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https://www.piwheels.org/simple/moleculekit/moleculekit-0.1.4-py3-none-any.whl#sha256=5784491ff294e145a00311f8239aaa0b92c12605db0508ee3e10469b80d4cadd (from https://www.piwheels.org/simple/moleculekit/) 2024-06-25T19:25:24,427 Skipping link: not a file: https://www.piwheels.org/simple/moleculekit/ 2024-06-25T19:25:24,427 Skipping link: not a file: https://pypi.org/simple/moleculekit/ 2024-06-25T19:25:24,469 Given no hashes to check 1 links for project 'moleculekit': discarding no candidates 2024-06-25T19:25:24,486 Collecting moleculekit==1.8.35 2024-06-25T19:25:24,488 Created temporary directory: /tmp/pip-unpack-gt3y5d3s 2024-06-25T19:25:24,532 Downloading moleculekit-1.8.35.tar.gz (6.8 MB) 2024-06-25T19:25:26,706 Added moleculekit==1.8.35 from https://files.pythonhosted.org/packages/26/6b/1104888679e9faf8b0e4e9b15586ea7532e171fe127c06e067c9ad563238/moleculekit-1.8.35.tar.gz to build tracker '/tmp/pip-build-tracker-i2at1th5' 2024-06-25T19:25:26,714 Created temporary directory: /tmp/pip-build-env-wy4x1a7g 2024-06-25T19:25:26,724 Installing build dependencies: started 2024-06-25T19:25:26,725 Running command pip subprocess to install build dependencies 2024-06-25T19:25:28,109 Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2024-06-25T19:25:28,624 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-06-25T19:25:30,100 Collecting setuptools 2024-06-25T19:25:30,119 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.1.1-py3-none-any.whl (883 kB) 2024-06-25T19:25:31,192 Collecting numpy>=1.18.5 2024-06-25T19:25:31,208 Using cached https://www.piwheels.org/simple/numpy/numpy-2.0.0-cp39-cp39-linux_armv7l.whl (5.8 MB) 2024-06-25T19:25:32,788 Collecting Cython>=0.29.21 2024-06-25T19:25:32,805 Using cached https://www.piwheels.org/simple/cython/Cython-3.0.10-cp39-cp39-linux_armv7l.whl (10.7 MB) 2024-06-25T19:25:33,178 Collecting toml 2024-06-25T19:25:33,197 Downloading https://www.piwheels.org/simple/toml/toml-0.10.2-py2.py3-none-any.whl (16 kB) 2024-06-25T19:25:33,381 Collecting versioneer==0.28 (from versioneer[toml]==0.28) 2024-06-25T19:25:33,395 Downloading https://www.piwheels.org/simple/versioneer/versioneer-0.28-py3-none-any.whl (45 kB) 2024-06-25T19:25:33,414 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.3/45.3 kB 3.7 MB/s eta 0:00:00 2024-06-25T19:25:33,545 Collecting tomli (from versioneer[toml]==0.28) 2024-06-25T19:25:33,571 Using cached https://www.piwheels.org/simple/tomli/tomli-2.0.1-py3-none-any.whl (12 kB) 2024-06-25T19:25:35,400 Installing collected packages: versioneer, tomli, toml, setuptools, numpy, Cython 2024-06-25T19:25:35,435 Creating /tmp/pip-build-env-wy4x1a7g/overlay/bin 2024-06-25T19:25:35,437 changing mode of /tmp/pip-build-env-wy4x1a7g/overlay/bin/versioneer to 755 2024-06-25T19:25:45,666 changing mode of /tmp/pip-build-env-wy4x1a7g/overlay/bin/f2py to 755 2024-06-25T19:25:45,668 changing mode of /tmp/pip-build-env-wy4x1a7g/overlay/bin/numpy-config to 755 2024-06-25T19:25:49,205 changing mode of /tmp/pip-build-env-wy4x1a7g/overlay/bin/cygdb to 755 2024-06-25T19:25:49,207 changing mode of /tmp/pip-build-env-wy4x1a7g/overlay/bin/cython to 755 2024-06-25T19:25:49,210 changing mode of /tmp/pip-build-env-wy4x1a7g/overlay/bin/cythonize to 755 2024-06-25T19:25:49,236 Successfully installed Cython-3.0.10 numpy-2.0.0 setuptools-70.1.1 toml-0.10.2 tomli-2.0.1 versioneer-0.28 2024-06-25T19:25:49,413 [notice] A new release of pip is available: 24.0 -> 24.1 2024-06-25T19:25:49,414 [notice] To update, run: python3 -m pip install --upgrade pip 2024-06-25T19:25:49,880 Installing build dependencies: finished with status 'done' 2024-06-25T19:25:49,885 Getting requirements to build wheel: started 2024-06-25T19:25:49,886 Running command Getting requirements to build wheel 2024-06-25T19:26:28,648 warning: moleculekit/wrapping/wrapping.pyx:47:4: Unreachable code 2024-06-25T19:26:38,057 Compiling moleculekit/interactions/hbonds/hbonds.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,057 Compiling moleculekit/interactions/pipi/pipi.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,057 Compiling moleculekit/interactions/cationpi/cationpi.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,057 Compiling moleculekit/interactions/sigmahole/sigmahole.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,057 Compiling moleculekit/wrapping/wrapping.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,058 Compiling moleculekit/bondguesser_utils/bondguesser_utils.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,058 Compiling moleculekit/atomselect_utils/atomselect_utils.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,058 Compiling moleculekit/distance_utils/distance_utils.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,058 Compiling moleculekit/occupancy_utils/occupancy_utils.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,058 Compiling moleculekit/cython_utils/cython_utils.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,058 Compiling moleculekit/fileformats/xtc/xtc.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2024-06-25T19:26:38,059 Compiling moleculekit/fileformats/xtc/trr.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2024-06-25T19:26:38,059 Compiling moleculekit/fileformats/dcd/dcd.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2024-06-25T19:26:38,059 Compiling moleculekit/fileformats/binpos/binpos.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2024-06-25T19:26:38,059 Compiling moleculekit/tmalign/tmalign_util.pyx because it depends on /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2024-06-25T19:26:38,059 [ 1/15] Cythonizing moleculekit/atomselect_utils/atomselect_utils.pyx 2024-06-25T19:26:38,059 [ 2/15] Cythonizing moleculekit/bondguesser_utils/bondguesser_utils.pyx 2024-06-25T19:26:38,060 [ 3/15] Cythonizing moleculekit/cython_utils/cython_utils.pyx 2024-06-25T19:26:38,060 [ 4/15] Cythonizing moleculekit/distance_utils/distance_utils.pyx 2024-06-25T19:26:38,060 [ 5/15] Cythonizing moleculekit/fileformats/dcd/dcd.pyx 2024-06-25T19:26:38,060 [ 6/15] Cythonizing moleculekit/interactions/cationpi/cationpi.pyx 2024-06-25T19:26:38,060 [ 7/15] Cythonizing moleculekit/interactions/hbonds/hbonds.pyx 2024-06-25T19:26:38,060 [ 8/15] Cythonizing moleculekit/interactions/pipi/pipi.pyx 2024-06-25T19:26:38,061 [ 9/15] Cythonizing moleculekit/interactions/sigmahole/sigmahole.pyx 2024-06-25T19:26:38,061 [10/15] Cythonizing moleculekit/occupancy_utils/occupancy_utils.pyx 2024-06-25T19:26:38,061 [11/15] Cythonizing moleculekit/tmalign/tmalign_util.pyx 2024-06-25T19:26:38,061 [12/15] Cythonizing moleculekit/wrapping/wrapping.pyx 2024-06-25T19:26:38,061 [13/15] Cythonizing moleculekit/fileformats/binpos/binpos.pyx 2024-06-25T19:26:38,061 [14/15] Cythonizing moleculekit/fileformats/xtc/trr.pyx 2024-06-25T19:26:38,061 [15/15] Cythonizing moleculekit/fileformats/xtc/xtc.pyx 2024-06-25T19:26:38,373 running egg_info 2024-06-25T19:26:38,380 writing moleculekit.egg-info/PKG-INFO 2024-06-25T19:26:38,383 writing dependency_links to moleculekit.egg-info/dependency_links.txt 2024-06-25T19:26:38,385 writing requirements to moleculekit.egg-info/requires.txt 2024-06-25T19:26:38,387 writing top-level names to moleculekit.egg-info/top_level.txt 2024-06-25T19:26:38,418 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,418 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,418 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,418 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,418 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,419 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,419 dependency 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the manifest: the path must be relative 2024-06-25T19:26:38,419 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,419 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,420 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,420 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,420 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,420 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,420 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,420 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,420 dependency /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in 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/tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,421 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,421 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,421 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,422 dependency /tmp/pip-build-env-wy4x1a7g/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-wy4x1a7g/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 2024-06-25T19:26:38,422 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,422 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,423 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,423 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,423 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,423 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,423 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,423 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,423 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,424 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,424 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,424 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,424 dependency /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in 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/tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,428 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,428 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,428 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,428 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,429 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,429 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,429 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,430 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,430 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,431 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,431 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,431 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,431 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,431 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:38,442 reading manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-06-25T19:26:38,475 reading manifest template 'MANIFEST.in' 2024-06-25T19:26:38,959 no previously-included directories found matching 'moleculekit/test-data' 2024-06-25T19:26:38,961 no previously-included directories found matching 'moleculekit/tests' 2024-06-25T19:26:38,963 no previously-included directories found matching 'package' 2024-06-25T19:26:38,963 adding license file 'LICENSE' 2024-06-25T19:26:38,991 writing manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-06-25T19:26:40,576 Getting requirements to build wheel: finished with status 'done' 2024-06-25T19:26:40,580 Created temporary directory: /tmp/pip-modern-metadata-lmkl_jow 2024-06-25T19:26:40,583 Preparing metadata (pyproject.toml): started 2024-06-25T19:26:40,584 Running command Preparing metadata (pyproject.toml) 2024-06-25T19:26:42,946 running dist_info 2024-06-25T19:26:42,947 creating /tmp/pip-modern-metadata-lmkl_jow/moleculekit.egg-info 2024-06-25T19:26:42,953 writing /tmp/pip-modern-metadata-lmkl_jow/moleculekit.egg-info/PKG-INFO 2024-06-25T19:26:42,957 writing dependency_links to /tmp/pip-modern-metadata-lmkl_jow/moleculekit.egg-info/dependency_links.txt 2024-06-25T19:26:42,959 writing requirements to /tmp/pip-modern-metadata-lmkl_jow/moleculekit.egg-info/requires.txt 2024-06-25T19:26:42,960 writing top-level names to /tmp/pip-modern-metadata-lmkl_jow/moleculekit.egg-info/top_level.txt 2024-06-25T19:26:42,961 writing manifest file '/tmp/pip-modern-metadata-lmkl_jow/moleculekit.egg-info/SOURCES.txt' 2024-06-25T19:26:42,986 dependency /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h won't be 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the manifest: the path must be relative 2024-06-25T19:26:42,998 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:42,998 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:43,004 reading manifest file '/tmp/pip-modern-metadata-lmkl_jow/moleculekit.egg-info/SOURCES.txt' 2024-06-25T19:26:43,007 reading manifest template 'MANIFEST.in' 2024-06-25T19:26:43,255 no previously-included directories found matching 'moleculekit/test-data' 2024-06-25T19:26:43,255 no previously-included directories found matching 'moleculekit/tests' 2024-06-25T19:26:43,256 no previously-included directories found matching 'package' 2024-06-25T19:26:43,256 adding license file 'LICENSE' 2024-06-25T19:26:43,270 writing manifest file '/tmp/pip-modern-metadata-lmkl_jow/moleculekit.egg-info/SOURCES.txt' 2024-06-25T19:26:43,279 creating '/tmp/pip-modern-metadata-lmkl_jow/moleculekit-1.8.35.dist-info' 2024-06-25T19:26:43,460 Preparing metadata (pyproject.toml): finished with status 'done' 2024-06-25T19:26:43,466 Source in /tmp/pip-wheel-vbudn77k/moleculekit_53245f833ce743f0a34eb2f0da096ced has version 1.8.35, which satisfies requirement moleculekit==1.8.35 from https://files.pythonhosted.org/packages/26/6b/1104888679e9faf8b0e4e9b15586ea7532e171fe127c06e067c9ad563238/moleculekit-1.8.35.tar.gz 2024-06-25T19:26:43,467 Removed moleculekit==1.8.35 from https://files.pythonhosted.org/packages/26/6b/1104888679e9faf8b0e4e9b15586ea7532e171fe127c06e067c9ad563238/moleculekit-1.8.35.tar.gz from build tracker '/tmp/pip-build-tracker-i2at1th5' 2024-06-25T19:26:43,473 Created temporary directory: /tmp/pip-unpack-ii1vt9ap 2024-06-25T19:26:43,474 Created temporary directory: /tmp/pip-unpack-to49cx6x 2024-06-25T19:26:43,482 Building wheels for collected packages: moleculekit 2024-06-25T19:26:43,486 Created temporary directory: /tmp/pip-wheel-er1hivg0 2024-06-25T19:26:43,487 Destination directory: /tmp/pip-wheel-er1hivg0 2024-06-25T19:26:43,489 Building wheel for moleculekit (pyproject.toml): started 2024-06-25T19:26:43,490 Running command Building wheel for moleculekit (pyproject.toml) 2024-06-25T19:26:45,749 running bdist_wheel 2024-06-25T19:26:45,764 running build 2024-06-25T19:26:45,765 running build_py 2024-06-25T19:26:45,772 creating build 2024-06-25T19:26:45,773 creating build/lib.linux-armv7l-cpython-39 2024-06-25T19:26:45,773 creating build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,774 copying moleculekit/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,776 copying moleculekit/vmdviewer.