2024-06-17T17:34:39,849 moleculekit/fileformats/xtc/src/xdrfile.cpp:1633:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:34:39,850 1633 | maxidx = (LASTIDX= num && num_of_bits < 32) 2024-06-17T17:35:05,020 | ~~~~~^~~~~~ 2024-06-17T17:35:05,020 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofints(int, unsigned int*)’: 2024-06-17T17:35:05,021 moleculekit/fileformats/xtc/src/xdrfile.cpp:505:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:35:05,021 505 | while (bytes[num_of_bytes] >= num) 2024-06-17T17:35:05,021 | ~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-06-17T17:35:05,023 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘void encodeints(int*, int, int, unsigned int*, unsigned int*)’: 2024-06-17T17:35:05,023 moleculekit/fileformats/xtc/src/xdrfile.cpp:614:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,023 614 | if (num_of_bits >= num_of_bytes * 8) 2024-06-17T17:35:05,023 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-06-17T17:35:05,023 moleculekit/fileformats/xtc/src/xdrfile.cpp:616:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,024 616 | for (i = 0; i < num_of_bytes; i++) 2024-06-17T17:35:05,024 | ~~^~~~~~~~~~~~~~ 2024-06-17T17:35:05,024 moleculekit/fileformats/xtc/src/xdrfile.cpp:624:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,024 624 | for (i = 0; i < num_of_bytes-1; i++) 2024-06-17T17:35:05,024 | ~~^~~~~~~~~~~~~~~~ 2024-06-17T17:35:05,024 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int decodebits(int*, int)’: 2024-06-17T17:35:05,025 moleculekit/fileformats/xtc/src/xdrfile.cpp:664:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:35:05,025 664 | if (lastbits < num_of_bits) 2024-06-17T17:35:05,025 | ~~~~~~~~~^~~~~~~~~~~~~ 2024-06-17T17:35:05,028 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_decompress_coord_float(float*, int*, float*, XDRFILE*)’: 2024-06-17T17:35:05,028 moleculekit/fileformats/xtc/src/xdrfile.cpp:785:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:35:05,028 785 | if(size3>xfp->buf1size) 2024-06-17T17:35:05,028 | ~~~~~^~~~~~~~~~~~~~ 2024-06-17T17:35:05,030 moleculekit/fileformats/xtc/src/xdrfile.cpp:842:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:35:05,030 842 | maxidx = (LASTIDX= size3 ) { return -1; } 2024-06-17T17:35:05,033 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:35:05,033 moleculekit/fileformats/xtc/src/xdrfile.cpp:935:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,033 935 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:35:05,033 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:35:05,033 moleculekit/fileformats/xtc/src/xdrfile.cpp:938:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,034 938 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:35:05,034 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:35:05,034 moleculekit/fileformats/xtc/src/xdrfile.cpp:945:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,034 945 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:35:05,034 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:35:05,034 moleculekit/fileformats/xtc/src/xdrfile.cpp:948:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,034 948 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:35:05,035 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:35:05,035 moleculekit/fileformats/xtc/src/xdrfile.cpp:951:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,035 951 | if(countmjh >= size3 ) { return -1; } 2024-06-17T17:35:05,035 | ~~~~~~~~~^~~~~~~~ 2024-06-17T17:35:05,035 moleculekit/fileformats/xtc/src/xdrfile.cpp:756:17: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-06-17T17:35:05,035 756 | int smallidx, minidx, maxidx; 2024-06-17T17:35:05,035 | ^~~~~~ 2024-06-17T17:35:05,035 moleculekit/fileformats/xtc/src/xdrfile.cpp:759:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-06-17T17:35:05,036 759 | int smallnum, smaller, larger, i, is_smaller, run; 2024-06-17T17:35:05,036 | ^~~~~~ 2024-06-17T17:35:05,036 moleculekit/fileformats/xtc/src/xdrfile.cpp:763:6: warning: unused variable ‘errval’ [-Wunused-variable] 2024-06-17T17:35:05,036 763 | int errval=1; 2024-06-17T17:35:05,036 | ^~~~~~ 2024-06-17T17:35:05,037 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_compress_coord_float(float*, int, float, XDRFILE*)’: 2024-06-17T17:35:05,037 moleculekit/fileformats/xtc/src/xdrfile.cpp:1011:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:35:05,037 1011 | if(size3>xfp->buf1size) 2024-06-17T17:35:05,037 | ~~~~~^~~~~~~~~~~~~~ 2024-06-17T17:35:05,039 moleculekit/fileformats/xtc/src/xdrfile.cpp:1068:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,039 1068 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-17T17:35:05,039 | ~~~~~~~~^~~~~~~ 2024-06-17T17:35:05,040 moleculekit/fileformats/xtc/src/xdrfile.cpp:1084:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,040 1084 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-17T17:35:05,040 | ~~~~~~~~^~~~~~~ 2024-06-17T17:35:05,040 moleculekit/fileformats/xtc/src/xdrfile.cpp:1098:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,040 1098 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-17T17:35:05,040 | ~~~~~~~~^~~~~~~ 2024-06-17T17:35:05,042 moleculekit/fileformats/xtc/src/xdrfile.cpp:1137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,042 1137 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2024-06-17T17:35:05,042 | ^ 2024-06-17T17:35:05,042 moleculekit/fileformats/xtc/src/xdrfile.cpp:1143:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:35:05,042 1143 | maxidx = (LASTIDXxfp->buf1size) 2024-06-17T17:35:05,050 | ~~~~~^~~~~~~~~~~~~~ 2024-06-17T17:35:05,051 moleculekit/fileformats/xtc/src/xdrfile.cpp:1377:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:35:05,051 1377 | maxidx = (LASTIDXxfp->buf1size) { 2024-06-17T17:35:05,057 | ~~~~~^~~~~~~~~~~~~~ 2024-06-17T17:35:05,061 moleculekit/fileformats/xtc/src/xdrfile.cpp:1628:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:35:05,061 1628 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2024-06-17T17:35:05,061 | ^ 2024-06-17T17:35:05,061 moleculekit/fileformats/xtc/src/xdrfile.cpp:1633:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:35:05,061 1633 | maxidx = (LASTIDX= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; 2024-06-17T17:35:39,750 | ^ 2024-06-17T17:35:39,757 moleculekit/fileformats/xtc/trr.c:12009:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,757 12009 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-17T17:35:39,757 | ^ 2024-06-17T17:35:39,758 moleculekit/fileformats/xtc/trr.c:2485:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,758 2485 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-06-17T17:35:39,758 | ^ 2024-06-17T17:35:39,764 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-06-17T17:35:39,764 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-06-17T17:35:39,764 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:35:39,770 moleculekit/fileformats/xtc/trr.c:12003:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,770 12003 | __pyx_t_28 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-06-17T17:35:39,770 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-06-17T17:35:39,777 moleculekit/fileformats/xtc/trr.c:11956:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,777 11956 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; 2024-06-17T17:35:39,777 | ^ 2024-06-17T17:35:39,784 moleculekit/fileformats/xtc/trr.c:11952:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,785 11952 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-17T17:35:39,785 | ^ 2024-06-17T17:35:39,785 moleculekit/fileformats/xtc/trr.c:2485:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,786 2485 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-06-17T17:35:39,786 | ^ 2024-06-17T17:35:39,791 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-06-17T17:35:39,792 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-06-17T17:35:39,792 | ^~~~~~~~~~~~~~~~~~~~ 2024-06-17T17:35:39,798 moleculekit/fileformats/xtc/trr.c:11946:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,798 11946 | __pyx_t_28 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-06-17T17:35:39,798 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-06-17T17:35:39,804 moleculekit/fileformats/xtc/trr.c:12345:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,804 12345 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-17T17:35:39,804 | ^ 2024-06-17T17:35:39,811 moleculekit/fileformats/xtc/trr.c:12341:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,811 12341 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-06-17T17:35:39,812 | ^ 2024-06-17T17:35:39,819 moleculekit/fileformats/xtc/trr.c:12186:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,819 12186 | } else if (unlikely(__pyx_t_35 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-17T17:35:39,819 | ^ 2024-06-17T17:35:39,826 moleculekit/fileformats/xtc/trr.c:12182:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,826 12182 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-06-17T17:35:39,826 | ^ 2024-06-17T17:35:39,832 moleculekit/fileformats/xtc/trr.c:12238:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,832 12238 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-17T17:35:39,832 | ^ 2024-06-17T17:35:39,839 moleculekit/fileformats/xtc/trr.c:12234:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:35:39,840 12234 | } else if (unlikely(__pyx_t_35 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-06-17T17:35:39,840 | ^ 2024-06-17T17:35:46,342 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/trr.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/trr.