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,778 copying moleculekit/rcsb.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,780 copying moleculekit/rdkitintegration.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,782 copying moleculekit/distance.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,783 copying moleculekit/align.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,785 copying moleculekit/viewer.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,787 copying moleculekit/home.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,793 copying moleculekit/_version.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,795 copying moleculekit/pymolgraphics.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,796 copying moleculekit/opm.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,799 copying moleculekit/config.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,800 copying moleculekit/version.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,802 copying moleculekit/bondguesser.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,804 copying moleculekit/readers.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,808 copying moleculekit/writers.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,810 copying moleculekit/molecule.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,815 copying moleculekit/util.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,818 copying moleculekit/vmdgraphics.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,820 copying moleculekit/periodictable.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,822 copying moleculekit/dihedral.py -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:45,825 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-25T19:26:45,826 copying moleculekit/fileformats/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-25T19:26:45,827 copying moleculekit/fileformats/netcdf.py -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-25T19:26:45,830 copying moleculekit/fileformats/utils.py -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-25T19:26:45,833 creating build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,834 copying moleculekit/projections/metrictmscore.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,836 copying moleculekit/projections/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,838 copying moleculekit/projections/metricdihedral.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,841 copying moleculekit/projections/metricrmsd.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,843 copying moleculekit/projections/projection.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,845 copying moleculekit/projections/metriccoordinate.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,847 copying moleculekit/projections/metricsecondarystructure.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,849 copying moleculekit/projections/metricsphericalcoordinate.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,851 copying moleculekit/projections/metricplumed2.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,854 copying moleculekit/projections/metricdistance.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,856 copying moleculekit/projections/metricshell.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,859 copying moleculekit/projections/metricsasa.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,862 copying moleculekit/projections/util.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,864 copying moleculekit/projections/metricgyration.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,867 copying moleculekit/projections/metricfluctuation.py -> build/lib.linux-armv7l-cpython-39/moleculekit/projections 2024-06-25T19:26:45,870 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions 2024-06-25T19:26:45,871 copying moleculekit/interactions/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions 2024-06-25T19:26:45,872 copying moleculekit/interactions/interactions.py -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions 2024-06-25T19:26:45,876 creating build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-25T19:26:45,877 copying moleculekit/smallmol/smallmolcdp.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-25T19:26:45,880 copying moleculekit/smallmol/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-25T19:26:45,882 copying moleculekit/smallmol/test_smallmol.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-25T19:26:45,884 copying moleculekit/smallmol/test_smallmollib.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-25T19:26:45,886 copying moleculekit/smallmol/smallmollib.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-25T19:26:45,888 copying moleculekit/smallmol/smallmol.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-25T19:26:45,891 copying moleculekit/smallmol/util.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol 2024-06-25T19:26:45,894 creating build/lib.linux-armv7l-cpython-39/moleculekit/pdbx 2024-06-25T19:26:45,895 copying moleculekit/pdbx/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx 2024-06-25T19:26:45,897 creating build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,898 copying moleculekit/tools/hhblitsprofile.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,900 copying moleculekit/tools/moleculechecks.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,902 copying moleculekit/tools/voxeldescriptors.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,904 copying moleculekit/tools/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,906 copying moleculekit/tools/sequencestructuralalignment.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,908 copying moleculekit/tools/modelling.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,910 copying moleculekit/tools/docking.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,912 copying moleculekit/tools/graphalignment.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,915 copying moleculekit/tools/preparation.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,918 copying moleculekit/tools/atomtyper.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,921 copying moleculekit/tools/detect.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,923 copying moleculekit/tools/crystalpacking.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,925 copying moleculekit/tools/preparation_customres.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,928 copying moleculekit/tools/autosegment.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools 2024-06-25T19:26:45,931 creating build/lib.linux-armv7l-cpython-39/moleculekit/ply 2024-06-25T19:26:45,932 copying moleculekit/ply/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/ply 2024-06-25T19:26:45,934 copying moleculekit/ply/yacc.py -> build/lib.linux-armv7l-cpython-39/moleculekit/ply 2024-06-25T19:26:45,940 copying moleculekit/ply/lex.py -> build/lib.linux-armv7l-cpython-39/moleculekit/ply 2024-06-25T19:26:45,944 creating build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-25T19:26:45,945 copying moleculekit/atomselect/languageparser.py -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-25T19:26:45,947 copying moleculekit/atomselect/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-25T19:26:45,948 copying moleculekit/atomselect/analyze.py -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-25T19:26:45,950 copying moleculekit/atomselect/atomselect.py -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect 2024-06-25T19:26:45,953 creating build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-25T19:26:45,954 copying moleculekit/smallmol/tools/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-25T19:26:45,956 copying moleculekit/smallmol/tools/test_tools.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-25T19:26:45,958 copying moleculekit/smallmol/tools/clustering.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-25T19:26:45,960 copying moleculekit/smallmol/tools/restrainedembed.py -> build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools 2024-06-25T19:26:45,963 creating build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-25T19:26:45,964 copying moleculekit/pdbx/reader/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-25T19:26:45,965 copying moleculekit/pdbx/reader/PdbxReader.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-25T19:26:45,967 copying moleculekit/pdbx/reader/PdbxContainers.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-25T19:26:45,970 copying moleculekit/pdbx/reader/PdbxParser.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader 2024-06-25T19:26:45,973 creating build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer 2024-06-25T19:26:45,974 copying moleculekit/pdbx/writer/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer 2024-06-25T19:26:45,975 copying moleculekit/pdbx/writer/PdbxWriter.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer 2024-06-25T19:26:45,978 creating build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-25T19:26:45,979 copying moleculekit/pdbx/tests/PdbxReadWriteTests.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-25T19:26:45,981 copying moleculekit/pdbx/tests/PdbxWriterTests.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-25T19:26:45,983 copying moleculekit/pdbx/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-25T19:26:45,984 copying moleculekit/pdbx/tests/PdbxReaderTests.py -> build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests 2024-06-25T19:26:45,987 creating build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools 2024-06-25T19:26:45,987 copying moleculekit/tools/obabel_tools/__init__.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools 2024-06-25T19:26:45,989 copying moleculekit/tools/obabel_tools/obabel_cli.py -> build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools 2024-06-25T19:26:45,991 running egg_info 2024-06-25T19:26:45,996 writing moleculekit.egg-info/PKG-INFO 2024-06-25T19:26:45,999 writing dependency_links to moleculekit.egg-info/dependency_links.txt 2024-06-25T19:26:46,001 writing requirements to moleculekit.egg-info/requires.txt 2024-06-25T19:26:46,002 writing top-level names to moleculekit.egg-info/top_level.txt 2024-06-25T19:26:46,020 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,020 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,020 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,020 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,020 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,020 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,021 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,021 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,021 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,021 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,021 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,021 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,021 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,022 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,022 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,022 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,022 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,022 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,022 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,022 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,022 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,023 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,023 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,023 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,023 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,023 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,023 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,023 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,023 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,024 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,024 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,024 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,024 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,024 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,024 