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:35:46,531 building 'moleculekit.dcd' extension 2024-06-17T17:35:46,532 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-17T17:35:46,533 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src 2024-06-17T17:35:46,535 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/dcd -Imoleculekit/fileformats/dcd/include/ -Imoleculekit/fileformats/dcd/ -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/fileformats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/dcd.o 2024-06-17T17:35:46,892 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:35:46,892 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:35:46,892 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:35:46,893 from moleculekit/fileformats/dcd/dcd.c:1256: 2024-06-17T17:35:46,893 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:35:46,893 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:35:46,893 | ^~~~~~~ 2024-06-17T17:35:47,936 In file included from moleculekit/fileformats/dcd/include/dcdplugin.h:1, 2024-06-17T17:35:47,937 from moleculekit/fileformats/dcd/dcd.c:1262: 2024-06-17T17:35:47,937 moleculekit/fileformats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2024-06-17T17:35:47,937 474 | static int fio_write_str(fio_fd fd, const char *str) { 2024-06-17T17:35:47,937 | ^~~~~~~~~~~~~ 2024-06-17T17:35:47,937 moleculekit/fileformats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2024-06-17T17:35:47,938 470 | static int fio_read_int32(fio_fd fd, int *i) { 2024-06-17T17:35:47,938 | ^~~~~~~~~~~~~~ 2024-06-17T17:35:47,938 moleculekit/fileformats/dcd/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 2024-06-17T17:35:47,938 466 | static int fio_write_int32(fio_fd fd, int i) { 2024-06-17T17:35:47,938 | ^~~~~~~~~~~~~~~ 2024-06-17T17:35:47,938 moleculekit/fileformats/dcd/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2024-06-17T17:35:47,939 457 | static fio_size_t fio_ftell(fio_fd fd) { 2024-06-17T17:35:47,939 | ^~~~~~~~~ 2024-06-17T17:35:47,939 moleculekit/fileformats/dcd/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 2024-06-17T17:35:47,939 450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { 2024-06-17T17:35:47,939 | ^~~~~~~~~ 2024-06-17T17:35:47,939 moleculekit/fileformats/dcd/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 2024-06-17T17:35:47,939 415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { 2024-06-17T17:35:47,939 | ^~~~~~~~~ 2024-06-17T17:35:47,940 moleculekit/fileformats/dcd/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2024-06-17T17:35:47,940 394 | static int fio_fclose(fio_fd fd) { 2024-06-17T17:35:47,940 | ^~~~~~~~~~ 2024-06-17T17:35:47,940 moleculekit/fileformats/dcd/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2024-06-17T17:35:47,940 366 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2024-06-17T17:35:47,940 | ^~~~~~~~ 2024-06-17T17:36:00,593 moleculekit/fileformats/dcd/dcd.c: In function ‘__pyx_pf_11moleculekit_3dcd_17DCDTrajectoryFile_18read’: 2024-06-17T17:36:00,593 moleculekit/fileformats/dcd/dcd.c:1158:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:36:00,593 1158 | #define PyInt_FromLong PyLong_FromLong 2024-06-17T17:36:00,593 | ^~~~~~~~~~~~~~~ 2024-06-17T17:36:00,598 moleculekit/fileformats/dcd/dcd.c:8476:7: note: ‘__pyx_v_i’ was declared here 2024-06-17T17:36:00,598 8476 | int __pyx_v_i; 2024-06-17T17:36:00,598 | ^~~~~~~~~ 2024-06-17T17:36:03,883 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/dcd -Imoleculekit/fileformats/dcd/include/ -Imoleculekit/fileformats/dcd/ -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/fileformats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src/dcdplugin.o 2024-06-17T17:36:04,063 moleculekit/fileformats/dcd/src/dcdplugin.c: In function ‘read_dcdheader’: 2024-06-17T17:36:04,064 moleculekit/fileformats/dcd/src/dcdplugin.c:150:55: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:36:04,064 150 | else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) 2024-06-17T17:36:04,064 | ^~ 2024-06-17T17:36:04,064 moleculekit/fileformats/dcd/src/dcdplugin.c:173:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:36:04,065 173 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) 2024-06-17T17:36:04,065 | ^~ 2024-06-17T17:36:04,065 moleculekit/fileformats/dcd/src/dcdplugin.c:194:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:36:04,065 194 | if (input_integer[0] != dcdcordmagic) 2024-06-17T17:36:04,065 | ^~ 2024-06-17T17:36:04,068 moleculekit/fileformats/dcd/src/dcdplugin.c:409:47: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:36:04,068 409 | if ((input_integer[0] + input_integer[1]) != ((*N) - (*NAMNF)) * 4) 2024-06-17T17:36:04,068 | ^~ 2024-06-17T17:36:04,069 moleculekit/fileformats/dcd/src/dcdplugin.c:428:47: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-17T17:36:04,069 428 | if ((input_integer[0] + input_integer[1]) != ((*N) - (*NAMNF)) * 4) 2024-06-17T17:36:04,069 | ^~ 2024-06-17T17:36:04,072 moleculekit/fileformats/dcd/src/dcdplugin.c: In function ‘read_dcdstep’: 2024-06-17T17:36:04,073 moleculekit/fileformats/dcd/src/dcdplugin.c:651:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:36:04,073 651 | if (tmpbuf[i] != sizeof(float) * N) 2024-06-17T17:36:04,073 | ^~ 2024-06-17T17:36:04,073 moleculekit/fileformats/dcd/src/dcdplugin.c:659:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-17T17:36:04,073 659 | if ((tmpbuf[2 * i] + tmpbuf[2 * i + 1]) != sizeof(float) * N) 2024-06-17T17:36:04,073 | ^~ 2024-06-17T17:36:04,096 In file included from moleculekit/fileformats/dcd/src/dcdplugin.c:55: 2024-06-17T17:36:04,096 At top level: 2024-06-17T17:36:04,097 moleculekit/fileformats/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2024-06-17T17:36:04,097 96 | static void swap2_aligned(void *v, long ndata) { 2024-06-17T17:36:04,097 | ^~~~~~~~~~~~~ 2024-06-17T17:36:04,097 moleculekit/fileformats/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2024-06-17T17:36:04,097 32 | static void swap2_unaligned(void *v, long ndata) { 2024-06-17T17:36:04,097 | ^~~~~~~~~~~~~~~ 2024-06-17T17:36:04,098 In file included from moleculekit/fileformats/dcd/src/dcdplugin.c:46: 2024-06-17T17:36:04,098 moleculekit/fileformats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2024-06-17T17:36:04,098 474 | static int fio_write_str(fio_fd fd, const char *str) { 2024-06-17T17:36:04,098 | ^~~~~~~~~~~~~ 2024-06-17T17:36:04,098 moleculekit/fileformats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2024-06-17T17:36:04,098 470 | static int fio_read_int32(fio_fd fd, int *i) { 2024-06-17T17:36:04,098 | ^~~~~~~~~~~~~~ 2024-06-17T17:36:05,205 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/dcd.o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src/dcdplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/dcd.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:36:05,348 building 'moleculekit.binpos' extension 2024-06-17T17:36:05,349 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-17T17:36:05,350 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src 2024-06-17T17:36:05,351 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/binpos -Imoleculekit/fileformats/binpos/include/ -Imoleculekit/fileformats/binpos/ -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/fileformats/binpos/binpos.c -o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/binpos.o 2024-06-17T17:36:05,699 In file included from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-17T17:36:05,700 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-17T17:36:05,700 from /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-17T17:36:05,700 from moleculekit/fileformats/binpos/binpos.c:1256: 2024-06-17T17:36:05,700 /tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-06-17T17:36:05,700 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-17T17:36:05,700 | ^~~~~~~ 2024-06-17T17:36:19,179 moleculekit/fileformats/binpos/binpos.c: In function ‘__pyx_pw_11moleculekit_6binpos_20BINPOSTrajectoryFile_7_read’: 2024-06-17T17:36:19,183 moleculekit/fileformats/binpos/binpos.c:8499:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:36:19,184 8499 | if (__pyx_t_1) { 2024-06-17T17:36:19,184 | ^ 2024-06-17T17:36:19,188 moleculekit/fileformats/binpos/binpos.c:7976:7: note: ‘__pyx_v_status’ was declared here 2024-06-17T17:36:19,188 7976 | int __pyx_v_status; 2024-06-17T17:36:19,188 | ^~~~~~~~~~~~~~ 2024-06-17T17:36:19,189 moleculekit/fileformats/binpos/binpos.c:1158:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-17T17:36:19,189 1158 | #define PyInt_FromLong PyLong_FromLong 2024-06-17T17:36:19,189 | ^~~~~~~~~~~~~~~ 2024-06-17T17:36:19,193 moleculekit/fileformats/binpos/binpos.c:7973:7: note: ‘__pyx_v_i’ was declared here 2024-06-17T17:36:19,193 7973 | int __pyx_v_i; 2024-06-17T17:36:19,194 | ^~~~~~~~~ 2024-06-17T17:36:21,483 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/fileformats/binpos -Imoleculekit/fileformats/binpos/include/ -Imoleculekit/fileformats/binpos/ -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/fileformats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src/binposplugin.o 2024-06-17T17:36:21,783 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/binpos.o build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src/binposplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/binpos.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:36:21,928 building 'moleculekit.tmalign' extension 2024-06-17T17:36:21,929 creating build/temp.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-17T17:36:21,930 creating build/temp.linux-armv7l-cpython-39/moleculekit/tmalign/src 2024-06-17T17:36:21,931 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/tmalign -Imoleculekit/tmalign/include/ -Imoleculekit/tmalign/ -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/tmalign/src/TMAlign.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/tmalign/src/TMAlign.o -w 2024-06-17T17:36:51,924 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imoleculekit/tmalign -Imoleculekit/tmalign/include/ -Imoleculekit/tmalign/ -I/tmp/pip-build-env-3we63uhk/overlay/lib/python3.9/site-packages/numpy/_core/include -I/usr/include/python3.9 -c moleculekit/tmalign/tmalign_util.cpp -o build/temp.linux-armv7l-cpython-39/moleculekit/tmalign/tmalign_util.o -w 2024-06-17T17:37:10,601 In file included from /usr/include/c++/10/vector:72, 2024-06-17T17:37:10,602 from moleculekit/tmalign/tmalign_util.cpp:1280: 2024-06-17T17:37:10,602 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2024-06-17T17:37:10,602 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-06-17T17:37:10,602 426 | vector<_Tp, _Alloc>:: 2024-06-17T17:37:10,602 | ^~~~~~~~~~~~~~~~~~~ 2024-06-17T17:37:11,182 In file included from /usr/include/c++/10/vector:67, 2024-06-17T17:37:11,182 from moleculekit/tmalign/tmalign_util.cpp:1280: 2024-06-17T17:37:11,182 /usr/include/c++/10/bits/stl_vector.h: In function ‘PyObject* __pyx_pw_11moleculekit_7tmalign_1tmalign(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’: 2024-06-17T17:37:11,183 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-06-17T17:37:11,183 1198 | _M_realloc_insert(end(), __x); 2024-06-17T17:37:11,183 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-17T17:37:11,183 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-06-17T17:37:11,183 1198 | _M_realloc_insert(end(), __x); 2024-06-17T17:37:11,183 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-17T17:37:11,184 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2024-06-17T17:37:11,184 1198 | _M_realloc_insert(end(), __x); 2024-06-17T17:37:11,184 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-17T17:37:13,670 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/moleculekit/tmalign/src/TMAlign.o build/temp.linux-armv7l-cpython-39/moleculekit/tmalign/tmalign_util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/moleculekit/tmalign.cpython-39-arm-linux-gnueabihf.so 2024-06-17T17:37:14,137 UPDATING build/lib.linux-armv7l-cpython-39/moleculekit/_version.py 2024-06-17T17:37:14,137 set build/lib.linux-armv7l-cpython-39/moleculekit/_version.py to '1.8.34' 2024-06-17T17:37:14,138 installing to build/bdist.linux-armv7l/wheel 2024-06-17T17:37:14,138 running install 2024-06-17T17:37:14,163 running install_lib 2024-06-17T17:37:14,170 creating build/bdist.linux-armv7l 2024-06-17T17:37:14,170 creating build/bdist.linux-armv7l/wheel 2024-06-17T17:37:14,172 creating build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,174 creating build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-06-17T17:37:14,175 copying build/lib.linux-armv7l-cpython-39/moleculekit/wrapping/wrapping.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-06-17T17:37:14,177 copying build/lib.linux-armv7l-cpython-39/moleculekit/wrapping/wrapping.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-06-17T17:37:14,213 creating build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-06-17T17:37:14,213 copying build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils/distance_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-06-17T17:37:14,244 copying build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils/distance_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-06-17T17:37:14,247 copying build/lib.linux-armv7l-cpython-39/moleculekit/wrapping.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,272 copying build/lib.linux-armv7l-cpython-39/moleculekit/vmd_wrapper -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,274 copying build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,277 copying build/lib.linux-armv7l-cpython-39/moleculekit/viewer.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,279 copying build/lib.linux-armv7l-cpython-39/moleculekit/distance.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,281 creating build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-06-17T17:37:14,282 copying build/lib.linux-armv7l-cpython-39/moleculekit/ply/yacc.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-06-17T17:37:14,287 copying build/lib.linux-armv7l-cpython-39/moleculekit/ply/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-06-17T17:37:14,289 copying build/lib.linux-armv7l-cpython-39/moleculekit/ply/lex.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-06-17T17:37:14,293 copying build/lib.linux-armv7l-cpython-39/moleculekit/dcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,316 copying build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,349 creating build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-06-17T17:37:14,350 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils/atomselect_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-06-17T17:37:14,399 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils/atomselect_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-06-17T17:37:14,404 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-06-17T17:37:14,406 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/tmalign_util.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-06-17T17:37:14,438 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/tmalign_util.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-06-17T17:37:14,441 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/tmalignlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-06-17T17:37:14,443 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign/src 2024-06-17T17:37:14,444 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/src/TMAlign.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign/src 2024-06-17T17:37:14,455 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign/include 2024-06-17T17:37:14,456 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/include/TMAlign.h -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign/include 2024-06-17T17:37:14,458 copying build/lib.linux-armv7l-cpython-39/moleculekit/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,460 copying build/lib.linux-armv7l-cpython-39/moleculekit/vmdgraphics.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,462 copying build/lib.linux-armv7l-cpython-39/moleculekit/config.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,465 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx 2024-06-17T17:37:14,466 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx 2024-06-17T17:37:14,468 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-17T17:37:14,468 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests/PdbxReadWriteTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-17T17:37:14,471 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-17T17:37:14,472 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests/PdbxReaderTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-17T17:37:14,474 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests/PdbxWriterTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-17T17:37:14,477 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-17T17:37:14,478 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-17T17:37:14,480 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader/PdbxContainers.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-17T17:37:14,484 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader/PdbxParser.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-17T17:37:14,490 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader/PdbxReader.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-17T17:37:14,494 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-06-17T17:37:14,495 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-06-17T17:37:14,497 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer/PdbxWriter.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-06-17T17:37:14,500 copying build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,532 creating build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,533 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/detect.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,537 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/hhblitsprofile.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,539 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,541 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/autosegment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,544 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/sequencestructuralalignment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,547 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/preparation.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,551 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/preparation_customres.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,554 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/modelling.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,557 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/graphalignment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,560 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/docking.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,563 creating build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-06-17T17:37:14,564 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-06-17T17:37:14,567 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools/obabel_cli.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-06-17T17:37:14,569 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/atomtyper.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,572 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/moleculechecks.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,575 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/voxeldescriptors.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,578 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/crystalpacking.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-17T17:37:14,581 copying build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,623 copying build/lib.linux-armv7l-cpython-39/moleculekit/writers.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,626 copying build/lib.linux-armv7l-cpython-39/moleculekit/periodictable.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,629 creating build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-06-17T17:37:14,630 copying build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils/bondguesser_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-06-17T17:37:14,632 copying build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils/bondguesser_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-06-17T17:37:14,657 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-17T17:37:14,658 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-17T17:37:14,660 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-17T17:37:14,688 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/interactions.py -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-17T17:37:14,690 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-17T17:37:14,717 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-17T17:37:14,749 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-17T17:37:14,785 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-06-17T17:37:14,786 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi/cationpi.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-06-17T17:37:14,788 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi/cationpi.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-06-17T17:37:14,823 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-06-17T17:37:14,824 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi/pipi.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-06-17T17:37:14,826 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi/pipi.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-06-17T17:37:14,859 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-06-17T17:37:14,860 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds/hbonds.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-06-17T17:37:14,863 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds/hbonds.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-06-17T17:37:14,897 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-06-17T17:37:14,898 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole/sigmahole.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-06-17T17:37:14,900 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole/sigmahole.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-06-17T17:37:14,933 creating build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-06-17T17:37:14,934 copying build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils/occupancy_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-06-17T17:37:14,936 copying build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils/occupancy_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-06-17T17:37:14,957 copying build/lib.linux-armv7l-cpython-39/moleculekit/readers.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:14,963 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,004 creating build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-17T17:37:15,005 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/test_smallmol.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-17T17:37:15,008 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-17T17:37:15,009 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/test_smallmollib.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-17T17:37:15,011 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/smallmol.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-17T17:37:15,015 creating build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-17T17:37:15,016 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools/restrainedembed.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-17T17:37:15,018 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-17T17:37:15,020 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools/clustering.