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,024 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,024 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,025 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,025 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,025 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,025 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,025 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,025 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,025 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,025 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,026 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,026 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,026 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,026 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,026 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,026 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,026 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,026 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,027 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,027 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,027 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,027 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,027 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,027 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,027 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,029 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,029 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,029 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,029 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,029 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,030 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,030 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,030 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,031 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,031 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,031 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,032 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,032 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,032 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,032 dependency /tmp/pip-build-env-wy4x1a7g/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 2024-06-25T19:26:46,038 reading manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-06-25T19:26:46,047 reading manifest template 'MANIFEST.in' 2024-06-25T19:26:46,300 no previously-included directories found matching 'moleculekit/test-data' 2024-06-25T19:26:46,301 no previously-included directories found matching 'moleculekit/tests' 2024-06-25T19:26:46,302 no previously-included directories found matching 'package' 2024-06-25T19:26:46,302 adding license file 'LICENSE' 2024-06-25T19:26:46,320 writing manifest file 'moleculekit.egg-info/SOURCES.txt' 2024-06-25T19:26:46,331 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.atomselect_utils' is absent from the `packages` configuration. 2024-06-25T19:26:46,331 !! 2024-06-25T19:26:46,331 ******************************************************************************** 2024-06-25T19:26:46,331 ############################ 2024-06-25T19:26:46,331 # Package would be ignored # 2024-06-25T19:26:46,332 ############################ 2024-06-25T19:26:46,332 Python recognizes 'moleculekit.atomselect_utils' as an importable package[^1], 2024-06-25T19:26:46,332 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,332 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,332 package, please make sure that 'moleculekit.atomselect_utils' is explicitly added 2024-06-25T19:26:46,332 to the `packages` configuration field. 2024-06-25T19:26:46,332 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,333 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,333 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,333 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,333 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,333 If you don't want 'moleculekit.atomselect_utils' to be distributed and are 2024-06-25T19:26:46,333 already explicitly excluding 'moleculekit.atomselect_utils' via 2024-06-25T19:26:46,334 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,334 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,334 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,334 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,334 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,335 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,335 even if it does not contain any `.py` files. 2024-06-25T19:26:46,335 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,335 directory, all directories are treated like packages. 2024-06-25T19:26:46,335 ******************************************************************************** 2024-06-25T19:26:46,335 !! 2024-06-25T19:26:46,335 check.warn(importable) 2024-06-25T19:26:46,336 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.bondguesser_utils' is absent from the `packages` configuration. 2024-06-25T19:26:46,336 !! 2024-06-25T19:26:46,336 ******************************************************************************** 2024-06-25T19:26:46,336 ############################ 2024-06-25T19:26:46,336 # Package would be ignored # 2024-06-25T19:26:46,336 ############################ 2024-06-25T19:26:46,336 Python recognizes 'moleculekit.bondguesser_utils' as an importable package[^1], 2024-06-25T19:26:46,337 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,337 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,337 package, please make sure that 'moleculekit.bondguesser_utils' is explicitly added 2024-06-25T19:26:46,337 to the `packages` configuration field. 2024-06-25T19:26:46,337 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,338 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,338 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,338 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,338 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,338 If you don't want 'moleculekit.bondguesser_utils' to be distributed and are 2024-06-25T19:26:46,338 already explicitly excluding 'moleculekit.bondguesser_utils' via 2024-06-25T19:26:46,339 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,339 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,339 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,339 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,339 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,340 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,340 even if it does not contain any `.py` files. 2024-06-25T19:26:46,340 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,340 directory, all directories are treated like packages. 2024-06-25T19:26:46,340 ******************************************************************************** 2024-06-25T19:26:46,340 !! 2024-06-25T19:26:46,340 check.warn(importable) 2024-06-25T19:26:46,341 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.cython_utils' is absent from the `packages` configuration. 2024-06-25T19:26:46,341 !! 2024-06-25T19:26:46,341 ******************************************************************************** 2024-06-25T19:26:46,341 ############################ 2024-06-25T19:26:46,341 # Package would be ignored # 2024-06-25T19:26:46,341 ############################ 2024-06-25T19:26:46,341 Python recognizes 'moleculekit.cython_utils' as an importable package[^1], 2024-06-25T19:26:46,341 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,342 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,342 package, please make sure that 'moleculekit.cython_utils' is explicitly added 2024-06-25T19:26:46,342 to the `packages` configuration field. 2024-06-25T19:26:46,342 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,342 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,342 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,343 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,343 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,343 If you don't want 'moleculekit.cython_utils' to be distributed and are 2024-06-25T19:26:46,343 already explicitly excluding 'moleculekit.cython_utils' via 2024-06-25T19:26:46,343 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,343 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,344 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,344 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,344 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,344 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,344 even if it does not contain any `.py` files. 2024-06-25T19:26:46,345 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,345 directory, all directories are treated like packages. 2024-06-25T19:26:46,345 ******************************************************************************** 2024-06-25T19:26:46,345 !! 2024-06-25T19:26:46,345 check.warn(importable) 2024-06-25T19:26:46,345 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.distance_utils' is absent from the `packages` configuration. 2024-06-25T19:26:46,346 !! 2024-06-25T19:26:46,346 ******************************************************************************** 2024-06-25T19:26:46,346 ############################ 2024-06-25T19:26:46,346 # Package would be ignored # 2024-06-25T19:26:46,346 ############################ 2024-06-25T19:26:46,346 Python recognizes 'moleculekit.distance_utils' as an importable package[^1], 2024-06-25T19:26:46,346 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,347 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,347 package, please make sure that 'moleculekit.distance_utils' is explicitly added 2024-06-25T19:26:46,347 to the `packages` configuration field. 2024-06-25T19:26:46,347 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,347 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,347 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,348 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,348 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,348 If you don't want 'moleculekit.distance_utils' to be distributed and are 2024-06-25T19:26:46,348 already explicitly excluding 'moleculekit.distance_utils' via 2024-06-25T19:26:46,348 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,348 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,349 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,349 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,349 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,349 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,349 even if it does not contain any `.py` files. 2024-06-25T19:26:46,350 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,350 directory, all directories are treated like packages. 2024-06-25T19:26:46,350 ******************************************************************************** 2024-06-25T19:26:46,350 !! 2024-06-25T19:26:46,350 check.warn(importable) 2024-06-25T19:26:46,350 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.binpos' is absent from the `packages` configuration. 2024-06-25T19:26:46,350 !! 2024-06-25T19:26:46,351 ******************************************************************************** 2024-06-25T19:26:46,351 ############################ 2024-06-25T19:26:46,351 # Package would be ignored # 2024-06-25T19:26:46,351 ############################ 2024-06-25T19:26:46,351 Python recognizes 'moleculekit.fileformats.binpos' as an importable package[^1], 2024-06-25T19:26:46,351 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,351 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,351 package, please make sure that 'moleculekit.fileformats.binpos' is explicitly added 2024-06-25T19:26:46,351 to the `packages` configuration field. 2024-06-25T19:26:46,352 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,352 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,352 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,352 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,352 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,353 If you don't want 'moleculekit.fileformats.binpos' to be distributed and are 2024-06-25T19:26:46,353 already explicitly excluding 'moleculekit.fileformats.binpos' via 2024-06-25T19:26:46,353 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,353 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,353 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,353 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,353 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,354 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,354 even if it does not contain any `.py` files. 2024-06-25T19:26:46,354 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,354 directory, all directories are treated like packages. 2024-06-25T19:26:46,354 ******************************************************************************** 2024-06-25T19:26:46,354 !! 2024-06-25T19:26:46,355 check.warn(importable) 2024-06-25T19:26:46,355 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.binpos.include' is absent from the `packages` configuration. 2024-06-25T19:26:46,355 !! 