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-17T17:37:15,022 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools/test_tools.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-17T17:37:15,025 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/smallmollib.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-17T17:37:15,027 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/smallmolcdp.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-17T17:37:15,029 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/util.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-17T17:37:15,032 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-06-17T17:37:15,033 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-06-17T17:37:15,035 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-06-17T17:37:15,036 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/dcd.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-06-17T17:37:15,053 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/dcd.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-06-17T17:37:15,056 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/src 2024-06-17T17:37:15,057 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src/dcdplugin.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/src 2024-06-17T17:37:15,060 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/dcdlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-06-17T17:37:15,062 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-17T17:37:15,063 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/fastio.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-17T17:37:15,065 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/dcdplugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-17T17:37:15,067 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/endianswap.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-17T17:37:15,069 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/largefiles.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-17T17:37:15,071 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/molfile_plugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-17T17:37:15,074 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-17T17:37:15,075 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/trr.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-17T17:37:15,078 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/xdrlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-17T17:37:15,080 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/trrlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-17T17:37:15,081 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/trr.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-17T17:37:15,107 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/xtclib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-17T17:37:15,109 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-17T17:37:15,110 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-17T17:37:15,114 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-17T17:37:15,117 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-17T17:37:15,119 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdr_seek.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-17T17:37:15,120 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-17T17:37:15,123 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/xtc.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-17T17:37:15,125 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-17T17:37:15,126 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xdr_seek.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-17T17:37:15,128 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-17T17:37:15,130 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/trr_header.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-17T17:37:15,132 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xtc.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-17T17:37:15,134 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-17T17:37:15,137 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-17T17:37:15,139 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-17T17:37:15,165 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-06-17T17:37:15,165 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/binposlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-06-17T17:37:15,167 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/binpos.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-06-17T17:37:15,170 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/binpos.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-06-17T17:37:15,187 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/src 2024-06-17T17:37:15,188 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src/binposplugin.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/src 2024-06-17T17:37:15,191 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-06-17T17:37:15,192 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include/largefiles.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-06-17T17:37:15,194 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include/molfile_plugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-06-17T17:37:15,197 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include/binposplugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-06-17T17:37:15,198 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/utils.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-06-17T17:37:15,200 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/netcdf.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-06-17T17:37:15,203 copying build/lib.linux-armv7l-cpython-39/moleculekit/align.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,205 copying build/lib.linux-armv7l-cpython-39/moleculekit/home.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,207 creating build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,208 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricfluctuation.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,211 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,212 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricshell.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,214 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricrmsd.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,216 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricdihedral.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,219 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metriccoordinate.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,221 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metrictmscore.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,223 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricsphericalcoordinate.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,225 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricsecondarystructure.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,227 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricgyration.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,230 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricplumed2.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,232 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricsasa.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,234 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/projection.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,236 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/util.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,238 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricdistance.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-17T17:37:15,240 copying build/lib.linux-armv7l-cpython-39/moleculekit/pymolgraphics.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,242 creating build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-06-17T17:37:15,243 copying build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils/cython_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-06-17T17:37:15,264 copying build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils/cython_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-06-17T17:37:15,266 copying build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,296 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,383 copying build/lib.linux-armv7l-cpython-39/moleculekit/opm.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,386 copying build/lib.linux-armv7l-cpython-39/moleculekit/vmdviewer.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,388 copying build/lib.linux-armv7l-cpython-39/moleculekit/_version.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,390 copying build/lib.linux-armv7l-cpython-39/moleculekit/version.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,392 copying build/lib.linux-armv7l-cpython-39/moleculekit/rcsb.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,395 creating build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-17T17:37:15,396 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-17T17:37:15,398 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect/analyze.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-17T17:37:15,400 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect/languageparser.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-17T17:37:15,402 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect/atomselect.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-17T17:37:15,405 copying build/lib.linux-armv7l-cpython-39/moleculekit/xtc.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,440 copying build/lib.linux-armv7l-cpython-39/moleculekit/logging.ini -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,442 copying build/lib.linux-armv7l-cpython-39/moleculekit/dihedral.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,444 copying build/lib.linux-armv7l-cpython-39/moleculekit/trr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,475 copying build/lib.linux-armv7l-cpython-39/moleculekit/binpos.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:15,489 creating build/bdist.linux-armv7l/wheel/moleculekit/share 2024-06-17T17:37:15,490 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/ALA.cif -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-06-17T17:37:15,492 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/backbone.cif -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-06-17T17:37:15,495 creating build/bdist.linux-armv7l/wheel/moleculekit/share/atomselect 2024-06-17T17:37:15,495 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/atomselect/atomselect.json -> build/bdist.linux-armv7l/wheel/moleculekit/share/atomselect 2024-06-17T17:37:15,498 creating build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr 2024-06-17T17:37:15,501 creating build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,502 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,504 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GHG.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,506 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DAH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,508 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,509 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DAH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,511 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/KYN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,513 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NAL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,514 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TPO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,516 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DA2.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,518 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,520 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MMO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,521 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/M3L.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,523 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HOX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,525 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,526 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DAB.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,528 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ESC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,530 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,532 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BTK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,534 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PTR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,535 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NCY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,537 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BCS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,539 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/OMX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,541 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/OCY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,542 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BB8.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,544 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,546 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,548 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ORM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,549 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/APD.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,551 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/P1L.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,553 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4PH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,555 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DAB.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,556 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HQA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,558 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DPP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,560 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/AHP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,562 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,563 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ABA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,565 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,566 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/YCM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,568 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MVA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,570 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BCS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,572 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,573 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CGU.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,575 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HLX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,577 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,578 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,580 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/YNM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,582 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DPP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,583 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/03Y.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,585 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ME0.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,587 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/5JP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,588 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BTK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,590 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2GX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,591 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,593 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HYP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,595 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/M3L.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,597 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,599 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IGL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,600 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NLE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,602 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,603 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/I2M.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,605 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4PH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,607 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2AS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,608 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,610 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ONL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,612 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PRK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,613 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GHG.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,615 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ESC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,617 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PRK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,619 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/KYN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,620 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TPO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,622 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0BN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,624 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2ML.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,626 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CCS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,627 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4IN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,629 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,631 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,633 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2AS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,634 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/SEP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,636 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/OMX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,638 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/004.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,639 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,641 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0A1.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,642 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/FGL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,644 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/D4P.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,646 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ME0.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,648 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HHK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,650 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ONL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,652 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/.gitkeep -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,653 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/1MH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,655 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,656 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GNC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,658 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HPE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,660 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/YNM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,661 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/FGL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,663 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HLU.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,665 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ABA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,666 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2GX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,668 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/OCY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,670 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GNC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,672 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PTR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,674 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/D4P.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,676 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HYP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,677 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PCA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,679 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HQA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,680 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,682 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TRO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,684 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,685 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TRO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,687 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MMO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,689 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/03Y.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,690 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,692 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/004.