2024-06-25T19:26:46,355 ******************************************************************************** 2024-06-25T19:26:46,355 ############################ 2024-06-25T19:26:46,355 # Package would be ignored # 2024-06-25T19:26:46,355 ############################ 2024-06-25T19:26:46,355 Python recognizes 'moleculekit.fileformats.binpos.include' as an importable package[^1], 2024-06-25T19:26:46,355 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,356 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,356 package, please make sure that 'moleculekit.fileformats.binpos.include' is explicitly added 2024-06-25T19:26:46,356 to the `packages` configuration field. 2024-06-25T19:26:46,356 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,356 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,356 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,357 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,357 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,357 If you don't want 'moleculekit.fileformats.binpos.include' to be distributed and are 2024-06-25T19:26:46,357 already explicitly excluding 'moleculekit.fileformats.binpos.include' via 2024-06-25T19:26:46,357 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,357 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,357 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,358 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,358 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,358 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,358 even if it does not contain any `.py` files. 2024-06-25T19:26:46,358 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,359 directory, all directories are treated like packages. 2024-06-25T19:26:46,359 ******************************************************************************** 2024-06-25T19:26:46,359 !! 2024-06-25T19:26:46,359 check.warn(importable) 2024-06-25T19:26:46,359 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.binpos.src' is absent from the `packages` configuration. 2024-06-25T19:26:46,359 !! 2024-06-25T19:26:46,359 ******************************************************************************** 2024-06-25T19:26:46,359 ############################ 2024-06-25T19:26:46,360 # Package would be ignored # 2024-06-25T19:26:46,360 ############################ 2024-06-25T19:26:46,360 Python recognizes 'moleculekit.fileformats.binpos.src' as an importable package[^1], 2024-06-25T19:26:46,360 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,360 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,360 package, please make sure that 'moleculekit.fileformats.binpos.src' is explicitly added 2024-06-25T19:26:46,360 to the `packages` configuration field. 2024-06-25T19:26:46,361 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,361 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,361 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,361 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,361 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,361 If you don't want 'moleculekit.fileformats.binpos.src' to be distributed and are 2024-06-25T19:26:46,362 already explicitly excluding 'moleculekit.fileformats.binpos.src' via 2024-06-25T19:26:46,362 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,362 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,362 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,362 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,362 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,363 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,363 even if it does not contain any `.py` files. 2024-06-25T19:26:46,363 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,363 directory, all directories are treated like packages. 2024-06-25T19:26:46,363 ******************************************************************************** 2024-06-25T19:26:46,363 !! 2024-06-25T19:26:46,363 check.warn(importable) 2024-06-25T19:26:46,363 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.dcd' is absent from the `packages` configuration. 2024-06-25T19:26:46,364 !! 2024-06-25T19:26:46,364 ******************************************************************************** 2024-06-25T19:26:46,364 ############################ 2024-06-25T19:26:46,364 # Package would be ignored # 2024-06-25T19:26:46,364 ############################ 2024-06-25T19:26:46,364 Python recognizes 'moleculekit.fileformats.dcd' as an importable package[^1], 2024-06-25T19:26:46,364 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,365 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,365 package, please make sure that 'moleculekit.fileformats.dcd' is explicitly added 2024-06-25T19:26:46,365 to the `packages` configuration field. 2024-06-25T19:26:46,365 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,365 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,365 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,365 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,366 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,366 If you don't want 'moleculekit.fileformats.dcd' to be distributed and are 2024-06-25T19:26:46,366 already explicitly excluding 'moleculekit.fileformats.dcd' via 2024-06-25T19:26:46,366 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,366 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,366 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,366 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,367 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,367 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,367 even if it does not contain any `.py` files. 2024-06-25T19:26:46,367 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,367 directory, all directories are treated like packages. 2024-06-25T19:26:46,367 ******************************************************************************** 2024-06-25T19:26:46,368 !! 2024-06-25T19:26:46,368 check.warn(importable) 2024-06-25T19:26:46,368 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.dcd.include' is absent from the `packages` configuration. 2024-06-25T19:26:46,368 !! 2024-06-25T19:26:46,368 ******************************************************************************** 2024-06-25T19:26:46,368 ############################ 2024-06-25T19:26:46,368 # Package would be ignored # 2024-06-25T19:26:46,368 ############################ 2024-06-25T19:26:46,369 Python recognizes 'moleculekit.fileformats.dcd.include' as an importable package[^1], 2024-06-25T19:26:46,369 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,369 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,369 package, please make sure that 'moleculekit.fileformats.dcd.include' is explicitly added 2024-06-25T19:26:46,369 to the `packages` configuration field. 2024-06-25T19:26:46,369 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,369 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,370 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,370 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,370 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,370 If you don't want 'moleculekit.fileformats.dcd.include' to be distributed and are 2024-06-25T19:26:46,370 already explicitly excluding 'moleculekit.fileformats.dcd.include' via 2024-06-25T19:26:46,370 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,371 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,371 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,371 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,371 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,372 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,372 even if it does not contain any `.py` files. 2024-06-25T19:26:46,372 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,372 directory, all directories are treated like packages. 2024-06-25T19:26:46,372 ******************************************************************************** 2024-06-25T19:26:46,372 !! 2024-06-25T19:26:46,373 check.warn(importable) 2024-06-25T19:26:46,373 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.dcd.src' is absent from the `packages` configuration. 2024-06-25T19:26:46,373 !! 2024-06-25T19:26:46,373 ******************************************************************************** 2024-06-25T19:26:46,373 ############################ 2024-06-25T19:26:46,373 # Package would be ignored # 2024-06-25T19:26:46,373 ############################ 2024-06-25T19:26:46,373 Python recognizes 'moleculekit.fileformats.dcd.src' as an importable package[^1], 2024-06-25T19:26:46,374 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,374 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,374 package, please make sure that 'moleculekit.fileformats.dcd.src' is explicitly added 2024-06-25T19:26:46,374 to the `packages` configuration field. 2024-06-25T19:26:46,374 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,374 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,374 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,375 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,375 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,375 If you don't want 'moleculekit.fileformats.dcd.src' to be distributed and are 2024-06-25T19:26:46,375 already explicitly excluding 'moleculekit.fileformats.dcd.src' via 2024-06-25T19:26:46,375 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,375 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,375 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,376 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,376 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,376 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,376 even if it does not contain any `.py` files. 2024-06-25T19:26:46,376 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,376 directory, all directories are treated like packages. 2024-06-25T19:26:46,377 ******************************************************************************** 2024-06-25T19:26:46,377 !! 2024-06-25T19:26:46,377 check.warn(importable) 2024-06-25T19:26:46,377 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.xtc' is absent from the `packages` configuration. 2024-06-25T19:26:46,377 !! 2024-06-25T19:26:46,377 ******************************************************************************** 2024-06-25T19:26:46,377 ############################ 2024-06-25T19:26:46,378 # Package would be ignored # 2024-06-25T19:26:46,378 ############################ 2024-06-25T19:26:46,378 Python recognizes 'moleculekit.fileformats.xtc' as an importable package[^1], 2024-06-25T19:26:46,378 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,378 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,378 package, please make sure that 'moleculekit.fileformats.xtc' is explicitly added 2024-06-25T19:26:46,378 to the `packages` configuration field. 2024-06-25T19:26:46,378 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,379 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,379 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,379 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,379 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,379 If you don't want 'moleculekit.fileformats.xtc' to be distributed and are 2024-06-25T19:26:46,379 already explicitly excluding 'moleculekit.fileformats.xtc' via 2024-06-25T19:26:46,380 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,380 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,380 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,380 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,380 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,380 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,381 even if it does not contain any `.py` files. 2024-06-25T19:26:46,381 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,381 directory, all directories are treated like packages. 2024-06-25T19:26:46,381 ******************************************************************************** 2024-06-25T19:26:46,381 !! 2024-06-25T19:26:46,381 check.warn(importable) 2024-06-25T19:26:46,381 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.xtc.include' is absent from the `packages` configuration. 2024-06-25T19:26:46,381 !! 2024-06-25T19:26:46,382 ******************************************************************************** 2024-06-25T19:26:46,382 ############################ 2024-06-25T19:26:46,382 # Package would be ignored # 2024-06-25T19:26:46,382 ############################ 2024-06-25T19:26:46,382 Python recognizes 'moleculekit.fileformats.xtc.include' as an importable package[^1], 2024-06-25T19:26:46,382 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,382 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,383 package, please make sure that 'moleculekit.fileformats.xtc.include' is explicitly added 2024-06-25T19:26:46,383 to the `packages` configuration field. 2024-06-25T19:26:46,383 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,383 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,383 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,383 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,384 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,384 If you don't want 'moleculekit.fileformats.xtc.include' to be distributed and are 2024-06-25T19:26:46,384 already explicitly excluding 'moleculekit.fileformats.xtc.include' via 2024-06-25T19:26:46,384 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,384 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,384 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,384 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,385 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,385 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,385 even if it does not contain any `.py` files. 