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,694 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IIL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,696 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NCY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,697 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,699 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,701 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,703 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,705 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2MR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,707 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,709 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0BN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,710 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,712 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TY2.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,713 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MVA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,715 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IIL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,717 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/AHP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,718 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4IN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,720 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,722 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IGL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,724 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2MR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,725 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BB8.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,727 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,728 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NVA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,730 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/AA4.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,732 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PCA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,733 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HTR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,735 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CGU.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,737 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,738 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HOX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,740 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,741 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,743 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/APD.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,745 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,746 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0AF.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,748 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0A1.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,750 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/YCM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,751 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HTR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,753 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/SEP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,755 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0AF.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,757 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/I2M.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,759 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CCS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,760 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HPE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,762 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HLU.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,763 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/1MH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,765 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,767 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HHK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,768 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IML.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,770 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NZC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,772 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/5JP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,773 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ORM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,775 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NZC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,777 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TY2.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,779 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HLX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,780 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2ML.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,782 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,784 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,786 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NLE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,787 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/P1L.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,790 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,791 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,793 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/AA4.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,794 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IML.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,796 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DA2.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,798 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NVA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,800 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NAL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-17T17:37:15,801 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/opm_sequences.json -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-06-17T17:37:16,053 copying build/lib.linux-armv7l-cpython-39/moleculekit/molecule.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:16,058 copying build/lib.linux-armv7l-cpython-39/moleculekit/rdkitintegration.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:16,061 copying build/lib.linux-armv7l-cpython-39/moleculekit/util.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-17T17:37:16,063 running install_egg_info 2024-06-17T17:37:16,070 Copying moleculekit.egg-info to build/bdist.linux-armv7l/wheel/moleculekit-1.8.34-py3.9.egg-info 2024-06-17T17:37:16,083 running install_scripts 2024-06-17T17:37:16,150 creating build/bdist.linux-armv7l/wheel/moleculekit-1.8.34.dist-info/WHEEL 2024-06-17T17:37:16,154 creating '/tmp/pip-wheel-0wfwgm3u/.tmp-eprci9v9/moleculekit-1.8.34-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-06-17T17:37:16,159 adding 'moleculekit/__init__.py' 2024-06-17T17:37:16,161 adding 'moleculekit/_version.py' 2024-06-17T17:37:16,164 adding 'moleculekit/align.py' 2024-06-17T17:37:16,487 adding 'moleculekit/atomselect_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:16,652 adding 'moleculekit/binpos.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:16,659 adding 'moleculekit/bondguesser.py' 2024-06-17T17:37:16,906 adding 'moleculekit/bondguesser_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:16,915 adding 'moleculekit/config.py' 2024-06-17T17:37:17,176 adding 'moleculekit/cython_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:17,349 adding 'moleculekit/dcd.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:17,356 adding 'moleculekit/dihedral.py' 2024-06-17T17:37:17,357 adding 'moleculekit/distance.py' 2024-06-17T17:37:17,689 adding 'moleculekit/distance_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:17,702 adding 'moleculekit/home.py' 2024-06-17T17:37:17,703 adding 'moleculekit/logging.ini' 2024-06-17T17:37:17,717 adding 'moleculekit/molecule.py' 2024-06-17T17:37:17,946 adding 'moleculekit/occupancy_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:17,955 adding 'moleculekit/opm.py' 2024-06-17T17:37:17,957 adding 'moleculekit/periodictable.py' 2024-06-17T17:37:17,959 adding 'moleculekit/pymolgraphics.py' 2024-06-17T17:37:17,960 adding 'moleculekit/rcsb.py' 2024-06-17T17:37:17,962 adding 'moleculekit/rdkitintegration.py' 2024-06-17T17:37:17,975 adding 'moleculekit/readers.py' 2024-06-17T17:37:18,585 adding 'moleculekit/tmalign.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:18,924 adding 'moleculekit/trr.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:18,937 adding 'moleculekit/util.py' 2024-06-17T17:37:18,938 adding 'moleculekit/version.py' 2024-06-17T17:37:18,940 adding 'moleculekit/viewer.py' 2024-06-17T17:37:18,941 adding 'moleculekit/vmd_wrapper' 2024-06-17T17:37:18,943 adding 'moleculekit/vmdgraphics.py' 2024-06-17T17:37:18,945 adding 'moleculekit/vmdviewer.py' 2024-06-17T17:37:19,202 adding 'moleculekit/wrapping.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:19,216 adding 'moleculekit/writers.py' 2024-06-17T17:37:19,488 adding 'moleculekit/xtc.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:19,497 adding 'moleculekit/atomselect/__init__.py' 2024-06-17T17:37:19,499 adding 'moleculekit/atomselect/analyze.py' 2024-06-17T17:37:19,501 adding 'moleculekit/atomselect/atomselect.py' 2024-06-17T17:37:19,503 adding 'moleculekit/atomselect/languageparser.py' 2024-06-17T17:37:19,609 adding 'moleculekit/atomselect_utils/atomselect_utils.cpp' 2024-06-17T17:37:19,620 adding 'moleculekit/atomselect_utils/atomselect_utils.pyx' 2024-06-17T17:37:19,715 adding 'moleculekit/bondguesser_utils/bondguesser_utils.cpp' 2024-06-17T17:37:19,724 adding 'moleculekit/bondguesser_utils/bondguesser_utils.pyx' 2024-06-17T17:37:19,815 adding 'moleculekit/cython_utils/cython_utils.cpp' 2024-06-17T17:37:19,824 adding 'moleculekit/cython_utils/cython_utils.pyx' 2024-06-17T17:37:19,930 adding 'moleculekit/distance_utils/distance_utils.cpp' 2024-06-17T17:37:19,941 adding 'moleculekit/distance_utils/distance_utils.pyx' 2024-06-17T17:37:19,943 adding 'moleculekit/fileformats/__init__.py' 2024-06-17T17:37:19,948 adding 'moleculekit/fileformats/netcdf.py' 2024-06-17T17:37:19,950 adding 'moleculekit/fileformats/utils.py' 2024-06-17T17:37:20,013 adding 'moleculekit/fileformats/binpos/binpos.c' 2024-06-17T17:37:20,020 adding 'moleculekit/fileformats/binpos/binpos.pyx' 2024-06-17T17:37:20,022 adding 'moleculekit/fileformats/binpos/binposlib.pxd' 2024-06-17T17:37:20,023 adding 'moleculekit/fileformats/binpos/include/binposplugin.h' 2024-06-17T17:37:20,025 adding 'moleculekit/fileformats/binpos/include/largefiles.h' 2024-06-17T17:37:20,030 adding 'moleculekit/fileformats/binpos/include/molfile_plugin.h' 2024-06-17T17:37:20,032 adding 'moleculekit/fileformats/binpos/src/binposplugin.c' 2024-06-17T17:37:20,097 adding 'moleculekit/fileformats/dcd/dcd.c' 2024-06-17T17:37:20,105 adding 'moleculekit/fileformats/dcd/dcd.pyx' 2024-06-17T17:37:20,107 adding 'moleculekit/fileformats/dcd/dcdlib.pxd' 2024-06-17T17:37:20,109 adding 'moleculekit/fileformats/dcd/include/dcdplugin.h' 2024-06-17T17:37:20,110 adding 'moleculekit/fileformats/dcd/include/endianswap.h' 2024-06-17T17:37:20,112 adding 'moleculekit/fileformats/dcd/include/fastio.h' 2024-06-17T17:37:20,113 adding 'moleculekit/fileformats/dcd/include/largefiles.h' 2024-06-17T17:37:20,119 adding 'moleculekit/fileformats/dcd/include/molfile_plugin.h' 2024-06-17T17:37:20,124 adding 'moleculekit/fileformats/dcd/src/dcdplugin.c' 2024-06-17T17:37:20,222 adding 'moleculekit/fileformats/xtc/trr.c' 2024-06-17T17:37:20,233 adding 'moleculekit/fileformats/xtc/trr.pyx' 2024-06-17T17:37:20,235 adding 'moleculekit/fileformats/xtc/trrlib.pxd' 2024-06-17T17:37:20,236 adding 'moleculekit/fileformats/xtc/xdrlib.pxd' 2024-06-17T17:37:20,328 adding 'moleculekit/fileformats/xtc/xtc.cpp' 2024-06-17T17:37:20,337 adding 'moleculekit/fileformats/xtc/xtc.pyx' 2024-06-17T17:37:20,339 adding 'moleculekit/fileformats/xtc/xtclib.pxd' 2024-06-17T17:37:20,342 adding 'moleculekit/fileformats/xtc/include/trr_header.h' 2024-06-17T17:37:20,343 adding 'moleculekit/fileformats/xtc/include/xdr_seek.h' 2024-06-17T17:37:20,346 adding 'moleculekit/fileformats/xtc/include/xdrfile.h' 2024-06-17T17:37:20,348 adding 'moleculekit/fileformats/xtc/include/xdrfile_trr.h' 2024-06-17T17:37:20,350 adding 'moleculekit/fileformats/xtc/include/xdrfile_xtc.h' 2024-06-17T17:37:20,352 adding 'moleculekit/fileformats/xtc/include/xtc.h' 2024-06-17T17:37:20,355 adding 'moleculekit/fileformats/xtc/src/xdr_seek.c' 2024-06-17T17:37:20,363 adding 'moleculekit/fileformats/xtc/src/xdrfile.cpp' 2024-06-17T17:37:20,366 adding 'moleculekit/fileformats/xtc/src/xdrfile_trr.c' 2024-06-17T17:37:20,368 adding 'moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp' 2024-06-17T17:37:20,370 adding 'moleculekit/fileformats/xtc/src/xtc.cpp' 2024-06-17T17:37:20,372 adding 'moleculekit/interactions/__init__.py' 2024-06-17T17:37:20,659 adding 'moleculekit/interactions/cationpi.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:20,930 adding 'moleculekit/interactions/hbonds.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:20,942 adding 'moleculekit/interactions/interactions.py' 2024-06-17T17:37:21,229 adding 'moleculekit/interactions/pipi.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:21,521 adding 'moleculekit/interactions/sigmahole.cpython-39-arm-linux-gnueabihf.so' 2024-06-17T17:37:21,625 adding 'moleculekit/interactions/cationpi/cationpi.cpp' 2024-06-17T17:37:21,634 adding 'moleculekit/interactions/cationpi/cationpi.pyx' 2024-06-17T17:37:21,728 adding 'moleculekit/interactions/hbonds/hbonds.cpp' 2024-06-17T17:37:21,737 adding 'moleculekit/interactions/hbonds/hbonds.pyx' 2024-06-17T17:37:21,831 adding 'moleculekit/interactions/pipi/pipi.cpp' 2024-06-17T17:37:21,841 adding 'moleculekit/interactions/pipi/pipi.pyx' 2024-06-17T17:37:21,935 adding 'moleculekit/interactions/sigmahole/sigmahole.cpp' 2024-06-17T17:37:21,945 adding 'moleculekit/interactions/sigmahole/sigmahole.pyx' 2024-06-17T17:37:22,035 adding 'moleculekit/occupancy_utils/occupancy_utils.cpp' 2024-06-17T17:37:22,043 adding 'moleculekit/occupancy_utils/occupancy_utils.pyx' 2024-06-17T17:37:22,045 adding 'moleculekit/pdbx/__init__.py' 2024-06-17T17:37:22,049 adding 'moleculekit/pdbx/reader/PdbxContainers.py' 2024-06-17T17:37:22,052 adding 'moleculekit/pdbx/reader/PdbxParser.py' 2024-06-17T17:37:22,054 adding 'moleculekit/pdbx/reader/PdbxReader.py' 2024-06-17T17:37:22,055 adding 'moleculekit/pdbx/reader/__init__.py' 2024-06-17T17:37:22,057 adding 'moleculekit/pdbx/tests/PdbxReadWriteTests.py' 2024-06-17T17:37:22,059 adding 'moleculekit/pdbx/tests/PdbxReaderTests.py' 2024-06-17T17:37:22,060 adding 'moleculekit/pdbx/tests/PdbxWriterTests.py' 2024-06-17T17:37:22,061 adding 'moleculekit/pdbx/tests/__init__.py' 2024-06-17T17:37:22,063 adding 'moleculekit/pdbx/writer/PdbxWriter.py' 2024-06-17T17:37:22,065 adding 'moleculekit/pdbx/writer/__init__.py' 2024-06-17T17:37:22,067 adding 'moleculekit/ply/__init__.py' 2024-06-17T17:37:22,071 adding 'moleculekit/ply/lex.py' 2024-06-17T17:37:22,083 adding 'moleculekit/ply/yacc.py' 2024-06-17T17:37:22,085 adding 'moleculekit/projections/__init__.py' 2024-06-17T17:37:22,087 adding 'moleculekit/projections/metriccoordinate.py' 2024-06-17T17:37:22,090 adding 'moleculekit/projections/metricdihedral.py' 2024-06-17T17:37:22,094 adding 'moleculekit/projections/metricdistance.py' 2024-06-17T17:37:22,097 adding 'moleculekit/projections/metricfluctuation.py' 2024-06-17T17:37:22,098 adding 'moleculekit/projections/metricgyration.py' 2024-06-17T17:37:22,102 adding 'moleculekit/projections/metricplumed2.py' 2024-06-17T17:37:22,104 adding 'moleculekit/projections/metricrmsd.py' 2024-06-17T17:37:22,106 adding 'moleculekit/projections/metricsasa.py' 2024-06-17T17:37:22,108 adding 'moleculekit/projections/metricsecondarystructure.py' 2024-06-17T17:37:22,110 adding 'moleculekit/projections/metricshell.py' 2024-06-17T17:37:22,112 adding 'moleculekit/projections/metricsphericalcoordinate.py' 2024-06-17T17:37:22,113 adding 'moleculekit/projections/metrictmscore.py' 2024-06-17T17:37:22,114 adding 'moleculekit/projections/projection.py' 2024-06-17T17:37:22,116 adding 'moleculekit/projections/util.py' 2024-06-17T17:37:22,118 adding 'moleculekit/share/ALA.cif' 2024-06-17T17:37:22,119 adding 'moleculekit/share/backbone.cif' 2024-06-17T17:37:23,437 adding 'moleculekit/share/opm_sequences.json' 2024-06-17T17:37:23,521 adding 'moleculekit/share/atomselect/atomselect.json' 2024-06-17T17:37:23,526 adding 'moleculekit/share/pdb2pqr/residues/.gitkeep' 2024-06-17T17:37:23,527 adding 'moleculekit/share/pdb2pqr/residues/004.dat' 2024-06-17T17:37:23,529 adding 'moleculekit/share/pdb2pqr/residues/004.xml' 2024-06-17T17:37:23,530 adding 'moleculekit/share/pdb2pqr/residues/03Y.dat' 2024-06-17T17:37:23,531 adding 'moleculekit/share/pdb2pqr/residues/03Y.xml' 2024-06-17T17:37:23,532 adding 'moleculekit/share/pdb2pqr/residues/0A1.dat' 2024-06-17T17:37:23,533 adding 'moleculekit/share/pdb2pqr/residues/0A1.xml' 2024-06-17T17:37:23,535 adding 'moleculekit/share/pdb2pqr/residues/0AF.dat' 2024-06-17T17:37:23,536 adding 'moleculekit/share/pdb2pqr/residues/0AF.xml' 2024-06-17T17:37:23,537 adding 'moleculekit/share/pdb2pqr/residues/0BN.dat' 2024-06-17T17:37:23,538 adding 'moleculekit/share/pdb2pqr/residues/0BN.xml' 2024-06-17T17:37:23,540 adding 'moleculekit/share/pdb2pqr/residues/1MH.dat' 2024-06-17T17:37:23,541 adding 'moleculekit/share/pdb2pqr/residues/1MH.xml' 2024-06-17T17:37:23,542 adding 'moleculekit/share/pdb2pqr/residues/2AS.dat' 2024-06-17T17:37:23,543 adding 'moleculekit/share/pdb2pqr/residues/2AS.xml' 2024-06-17T17:37:23,545 adding 'moleculekit/share/pdb2pqr/residues/2GX.dat' 2024-06-17T17:37:23,546 adding 'moleculekit/share/pdb2pqr/residues/2GX.xml' 2024-06-17T17:37:23,547 adding 'moleculekit/share/pdb2pqr/residues/2ML.dat' 2024-06-17T17:37:23,548 adding 'moleculekit/share/pdb2pqr/residues/2ML.xml' 2024-06-17T17:37:23,550 adding 'moleculekit/share/pdb2pqr/residues/2MR.dat' 2024-06-17T17:37:23,551 adding 'moleculekit/share/pdb2pqr/residues/2MR.xml' 2024-06-17T17:37:23,552 adding 'moleculekit/share/pdb2pqr/residues/4IN.dat' 2024-06-17T17:37:23,553 adding 'moleculekit/share/pdb2pqr/residues/4IN.xml' 2024-06-17T17:37:23,555 adding 'moleculekit/share/pdb2pqr/residues/4PH.dat' 2024-06-17T17:37:23,556 adding 'moleculekit/share/pdb2pqr/residues/4PH.xml' 2024-06-17T17:37:23,557 adding 'moleculekit/share/pdb2pqr/residues/4PQ.dat' 2024-06-17T17:37:23,559 adding 'moleculekit/share/pdb2pqr/residues/4PQ.xml' 2024-06-17T17:37:23,560 adding 'moleculekit/share/pdb2pqr/residues/5JP.dat' 2024-06-17T17:37:23,561 adding 'moleculekit/share/pdb2pqr/residues/5JP.xml' 2024-06-17T17:37:23,562 adding 'moleculekit/share/pdb2pqr/residues/AA4.dat' 2024-06-17T17:37:23,563 adding 'moleculekit/share/pdb2pqr/residues/AA4.xml' 2024-06-17T17:37:23,565 adding 'moleculekit/share/pdb2pqr/residues/ABA.dat' 2024-06-17T17:37:23,566 adding 'moleculekit/share/pdb2pqr/residues/ABA.xml' 2024-06-17T17:37:23,567 adding 'moleculekit/share/pdb2pqr/residues/AHP.dat' 2024-06-17T17:37:23,568 adding 'moleculekit/share/pdb2pqr/residues/AHP.xml' 2024-06-17T17:37:23,570 adding 'moleculekit/share/pdb2pqr/residues/ALC.dat' 2024-06-17T17:37:23,571 adding 'moleculekit/share/pdb2pqr/residues/ALC.xml' 2024-06-17T17:37:23,572 adding 'moleculekit/share/pdb2pqr/residues/ALN.dat' 2024-06-17T17:37:23,573 adding 'moleculekit/share/pdb2pqr/residues/ALN.xml' 2024-06-17T17:37:23,575 adding 'moleculekit/share/pdb2pqr/residues/ALY.dat' 2024-06-17T17:37:23,576 adding 'moleculekit/share/pdb2pqr/residues/ALY.xml' 2024-06-17T17:37:23,577 adding 'moleculekit/share/pdb2pqr/residues/APD.dat' 2024-06-17T17:37:23,578 adding 'moleculekit/share/pdb2pqr/residues/APD.xml' 2024-06-17T17:37:23,580 adding 'moleculekit/share/pdb2pqr/residues/BB8.dat' 2024-06-17T17:37:23,581 adding 'moleculekit/share/pdb2pqr/residues/BB8.xml' 2024-06-17T17:37:23,582 adding 'moleculekit/share/pdb2pqr/residues/BCS.dat' 2024-06-17T17:37:23,583 adding 'moleculekit/share/pdb2pqr/residues/BCS.xml' 2024-06-17T17:37:23,585 adding 'moleculekit/share/pdb2pqr/residues/BTK.dat' 2024-06-17T17:37:23,586 adding 'moleculekit/share/pdb2pqr/residues/BTK.xml' 2024-06-17T17:37:23,587 adding 'moleculekit/share/pdb2pqr/residues/CCS.dat' 2024-06-17T17:37:23,589 adding 'moleculekit/share/pdb2pqr/residues/CCS.xml' 2024-06-17T17:37:23,590 adding 'moleculekit/share/pdb2pqr/residues/CGU.dat' 2024-06-17T17:37:23,591 adding 'moleculekit/share/pdb2pqr/residues/CGU.xml' 2024-06-17T17:37:23,592 adding 'moleculekit/share/pdb2pqr/residues/CSA.dat' 2024-06-17T17:37:23,593 adding 'moleculekit/share/pdb2pqr/residues/CSA.xml' 2024-06-17T17:37:23,595 adding 'moleculekit/share/pdb2pqr/residues/CSO.dat' 2024-06-17T17:37:23,596 adding 'moleculekit/share/pdb2pqr/residues/CSO.xml' 2024-06-17T17:37:23,597 adding 'moleculekit/share/pdb2pqr/residues/CSP.dat' 2024-06-17T17:37:23,598 adding 'moleculekit/share/pdb2pqr/residues/CSP.xml' 2024-06-17T17:37:23,599 adding 'moleculekit/share/pdb2pqr/residues/CSS.dat' 2024-06-17T17:37:23,601 adding 'moleculekit/share/pdb2pqr/residues/CSS.xml' 2024-06-17T17:37:23,602 adding 'moleculekit/share/pdb2pqr/residues/D4P.dat' 2024-06-17T17:37:23,603 adding 'moleculekit/share/pdb2pqr/residues/D4P.xml' 2024-06-17T17:37:23,604 adding 'moleculekit/share/pdb2pqr/residues/DA2.dat' 2024-06-17T17:37:23,606 adding 'moleculekit/share/pdb2pqr/residues/DA2.xml' 2024-06-17T17:37:23,607 adding 'moleculekit/share/pdb2pqr/residues/DAB.dat' 2024-06-17T17:37:23,608 adding 'moleculekit/share/pdb2pqr/residues/DAB.xml' 2024-06-17T17:37:23,609 adding 'moleculekit/share/pdb2pqr/residues/DAH.dat' 2024-06-17T17:37:23,611 adding 'moleculekit/share/pdb2pqr/residues/DAH.xml' 2024-06-17T17:37:23,612 adding 'moleculekit/share/pdb2pqr/residues/DPP.dat' 2024-06-17T17:37:23,613 adding 'moleculekit/share/pdb2pqr/residues/DPP.xml' 2024-06-17T17:37:23,615 