2024-06-25T19:26:46,385 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,385 directory, all directories are treated like packages. 2024-06-25T19:26:46,385 ******************************************************************************** 2024-06-25T19:26:46,386 !! 2024-06-25T19:26:46,386 check.warn(importable) 2024-06-25T19:26:46,386 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.fileformats.xtc.src' is absent from the `packages` configuration. 2024-06-25T19:26:46,386 !! 2024-06-25T19:26:46,386 ******************************************************************************** 2024-06-25T19:26:46,386 ############################ 2024-06-25T19:26:46,386 # Package would be ignored # 2024-06-25T19:26:46,386 ############################ 2024-06-25T19:26:46,387 Python recognizes 'moleculekit.fileformats.xtc.src' as an importable package[^1], 2024-06-25T19:26:46,387 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,387 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,387 package, please make sure that 'moleculekit.fileformats.xtc.src' is explicitly added 2024-06-25T19:26:46,387 to the `packages` configuration field. 2024-06-25T19:26:46,387 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,388 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,388 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,388 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,388 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,388 If you don't want 'moleculekit.fileformats.xtc.src' to be distributed and are 2024-06-25T19:26:46,388 already explicitly excluding 'moleculekit.fileformats.xtc.src' via 2024-06-25T19:26:46,389 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,389 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,389 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,389 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,389 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,390 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,390 even if it does not contain any `.py` files. 2024-06-25T19:26:46,390 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,390 directory, all directories are treated like packages. 2024-06-25T19:26:46,390 ******************************************************************************** 2024-06-25T19:26:46,390 !! 2024-06-25T19:26:46,390 check.warn(importable) 2024-06-25T19:26:46,391 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.cationpi' is absent from the `packages` configuration. 2024-06-25T19:26:46,391 !! 2024-06-25T19:26:46,391 ******************************************************************************** 2024-06-25T19:26:46,391 ############################ 2024-06-25T19:26:46,391 # Package would be ignored # 2024-06-25T19:26:46,391 ############################ 2024-06-25T19:26:46,392 Python recognizes 'moleculekit.interactions.cationpi' as an importable package[^1], 2024-06-25T19:26:46,392 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,392 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,392 package, please make sure that 'moleculekit.interactions.cationpi' is explicitly added 2024-06-25T19:26:46,392 to the `packages` configuration field. 2024-06-25T19:26:46,392 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,393 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,393 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,393 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,393 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,394 If you don't want 'moleculekit.interactions.cationpi' to be distributed and are 2024-06-25T19:26:46,394 already explicitly excluding 'moleculekit.interactions.cationpi' via 2024-06-25T19:26:46,394 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,394 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,394 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,395 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,395 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,395 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,395 even if it does not contain any `.py` files. 2024-06-25T19:26:46,396 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,396 directory, all directories are treated like packages. 2024-06-25T19:26:46,396 ******************************************************************************** 2024-06-25T19:26:46,396 !! 2024-06-25T19:26:46,396 check.warn(importable) 2024-06-25T19:26:46,396 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.hbonds' is absent from the `packages` configuration. 2024-06-25T19:26:46,396 !! 2024-06-25T19:26:46,397 ******************************************************************************** 2024-06-25T19:26:46,397 ############################ 2024-06-25T19:26:46,397 # Package would be ignored # 2024-06-25T19:26:46,397 ############################ 2024-06-25T19:26:46,398 Python recognizes 'moleculekit.interactions.hbonds' as an importable package[^1], 2024-06-25T19:26:46,398 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,398 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,398 package, please make sure that 'moleculekit.interactions.hbonds' is explicitly added 2024-06-25T19:26:46,398 to the `packages` configuration field. 2024-06-25T19:26:46,399 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,399 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,399 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,399 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,400 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,400 If you don't want 'moleculekit.interactions.hbonds' to be distributed and are 2024-06-25T19:26:46,400 already explicitly excluding 'moleculekit.interactions.hbonds' via 2024-06-25T19:26:46,400 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,400 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,400 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,401 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,401 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,402 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,402 even if it does not contain any `.py` files. 2024-06-25T19:26:46,402 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,402 directory, all directories are treated like packages. 2024-06-25T19:26:46,402 ******************************************************************************** 2024-06-25T19:26:46,402 !! 2024-06-25T19:26:46,403 check.warn(importable) 2024-06-25T19:26:46,403 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.pipi' is absent from the `packages` configuration. 2024-06-25T19:26:46,403 !! 2024-06-25T19:26:46,403 ******************************************************************************** 2024-06-25T19:26:46,403 ############################ 2024-06-25T19:26:46,403 # Package would be ignored # 2024-06-25T19:26:46,403 ############################ 2024-06-25T19:26:46,403 Python recognizes 'moleculekit.interactions.pipi' as an importable package[^1], 2024-06-25T19:26:46,404 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,404 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,404 package, please make sure that 'moleculekit.interactions.pipi' is explicitly added 2024-06-25T19:26:46,404 to the `packages` configuration field. 2024-06-25T19:26:46,404 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,404 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,404 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,405 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,405 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,405 If you don't want 'moleculekit.interactions.pipi' to be distributed and are 2024-06-25T19:26:46,405 already explicitly excluding 'moleculekit.interactions.pipi' via 2024-06-25T19:26:46,405 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,405 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,406 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,406 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,406 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,406 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,406 even if it does not contain any `.py` files. 2024-06-25T19:26:46,407 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,407 directory, all directories are treated like packages. 2024-06-25T19:26:46,407 ******************************************************************************** 2024-06-25T19:26:46,407 !! 2024-06-25T19:26:46,407 check.warn(importable) 2024-06-25T19:26:46,407 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.interactions.sigmahole' is absent from the `packages` configuration. 2024-06-25T19:26:46,407 !! 2024-06-25T19:26:46,407 ******************************************************************************** 2024-06-25T19:26:46,408 ############################ 2024-06-25T19:26:46,408 # Package would be ignored # 2024-06-25T19:26:46,408 ############################ 2024-06-25T19:26:46,409 Python recognizes 'moleculekit.interactions.sigmahole' as an importable package[^1], 2024-06-25T19:26:46,411 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,412 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,413 package, please make sure that 'moleculekit.interactions.sigmahole' is explicitly added 2024-06-25T19:26:46,413 to the `packages` configuration field. 2024-06-25T19:26:46,413 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,413 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,414 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,414 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,414 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,415 If you don't want 'moleculekit.interactions.sigmahole' to be distributed and are 2024-06-25T19:26:46,415 already explicitly excluding 'moleculekit.interactions.sigmahole' via 2024-06-25T19:26:46,415 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,415 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,415 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,415 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,416 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,416 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,416 even if it does not contain any `.py` files. 2024-06-25T19:26:46,416 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,417 directory, all directories are treated like packages. 2024-06-25T19:26:46,417 ******************************************************************************** 2024-06-25T19:26:46,417 !! 2024-06-25T19:26:46,417 check.warn(importable) 2024-06-25T19:26:46,417 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.occupancy_utils' is absent from the `packages` configuration. 2024-06-25T19:26:46,418 !! 2024-06-25T19:26:46,418 ******************************************************************************** 2024-06-25T19:26:46,418 ############################ 2024-06-25T19:26:46,418 # Package would be ignored # 2024-06-25T19:26:46,418 ############################ 2024-06-25T19:26:46,419 Python recognizes 'moleculekit.occupancy_utils' as an importable package[^1], 2024-06-25T19:26:46,419 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,419 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,419 package, please make sure that 'moleculekit.occupancy_utils' is explicitly added 2024-06-25T19:26:46,419 to the `packages` configuration field. 2024-06-25T19:26:46,419 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,420 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,420 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,420 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,420 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,420 If you don't want 'moleculekit.occupancy_utils' to be distributed and are 2024-06-25T19:26:46,421 already explicitly excluding 'moleculekit.occupancy_utils' via 2024-06-25T19:26:46,421 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,421 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,421 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,421 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,421 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,422 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,422 even if it does not contain any `.py` files. 2024-06-25T19:26:46,422 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,422 directory, all directories are treated like packages. 2024-06-25T19:26:46,422 ******************************************************************************** 2024-06-25T19:26:46,422 !! 2024-06-25T19:26:46,423 check.warn(importable) 2024-06-25T19:26:46,423 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.share' is absent from the `packages` configuration. 2024-06-25T19:26:46,423 !! 2024-06-25T19:26:46,423 ******************************************************************************** 2024-06-25T19:26:46,423 ############################ 2024-06-25T19:26:46,423 # Package would be ignored # 2024-06-25T19:26:46,423 ############################ 2024-06-25T19:26:46,424 Python recognizes 'moleculekit.share' as an importable package[^1], 2024-06-25T19:26:46,424 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,424 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,424 package, please make sure that 'moleculekit.share' is explicitly added 2024-06-25T19:26:46,424 to the `packages` configuration field. 2024-06-25T19:26:46,424 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,425 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,425 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,425 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,425 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,425 If you don't want 'moleculekit.share' to be distributed and are 2024-06-25T19:26:46,426 already explicitly excluding 'moleculekit.share' via 2024-06-25T19:26:46,426 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,426 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,426 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,426 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,426 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,427 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,427 even if it does not contain any `.py` files. 2024-06-25T19:26:46,427 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,427 directory, all directories are treated like packages. 2024-06-25T19:26:46,427 ******************************************************************************** 2024-06-25T19:26:46,427 !! 2024-06-25T19:26:46,428 check.warn(importable) 2024-06-25T19:26:46,428 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.share.atomselect' is absent from the `packages` configuration. 2024-06-25T19:26:46,428 !! 2024-06-25T19:26:46,428 ******************************************************************************** 2024-06-25T19:26:46,428 ############################ 2024-06-25T19:26:46,428 # Package would be ignored # 2024-06-25T19:26:46,428 ############################ 2024-06-25T19:26:46,429 Python recognizes 'moleculekit.share.atomselect' as an importable package[^1], 2024-06-25T19:26:46,429 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,429 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,429 package, please make sure that 'moleculekit.share.atomselect' is explicitly added 2024-06-25T19:26:46,429 to the `packages` configuration field. 2024-06-25T19:26:46,429 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,429 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,430 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,430 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,430 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,430 If you don't want 'moleculekit.share.atomselect' to be distributed and are 2024-06-25T19:26:46,430 already explicitly excluding 'moleculekit.share.atomselect' via 2024-06-25T19:26:46,430 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,431 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,431 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,431 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,431 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,432 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,432 even if it does not contain any `.py` files. 2024-06-25T19:26:46,432 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,432 directory, all directories are treated like packages. 2024-06-25T19:26:46,432 ******************************************************************************** 2024-06-25T19:26:46,432 !! 2024-06-25T19:26:46,432 check.warn(importable) 2024-06-25T19:26:46,432 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.share.pdb2pqr.residues' is absent from the `packages` configuration. 2024-06-25T19:26:46,433 !! 2024-06-25T19:26:46,433 ******************************************************************************** 2024-06-25T19:26:46,433 ############################ 2024-06-25T19:26:46,433 # Package would be ignored # 2024-06-25T19:26:46,433 ############################ 2024-06-25T19:26:46,433 Python recognizes 'moleculekit.share.pdb2pqr.residues' as an importable package[^1], 2024-06-25T19:26:46,433 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,434 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,434 package, please make sure that 'moleculekit.share.pdb2pqr.residues' is explicitly added 2024-06-25T19:26:46,434 to the `packages` configuration field. 2024-06-25T19:26:46,434 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,434 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,435 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,435 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,435 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,435 If you don't want 'moleculekit.share.pdb2pqr.residues' to be distributed and are 2024-06-25T19:26:46,435 already explicitly excluding 'moleculekit.share.pdb2pqr.residues' via 2024-06-25T19:26:46,436 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,436 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,436 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,436 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,436 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,437 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,437 even if it does not contain any `.py` files. 2024-06-25T19:26:46,437 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,437 directory, all directories are treated like packages. 2024-06-25T19:26:46,437 ******************************************************************************** 2024-06-25T19:26:46,437 !! 2024-06-25T19:26:46,438 check.warn(importable) 2024-06-25T19:26:46,438 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign' is absent from the `packages` configuration. 2024-06-25T19:26:46,438 !! 2024-06-25T19:26:46,438 ******************************************************************************** 2024-06-25T19:26:46,438 ############################ 2024-06-25T19:26:46,438 # Package would be ignored # 2024-06-25T19:26:46,438 ############################ 2024-06-25T19:26:46,438 Python recognizes 'moleculekit.tmalign' as an importable package[^1], 2024-06-25T19:26:46,439 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,439 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,439 package, please make sure that 'moleculekit.tmalign' is explicitly added 2024-06-25T19:26:46,439 to the `packages` configuration field. 2024-06-25T19:26:46,439 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,439 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,440 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,440 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,440 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,440 If you don't want 'moleculekit.tmalign' to be distributed and are 2024-06-25T19:26:46,440 already explicitly excluding 'moleculekit.tmalign' via 2024-06-25T19:26:46,441 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,441 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,441 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,441 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,441 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,442 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,442 even if it does not contain any `.py` files. 2024-06-25T19:26:46,442 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,442 directory, all directories are treated like packages. 2024-06-25T19:26:46,442 ******************************************************************************** 2024-06-25T19:26:46,443 !! 2024-06-25T19:26:46,443 check.warn(importable) 2024-06-25T19:26:46,443 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign.include' is absent from the `packages` configuration. 2024-06-25T19:26:46,443 !! 2024-06-25T19:26:46,443 ******************************************************************************** 2024-06-25T19:26:46,443 ############################ 2024-06-25T19:26:46,444 # Package would be ignored # 2024-06-25T19:26:46,444 ############################ 2024-06-25T19:26:46,444 Python recognizes 'moleculekit.tmalign.include' as an importable package[^1], 2024-06-25T19:26:46,444 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,444 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,444 package, please make sure that 'moleculekit.tmalign.include' is explicitly added 2024-06-25T19:26:46,445 to the `packages` configuration field. 2024-06-25T19:26:46,445 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,445 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,445 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,446 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,446 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,446 If you don't want 'moleculekit.tmalign.include' to be distributed and are 2024-06-25T19:26:46,446 already explicitly excluding 'moleculekit.tmalign.include' via 2024-06-25T19:26:46,446 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,447 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,447 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,447 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,447 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,448 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,448 even if it does not contain any `.py` files. 2024-06-25T19:26:46,448 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,448 directory, all directories are treated like packages. 2024-06-25T19:26:46,448 ******************************************************************************** 2024-06-25T19:26:46,448 !! 2024-06-25T19:26:46,448 check.warn(importable) 2024-06-25T19:26:46,448 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.tmalign.src' is absent from the `packages` configuration. 2024-06-25T19:26:46,449 !! 2024-06-25T19:26:46,449 ******************************************************************************** 2024-06-25T19:26:46,449 ############################ 2024-06-25T19:26:46,449 # Package would be ignored # 2024-06-25T19:26:46,449 ############################ 2024-06-25T19:26:46,449 Python recognizes 'moleculekit.tmalign.src' as an importable package[^1], 2024-06-25T19:26:46,449 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,450 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,450 package, please make sure that 'moleculekit.tmalign.src' is explicitly added 2024-06-25T19:26:46,450 to the `packages` configuration field. 2024-06-25T19:26:46,450 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,450 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,450 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,450 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,451 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,451 If you don't want 'moleculekit.tmalign.src' to be distributed and are 2024-06-25T19:26:46,451 already explicitly excluding 'moleculekit.tmalign.src' via 2024-06-25T19:26:46,451 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,451 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,452 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,452 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,452 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,452 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,452 even if it does not contain any `.py` files. 2024-06-25T19:26:46,453 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,453 directory, all directories are treated like packages. 2024-06-25T19:26:46,453 ******************************************************************************** 2024-06-25T19:26:46,453 !! 2024-06-25T19:26:46,453 check.warn(importable) 2024-06-25T19:26:46,453 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'moleculekit.wrapping' is absent from the `packages` configuration. 2024-06-25T19:26:46,453 !! 2024-06-25T19:26:46,454 ******************************************************************************** 2024-06-25T19:26:46,454 ############################ 2024-06-25T19:26:46,454 # Package would be ignored # 2024-06-25T19:26:46,454 ############################ 2024-06-25T19:26:46,454 Python recognizes 'moleculekit.wrapping' as an importable package[^1], 2024-06-25T19:26:46,454 but it is absent from setuptools' `packages` configuration. 2024-06-25T19:26:46,455 This leads to an ambiguous overall configuration. If you want to distribute this 2024-06-25T19:26:46,455 package, please make sure that 'moleculekit.wrapping' is explicitly added 2024-06-25T19:26:46,455 to the `packages` configuration field. 2024-06-25T19:26:46,455 Alternatively, you can also rely on setuptools' discovery methods 2024-06-25T19:26:46,455 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-06-25T19:26:46,455 instead of `find_packages(...)`/`find:`). 2024-06-25T19:26:46,456 You can read more about "package discovery" on setuptools documentation page: 2024-06-25T19:26:46,456 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-06-25T19:26:46,456 If you don't want 'moleculekit.wrapping' to be distributed and are 2024-06-25T19:26:46,456 already explicitly excluding 'moleculekit.wrapping' via 2024-06-25T19:26:46,456 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-06-25T19:26:46,456 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-06-25T19:26:46,456 combination with a more fine grained `package-data` configuration. 2024-06-25T19:26:46,457 You can read more about "package data files" on setuptools documentation page: 2024-06-25T19:26:46,457 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-06-25T19:26:46,457 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-06-25T19:26:46,457 even if it does not contain any `.py` files. 2024-06-25T19:26:46,457 On the other hand, currently there is no concept of package data 2024-06-25T19:26:46,458 directory, all directories are treated like packages. 