adding 'moleculekit/share/pdb2pqr/residues/ESC.dat' 2024-06-17T17:37:23,616 adding 'moleculekit/share/pdb2pqr/residues/ESC.xml' 2024-06-17T17:37:23,618 adding 'moleculekit/share/pdb2pqr/residues/FGL.dat' 2024-06-17T17:37:23,619 adding 'moleculekit/share/pdb2pqr/residues/FGL.xml' 2024-06-17T17:37:23,620 adding 'moleculekit/share/pdb2pqr/residues/GHG.dat' 2024-06-17T17:37:23,622 adding 'moleculekit/share/pdb2pqr/residues/GHG.xml' 2024-06-17T17:37:23,623 adding 'moleculekit/share/pdb2pqr/residues/GME.dat' 2024-06-17T17:37:23,624 adding 'moleculekit/share/pdb2pqr/residues/GME.xml' 2024-06-17T17:37:23,625 adding 'moleculekit/share/pdb2pqr/residues/GNC.dat' 2024-06-17T17:37:23,627 adding 'moleculekit/share/pdb2pqr/residues/GNC.xml' 2024-06-17T17:37:23,628 adding 'moleculekit/share/pdb2pqr/residues/HHK.dat' 2024-06-17T17:37:23,629 adding 'moleculekit/share/pdb2pqr/residues/HHK.xml' 2024-06-17T17:37:23,631 adding 'moleculekit/share/pdb2pqr/residues/HLU.dat' 2024-06-17T17:37:23,632 adding 'moleculekit/share/pdb2pqr/residues/HLU.xml' 2024-06-17T17:37:23,633 adding 'moleculekit/share/pdb2pqr/residues/HLX.dat' 2024-06-17T17:37:23,634 adding 'moleculekit/share/pdb2pqr/residues/HLX.xml' 2024-06-17T17:37:23,636 adding 'moleculekit/share/pdb2pqr/residues/HOX.dat' 2024-06-17T17:37:23,637 adding 'moleculekit/share/pdb2pqr/residues/HOX.xml' 2024-06-17T17:37:23,638 adding 'moleculekit/share/pdb2pqr/residues/HPE.dat' 2024-06-17T17:37:23,639 adding 'moleculekit/share/pdb2pqr/residues/HPE.xml' 2024-06-17T17:37:23,641 adding 'moleculekit/share/pdb2pqr/residues/HQA.dat' 2024-06-17T17:37:23,642 adding 'moleculekit/share/pdb2pqr/residues/HQA.xml' 2024-06-17T17:37:23,643 adding 'moleculekit/share/pdb2pqr/residues/HTR.dat' 2024-06-17T17:37:23,644 adding 'moleculekit/share/pdb2pqr/residues/HTR.xml' 2024-06-17T17:37:23,646 adding 'moleculekit/share/pdb2pqr/residues/HYP.dat' 2024-06-17T17:37:23,647 adding 'moleculekit/share/pdb2pqr/residues/HYP.xml' 2024-06-17T17:37:23,648 adding 'moleculekit/share/pdb2pqr/residues/I2M.dat' 2024-06-17T17:37:23,649 adding 'moleculekit/share/pdb2pqr/residues/I2M.xml' 2024-06-17T17:37:23,651 adding 'moleculekit/share/pdb2pqr/residues/IGL.dat' 2024-06-17T17:37:23,652 adding 'moleculekit/share/pdb2pqr/residues/IGL.xml' 2024-06-17T17:37:23,653 adding 'moleculekit/share/pdb2pqr/residues/IIL.dat' 2024-06-17T17:37:23,654 adding 'moleculekit/share/pdb2pqr/residues/IIL.xml' 2024-06-17T17:37:23,656 adding 'moleculekit/share/pdb2pqr/residues/IML.dat' 2024-06-17T17:37:23,657 adding 'moleculekit/share/pdb2pqr/residues/IML.xml' 2024-06-17T17:37:23,658 adding 'moleculekit/share/pdb2pqr/residues/KYN.dat' 2024-06-17T17:37:23,659 adding 'moleculekit/share/pdb2pqr/residues/KYN.xml' 2024-06-17T17:37:23,661 adding 'moleculekit/share/pdb2pqr/residues/LME.dat' 2024-06-17T17:37:23,662 adding 'moleculekit/share/pdb2pqr/residues/LME.xml' 2024-06-17T17:37:23,663 adding 'moleculekit/share/pdb2pqr/residues/LMQ.dat' 2024-06-17T17:37:23,664 adding 'moleculekit/share/pdb2pqr/residues/LMQ.xml' 2024-06-17T17:37:23,665 adding 'moleculekit/share/pdb2pqr/residues/LYZ.dat' 2024-06-17T17:37:23,667 adding 'moleculekit/share/pdb2pqr/residues/LYZ.xml' 2024-06-17T17:37:23,668 adding 'moleculekit/share/pdb2pqr/residues/M3L.dat' 2024-06-17T17:37:23,669 adding 'moleculekit/share/pdb2pqr/residues/M3L.xml' 2024-06-17T17:37:23,671 adding 'moleculekit/share/pdb2pqr/residues/ME0.dat' 2024-06-17T17:37:23,672 adding 'moleculekit/share/pdb2pqr/residues/ME0.xml' 2024-06-17T17:37:23,673 adding 'moleculekit/share/pdb2pqr/residues/MEA.dat' 2024-06-17T17:37:23,674 adding 'moleculekit/share/pdb2pqr/residues/MEA.xml' 2024-06-17T17:37:23,676 adding 'moleculekit/share/pdb2pqr/residues/MEN.dat' 2024-06-17T17:37:23,677 adding 'moleculekit/share/pdb2pqr/residues/MEN.xml' 2024-06-17T17:37:23,678 adding 'moleculekit/share/pdb2pqr/residues/MEQ.dat' 2024-06-17T17:37:23,680 adding 'moleculekit/share/pdb2pqr/residues/MEQ.xml' 2024-06-17T17:37:23,681 adding 'moleculekit/share/pdb2pqr/residues/MLE.dat' 2024-06-17T17:37:23,682 adding 'moleculekit/share/pdb2pqr/residues/MLE.xml' 2024-06-17T17:37:23,683 adding 'moleculekit/share/pdb2pqr/residues/MLY.dat' 2024-06-17T17:37:23,685 adding 'moleculekit/share/pdb2pqr/residues/MLY.xml' 2024-06-17T17:37:23,686 adding 'moleculekit/share/pdb2pqr/residues/MLZ.dat' 2024-06-17T17:37:23,687 adding 'moleculekit/share/pdb2pqr/residues/MLZ.xml' 2024-06-17T17:37:23,688 adding 'moleculekit/share/pdb2pqr/residues/MME.dat' 2024-06-17T17:37:23,690 adding 'moleculekit/share/pdb2pqr/residues/MME.xml' 2024-06-17T17:37:23,691 adding 'moleculekit/share/pdb2pqr/residues/MMO.dat' 2024-06-17T17:37:23,692 adding 'moleculekit/share/pdb2pqr/residues/MMO.xml' 2024-06-17T17:37:23,693 adding 'moleculekit/share/pdb2pqr/residues/MVA.dat' 2024-06-17T17:37:23,695 adding 'moleculekit/share/pdb2pqr/residues/MVA.xml' 2024-06-17T17:37:23,696 adding 'moleculekit/share/pdb2pqr/residues/NAL.dat' 2024-06-17T17:37:23,697 adding 'moleculekit/share/pdb2pqr/residues/NAL.xml' 2024-06-17T17:37:23,698 adding 'moleculekit/share/pdb2pqr/residues/NCY.dat' 2024-06-17T17:37:23,700 adding 'moleculekit/share/pdb2pqr/residues/NCY.xml' 2024-06-17T17:37:23,701 adding 'moleculekit/share/pdb2pqr/residues/NLE.dat' 2024-06-17T17:37:23,702 adding 'moleculekit/share/pdb2pqr/residues/NLE.xml' 2024-06-17T17:37:23,703 adding 'moleculekit/share/pdb2pqr/residues/NVA.dat' 2024-06-17T17:37:23,705 adding 'moleculekit/share/pdb2pqr/residues/NVA.xml' 2024-06-17T17:37:23,706 adding 'moleculekit/share/pdb2pqr/residues/NZC.dat' 2024-06-17T17:37:23,707 adding 'moleculekit/share/pdb2pqr/residues/NZC.xml' 2024-06-17T17:37:23,709 adding 'moleculekit/share/pdb2pqr/residues/OCY.dat' 2024-06-17T17:37:23,710 adding 'moleculekit/share/pdb2pqr/residues/OCY.xml' 2024-06-17T17:37:23,711 adding 'moleculekit/share/pdb2pqr/residues/OMX.dat' 2024-06-17T17:37:23,713 adding 'moleculekit/share/pdb2pqr/residues/OMX.xml' 2024-06-17T17:37:23,714 adding 'moleculekit/share/pdb2pqr/residues/ONL.dat' 2024-06-17T17:37:23,715 adding 'moleculekit/share/pdb2pqr/residues/ONL.xml' 2024-06-17T17:37:23,716 adding 'moleculekit/share/pdb2pqr/residues/ORM.dat' 2024-06-17T17:37:23,717 adding 'moleculekit/share/pdb2pqr/residues/ORM.xml' 2024-06-17T17:37:23,719 adding 'moleculekit/share/pdb2pqr/residues/P1L.dat' 2024-06-17T17:37:23,720 adding 'moleculekit/share/pdb2pqr/residues/P1L.xml' 2024-06-17T17:37:23,721 adding 'moleculekit/share/pdb2pqr/residues/PCA.dat' 2024-06-17T17:37:23,723 adding 'moleculekit/share/pdb2pqr/residues/PCA.xml' 2024-06-17T17:37:23,724 adding 'moleculekit/share/pdb2pqr/residues/PRK.dat' 2024-06-17T17:37:23,725 adding 'moleculekit/share/pdb2pqr/residues/PRK.xml' 2024-06-17T17:37:23,726 adding 'moleculekit/share/pdb2pqr/residues/PTR.dat' 2024-06-17T17:37:23,728 adding 'moleculekit/share/pdb2pqr/residues/PTR.xml' 2024-06-17T17:37:23,729 adding 'moleculekit/share/pdb2pqr/residues/SEP.dat' 2024-06-17T17:37:23,730 adding 'moleculekit/share/pdb2pqr/residues/SEP.xml' 2024-06-17T17:37:23,731 adding 'moleculekit/share/pdb2pqr/residues/TPO.dat' 2024-06-17T17:37:23,733 adding 'moleculekit/share/pdb2pqr/residues/TPO.xml' 2024-06-17T17:37:23,734 adding 'moleculekit/share/pdb2pqr/residues/TRO.dat' 2024-06-17T17:37:23,735 adding 'moleculekit/share/pdb2pqr/residues/TRO.xml' 2024-06-17T17:37:23,737 adding 'moleculekit/share/pdb2pqr/residues/TY2.dat' 2024-06-17T17:37:23,738 adding 'moleculekit/share/pdb2pqr/residues/TY2.xml' 2024-06-17T17:37:23,739 adding 'moleculekit/share/pdb2pqr/residues/TYQ.dat' 2024-06-17T17:37:23,740 adding 'moleculekit/share/pdb2pqr/residues/TYQ.xml' 2024-06-17T17:37:23,742 adding 'moleculekit/share/pdb2pqr/residues/YCM.dat' 2024-06-17T17:37:23,743 adding 'moleculekit/share/pdb2pqr/residues/YCM.xml' 2024-06-17T17:37:23,744 adding 'moleculekit/share/pdb2pqr/residues/YNM.dat' 2024-06-17T17:37:23,745 adding 'moleculekit/share/pdb2pqr/residues/YNM.xml' 2024-06-17T17:37:23,747 adding 'moleculekit/smallmol/__init__.py' 2024-06-17T17:37:23,753 adding 'moleculekit/smallmol/smallmol.py' 2024-06-17T17:37:23,755 adding 'moleculekit/smallmol/smallmolcdp.py' 2024-06-17T17:37:23,757 adding 'moleculekit/smallmol/smallmollib.py' 2024-06-17T17:37:23,759 adding 'moleculekit/smallmol/test_smallmol.py' 2024-06-17T17:37:23,761 adding 'moleculekit/smallmol/test_smallmollib.py' 2024-06-17T17:37:23,763 adding 'moleculekit/smallmol/util.py' 2024-06-17T17:37:23,765 adding 'moleculekit/smallmol/tools/__init__.py' 2024-06-17T17:37:23,766 adding 'moleculekit/smallmol/tools/clustering.py' 2024-06-17T17:37:23,768 adding 'moleculekit/smallmol/tools/restrainedembed.py' 2024-06-17T17:37:23,770 adding 'moleculekit/smallmol/tools/test_tools.py' 2024-06-17T17:37:23,862 adding 'moleculekit/tmalign/tmalign_util.cpp' 2024-06-17T17:37:23,871 adding 'moleculekit/tmalign/tmalign_util.pyx' 2024-06-17T17:37:23,872 adding 'moleculekit/tmalign/tmalignlib.pxd' 2024-06-17T17:37:23,874 adding 'moleculekit/tmalign/include/TMAlign.h' 2024-06-17T17:37:23,891 adding 'moleculekit/tmalign/src/TMAlign.cpp' 2024-06-17T17:37:23,894 adding 'moleculekit/tools/__init__.py' 2024-06-17T17:37:23,897 adding 'moleculekit/tools/atomtyper.py' 2024-06-17T17:37:23,899 adding 'moleculekit/tools/autosegment.py' 2024-06-17T17:37:23,901 adding 'moleculekit/tools/crystalpacking.py' 2024-06-17T17:37:23,905 adding 'moleculekit/tools/detect.py' 2024-06-17T17:37:23,907 adding 'moleculekit/tools/docking.py' 2024-06-17T17:37:23,909 adding 'moleculekit/tools/graphalignment.py' 2024-06-17T17:37:23,910 adding 'moleculekit/tools/hhblitsprofile.py' 2024-06-17T17:37:23,912 adding 'moleculekit/tools/modelling.py' 2024-06-17T17:37:23,913 adding 'moleculekit/tools/moleculechecks.py' 2024-06-17T17:37:23,920 adding 'moleculekit/tools/preparation.py' 2024-06-17T17:37:23,922 adding 'moleculekit/tools/preparation_customres.py' 2024-06-17T17:37:23,924 adding 'moleculekit/tools/sequencestructuralalignment.py' 2024-06-17T17:37:23,927 adding 'moleculekit/tools/voxeldescriptors.py' 2024-06-17T17:37:23,929 adding 'moleculekit/tools/obabel_tools/__init__.py' 2024-06-17T17:37:23,930 adding 'moleculekit/tools/obabel_tools/obabel_cli.py' 2024-06-17T17:37:24,025 adding 'moleculekit/wrapping/wrapping.cpp' 2024-06-17T17:37:24,034 adding 'moleculekit/wrapping/wrapping.pyx' 2024-06-17T17:37:24,037 adding 'moleculekit-1.8.34.dist-info/LICENSE' 2024-06-17T17:37:24,038 adding 'moleculekit-1.8.34.dist-info/METADATA' 2024-06-17T17:37:24,039 adding 'moleculekit-1.8.34.dist-info/WHEEL' 2024-06-17T17:37:24,040 adding 'moleculekit-1.8.34.dist-info/top_level.txt' 2024-06-17T17:37:24,045 adding 'moleculekit-1.8.34.dist-info/RECORD' 2024-06-17T17:37:24,278 removing build/bdist.linux-armv7l/wheel 2024-06-17T17:37:24,562 Building wheel for moleculekit (pyproject.toml): finished with status 'done' 2024-06-17T17:37:24,888 Created wheel for moleculekit: filename=moleculekit-1.8.34-cp39-cp39-linux_armv7l.whl size=14926654 sha256=3e3ca8c16ef993abbd889b734326ba2303227bdd4797f95337551e5a57b7c4ab 2024-06-17T17:37:24,889 Stored in directory: /tmp/pip-ephem-wheel-cache-0bhbj2eh/wheels/19/29/d6/132e6f7186db91afdf7a2525f1a195303ca2484630b9aa1e01 2024-06-17T17:37:24,916 Successfully built moleculekit 2024-06-17T17:37:25,373 Removed build tracker: '/tmp/pip-build-tracker-0ss4s881'