2024-06-25T19:26:46,458 ******************************************************************************** 2024-06-25T19:26:46,458 !! 2024-06-25T19:26:46,458 check.warn(importable) 2024-06-25T19:26:46,458 copying moleculekit/logging.ini -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:46,458 copying moleculekit/vmd_wrapper -> build/lib.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:46,458 creating build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils 2024-06-25T19:26:46,458 copying moleculekit/atomselect_utils/atomselect_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils 2024-06-25T19:26:46,459 copying moleculekit/atomselect_utils/atomselect_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils 2024-06-25T19:26:46,459 creating build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils 2024-06-25T19:26:46,459 copying moleculekit/bondguesser_utils/bondguesser_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils 2024-06-25T19:26:46,459 copying moleculekit/bondguesser_utils/bondguesser_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils 2024-06-25T19:26:46,459 creating build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils 2024-06-25T19:26:46,459 copying moleculekit/cython_utils/cython_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils 2024-06-25T19:26:46,474 copying moleculekit/cython_utils/cython_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils 2024-06-25T19:26:46,476 creating build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils 2024-06-25T19:26:46,477 copying moleculekit/distance_utils/distance_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils 2024-06-25T19:26:46,503 copying moleculekit/distance_utils/distance_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils 2024-06-25T19:26:46,506 creating build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils 2024-06-25T19:26:46,506 copying moleculekit/occupancy_utils/occupancy_utils.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils 2024-06-25T19:26:46,533 copying moleculekit/occupancy_utils/occupancy_utils.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils 2024-06-25T19:26:46,535 creating build/lib.linux-armv7l-cpython-39/moleculekit/share 2024-06-25T19:26:46,536 copying moleculekit/share/ALA.cif -> build/lib.linux-armv7l-cpython-39/moleculekit/share 2024-06-25T19:26:46,538 copying moleculekit/share/backbone.cif -> build/lib.linux-armv7l-cpython-39/moleculekit/share 2024-06-25T19:26:46,540 copying moleculekit/share/opm_sequences.json -> build/lib.linux-armv7l-cpython-39/moleculekit/share 2024-06-25T19:26:46,756 creating build/lib.linux-armv7l-cpython-39/moleculekit/share/atomselect 2024-06-25T19:26:46,757 copying moleculekit/share/atomselect/atomselect.json -> build/lib.linux-armv7l-cpython-39/moleculekit/share/atomselect 2024-06-25T19:26:46,759 creating build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr 2024-06-25T19:26:46,760 creating build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,761 copying moleculekit/share/pdb2pqr/residues/.gitkeep -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,763 copying moleculekit/share/pdb2pqr/residues/004.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,764 copying moleculekit/share/pdb2pqr/residues/004.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,767 copying moleculekit/share/pdb2pqr/residues/03Y.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,768 copying moleculekit/share/pdb2pqr/residues/03Y.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,770 copying moleculekit/share/pdb2pqr/residues/0A1.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,772 copying moleculekit/share/pdb2pqr/residues/0A1.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,774 copying moleculekit/share/pdb2pqr/residues/0AF.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,776 copying moleculekit/share/pdb2pqr/residues/0AF.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,778 copying moleculekit/share/pdb2pqr/residues/0BN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,780 copying moleculekit/share/pdb2pqr/residues/0BN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,782 copying moleculekit/share/pdb2pqr/residues/1MH.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,784 copying moleculekit/share/pdb2pqr/residues/1MH.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,786 copying moleculekit/share/pdb2pqr/residues/2AS.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,788 copying moleculekit/share/pdb2pqr/residues/2AS.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,790 copying moleculekit/share/pdb2pqr/residues/2GX.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,792 copying moleculekit/share/pdb2pqr/residues/2GX.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,795 copying moleculekit/share/pdb2pqr/residues/2ML.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,797 copying moleculekit/share/pdb2pqr/residues/2ML.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,799 copying moleculekit/share/pdb2pqr/residues/2MR.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,802 copying moleculekit/share/pdb2pqr/residues/2MR.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,804 copying moleculekit/share/pdb2pqr/residues/4IN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,806 copying moleculekit/share/pdb2pqr/residues/4IN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,809 copying moleculekit/share/pdb2pqr/residues/4PH.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,812 copying moleculekit/share/pdb2pqr/residues/4PH.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,815 copying moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,818 copying moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,821 copying moleculekit/share/pdb2pqr/residues/5JP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,823 copying moleculekit/share/pdb2pqr/residues/5JP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,826 copying moleculekit/share/pdb2pqr/residues/AA4.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,829 copying moleculekit/share/pdb2pqr/residues/AA4.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,832 copying moleculekit/share/pdb2pqr/residues/ABA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,835 copying moleculekit/share/pdb2pqr/residues/ABA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,838 copying moleculekit/share/pdb2pqr/residues/AHP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,841 copying moleculekit/share/pdb2pqr/residues/AHP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,844 copying moleculekit/share/pdb2pqr/residues/ALC.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,847 copying moleculekit/share/pdb2pqr/residues/ALC.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,850 copying moleculekit/share/pdb2pqr/residues/ALN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,852 copying moleculekit/share/pdb2pqr/residues/ALN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,855 copying moleculekit/share/pdb2pqr/residues/ALY.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,858 copying moleculekit/share/pdb2pqr/residues/ALY.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,861 copying moleculekit/share/pdb2pqr/residues/APD.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,864 copying moleculekit/share/pdb2pqr/residues/APD.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,867 copying moleculekit/share/pdb2pqr/residues/BB8.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,870 copying moleculekit/share/pdb2pqr/residues/BB8.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,873 copying moleculekit/share/pdb2pqr/residues/BCS.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,875 copying moleculekit/share/pdb2pqr/residues/BCS.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,878 copying moleculekit/share/pdb2pqr/residues/BTK.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,881 copying moleculekit/share/pdb2pqr/residues/BTK.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,884 copying moleculekit/share/pdb2pqr/residues/CCS.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,887 copying moleculekit/share/pdb2pqr/residues/CCS.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,890 copying moleculekit/share/pdb2pqr/residues/CGU.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,893 copying moleculekit/share/pdb2pqr/residues/CGU.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,895 copying moleculekit/share/pdb2pqr/residues/CSA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,898 copying moleculekit/share/pdb2pqr/residues/CSA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,901 copying moleculekit/share/pdb2pqr/residues/CSO.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,904 copying moleculekit/share/pdb2pqr/residues/CSO.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,907 copying moleculekit/share/pdb2pqr/residues/CSP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,909 copying moleculekit/share/pdb2pqr/residues/CSP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,912 copying moleculekit/share/pdb2pqr/residues/CSS.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,914 copying moleculekit/share/pdb2pqr/residues/CSS.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,916 copying moleculekit/share/pdb2pqr/residues/D4P.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,918 copying moleculekit/share/pdb2pqr/residues/D4P.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,920 copying moleculekit/share/pdb2pqr/residues/DA2.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,923 copying moleculekit/share/pdb2pqr/residues/DA2.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,926 copying moleculekit/share/pdb2pqr/residues/DAB.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,928 copying moleculekit/share/pdb2pqr/residues/DAB.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,931 copying moleculekit/share/pdb2pqr/residues/DAH.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,933 copying moleculekit/share/pdb2pqr/residues/DAH.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,935 copying moleculekit/share/pdb2pqr/residues/DPP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,938 copying moleculekit/share/pdb2pqr/residues/DPP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,940 copying moleculekit/share/pdb2pqr/residues/ESC.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,942 copying moleculekit/share/pdb2pqr/residues/ESC.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,944 copying moleculekit/share/pdb2pqr/residues/FGL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,946 copying moleculekit/share/pdb2pqr/residues/FGL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,948 copying moleculekit/share/pdb2pqr/residues/GHG.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,950 copying moleculekit/share/pdb2pqr/residues/GHG.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,953 copying moleculekit/share/pdb2pqr/residues/GME.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,955 copying moleculekit/share/pdb2pqr/residues/GME.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,957 copying moleculekit/share/pdb2pqr/residues/GNC.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,959 copying moleculekit/share/pdb2pqr/residues/GNC.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,961 copying moleculekit/share/pdb2pqr/residues/HHK.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,963 copying moleculekit/share/pdb2pqr/residues/HHK.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,966 copying moleculekit/share/pdb2pqr/residues/HLU.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,968 copying moleculekit/share/pdb2pqr/residues/HLU.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,971 copying moleculekit/share/pdb2pqr/residues/HLX.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,973 copying moleculekit/share/pdb2pqr/residues/HLX.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,975 copying moleculekit/share/pdb2pqr/residues/HOX.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,978 copying moleculekit/share/pdb2pqr/residues/HOX.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,980 copying moleculekit/share/pdb2pqr/residues/HPE.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,982 copying moleculekit/share/pdb2pqr/residues/HPE.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,984 copying moleculekit/share/pdb2pqr/residues/HQA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,986 copying moleculekit/share/pdb2pqr/residues/HQA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,989 copying moleculekit/share/pdb2pqr/residues/HTR.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,991 copying moleculekit/share/pdb2pqr/residues/HTR.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,993 copying moleculekit/share/pdb2pqr/residues/HYP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,996 copying moleculekit/share/pdb2pqr/residues/HYP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:46,998 copying moleculekit/share/pdb2pqr/residues/I2M.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,000 copying moleculekit/share/pdb2pqr/residues/I2M.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,002 copying moleculekit/share/pdb2pqr/residues/IGL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,005 copying moleculekit/share/pdb2pqr/residues/IGL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,007 copying moleculekit/share/pdb2pqr/residues/IIL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,009 copying moleculekit/share/pdb2pqr/residues/IIL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,011 copying moleculekit/share/pdb2pqr/residues/IML.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,014 copying moleculekit/share/pdb2pqr/residues/IML.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,016 copying moleculekit/share/pdb2pqr/residues/KYN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,018 copying moleculekit/share/pdb2pqr/residues/KYN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,020 copying moleculekit/share/pdb2pqr/residues/LME.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,023 copying moleculekit/share/pdb2pqr/residues/LME.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,025 copying moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,027 copying moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,030 copying moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,032 copying moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,034 copying moleculekit/share/pdb2pqr/residues/M3L.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,037 copying moleculekit/share/pdb2pqr/residues/M3L.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,039 copying moleculekit/share/pdb2pqr/residues/ME0.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,042 copying moleculekit/share/pdb2pqr/residues/ME0.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,044 copying moleculekit/share/pdb2pqr/residues/MEA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,046 copying moleculekit/share/pdb2pqr/residues/MEA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,048 copying moleculekit/share/pdb2pqr/residues/MEN.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,050 copying moleculekit/share/pdb2pqr/residues/MEN.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,052 copying moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,055 copying moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,057 copying moleculekit/share/pdb2pqr/residues/MLE.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,059 copying moleculekit/share/pdb2pqr/residues/MLE.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,061 copying moleculekit/share/pdb2pqr/residues/MLY.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,063 copying moleculekit/share/pdb2pqr/residues/MLY.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,066 copying moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,068 copying moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,071 copying moleculekit/share/pdb2pqr/residues/MME.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,073 copying moleculekit/share/pdb2pqr/residues/MME.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,075 copying moleculekit/share/pdb2pqr/residues/MMO.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,078 copying moleculekit/share/pdb2pqr/residues/MMO.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,080 copying moleculekit/share/pdb2pqr/residues/MVA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,082 copying moleculekit/share/pdb2pqr/residues/MVA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,084 copying moleculekit/share/pdb2pqr/residues/NAL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,086 copying moleculekit/share/pdb2pqr/residues/NAL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,089 copying moleculekit/share/pdb2pqr/residues/NCY.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,091 copying moleculekit/share/pdb2pqr/residues/NCY.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,093 copying moleculekit/share/pdb2pqr/residues/NLE.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,095 copying moleculekit/share/pdb2pqr/residues/NLE.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,097 copying moleculekit/share/pdb2pqr/residues/NVA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,099 copying moleculekit/share/pdb2pqr/residues/NVA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,102 copying moleculekit/share/pdb2pqr/residues/NZC.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,104 copying moleculekit/share/pdb2pqr/residues/NZC.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,106 copying moleculekit/share/pdb2pqr/residues/OCY.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,108 copying moleculekit/share/pdb2pqr/residues/OCY.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,111 copying moleculekit/share/pdb2pqr/residues/OMX.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,113 copying moleculekit/share/pdb2pqr/residues/OMX.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,115 copying moleculekit/share/pdb2pqr/residues/ONL.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,118 copying moleculekit/share/pdb2pqr/residues/ONL.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,120 copying moleculekit/share/pdb2pqr/residues/ORM.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,122 copying moleculekit/share/pdb2pqr/residues/ORM.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,124 copying moleculekit/share/pdb2pqr/residues/P1L.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,127 copying moleculekit/share/pdb2pqr/residues/P1L.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,129 copying moleculekit/share/pdb2pqr/residues/PCA.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,131 copying moleculekit/share/pdb2pqr/residues/PCA.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,134 copying moleculekit/share/pdb2pqr/residues/PRK.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,136 copying moleculekit/share/pdb2pqr/residues/PRK.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,139 copying moleculekit/share/pdb2pqr/residues/PTR.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,141 copying moleculekit/share/pdb2pqr/residues/PTR.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,143 copying moleculekit/share/pdb2pqr/residues/SEP.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,146 copying moleculekit/share/pdb2pqr/residues/SEP.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,148 copying moleculekit/share/pdb2pqr/residues/TPO.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,150 copying moleculekit/share/pdb2pqr/residues/TPO.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,153 copying moleculekit/share/pdb2pqr/residues/TRO.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,155 copying moleculekit/share/pdb2pqr/residues/TRO.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,157 copying moleculekit/share/pdb2pqr/residues/TY2.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,159 copying moleculekit/share/pdb2pqr/residues/TY2.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,162 copying moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,164 copying moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,166 copying moleculekit/share/pdb2pqr/residues/YCM.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,168 copying moleculekit/share/pdb2pqr/residues/YCM.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,171 copying moleculekit/share/pdb2pqr/residues/YNM.dat -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,173 copying moleculekit/share/pdb2pqr/residues/YNM.xml -> build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues 2024-06-25T19:26:47,175 creating build/lib.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-25T19:26:47,177 copying moleculekit/tmalign/tmalign_util.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-25T19:26:47,197 copying moleculekit/tmalign/tmalign_util.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-25T19:26:47,199 copying moleculekit/tmalign/tmalignlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-25T19:26:47,201 creating build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/include 2024-06-25T19:26:47,202 copying moleculekit/tmalign/include/TMAlign.h -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/include 2024-06-25T19:26:47,204 creating build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/src 2024-06-25T19:26:47,205 copying moleculekit/tmalign/src/TMAlign.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/src 2024-06-25T19:26:47,211 creating build/lib.linux-armv7l-cpython-39/moleculekit/wrapping 2024-06-25T19:26:47,211 copying moleculekit/wrapping/wrapping.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/wrapping 2024-06-25T19:26:47,233 copying moleculekit/wrapping/wrapping.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/wrapping 2024-06-25T19:26:47,235 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-25T19:26:47,236 copying moleculekit/fileformats/binpos/binpos.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-25T19:26:47,254 copying moleculekit/fileformats/binpos/binpos.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-25T19:26:47,257 copying moleculekit/fileformats/binpos/binposlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-25T19:26:47,259 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include 2024-06-25T19:26:47,260 copying moleculekit/fileformats/binpos/include/binposplugin.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include 2024-06-25T19:26:47,263 copying moleculekit/fileformats/binpos/include/largefiles.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include 2024-06-25T19:26:47,265 copying moleculekit/fileformats/binpos/include/molfile_plugin.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include 2024-06-25T19:26:47,269 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src 2024-06-25T19:26:47,270 copying moleculekit/fileformats/binpos/src/binposplugin.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src 2024-06-25T19:26:47,272 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-25T19:26:47,273 copying moleculekit/fileformats/dcd/dcd.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-25T19:26:47,295 copying moleculekit/fileformats/dcd/dcd.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-25T19:26:47,298 copying moleculekit/fileformats/dcd/dcdlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-25T19:26:47,300 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-25T19:26:47,301 copying moleculekit/fileformats/dcd/include/dcdplugin.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-25T19:26:47,303 copying moleculekit/fileformats/dcd/include/endianswap.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-25T19:26:47,306 copying moleculekit/fileformats/dcd/include/fastio.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-25T19:26:47,309 copying moleculekit/fileformats/dcd/include/largefiles.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-25T19:26:47,311 copying moleculekit/fileformats/dcd/include/molfile_plugin.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include 2024-06-25T19:26:47,314 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src 2024-06-25T19:26:47,315 copying moleculekit/fileformats/dcd/src/dcdplugin.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src 2024-06-25T19:26:47,319 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:26:47,320 copying moleculekit/fileformats/xtc/trr.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:26:47,344 copying moleculekit/fileformats/xtc/trr.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:26:47,347 copying moleculekit/fileformats/xtc/trrlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:26:47,349 copying moleculekit/fileformats/xtc/xdrlib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:26:47,350 copying moleculekit/fileformats/xtc/xtc.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:26:47,371 copying moleculekit/fileformats/xtc/xtc.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:26:47,373 copying moleculekit/fileformats/xtc/xtclib.pxd -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:26:47,374 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-25T19:26:47,375 copying moleculekit/fileformats/xtc/include/trr_header.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-25T19:26:47,377 copying moleculekit/fileformats/xtc/include/xdr_seek.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-25T19:26:47,379 copying moleculekit/fileformats/xtc/include/xdrfile.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-25T19:26:47,382 copying moleculekit/fileformats/xtc/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-25T19:26:47,384 copying moleculekit/fileformats/xtc/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-25T19:26:47,386 copying moleculekit/fileformats/xtc/include/xtc.h -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include 2024-06-25T19:26:47,388 creating build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-25T19:26:47,389 copying moleculekit/fileformats/xtc/src/xdr_seek.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-25T19:26:47,391 copying moleculekit/fileformats/xtc/src/xdrfile.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-25T19:26:47,394 copying moleculekit/fileformats/xtc/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-25T19:26:47,397 copying moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-25T19:26:47,400 copying moleculekit/fileformats/xtc/src/xtc.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-25T19:26:47,403 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi 2024-06-25T19:26:47,404 copying moleculekit/interactions/cationpi/cationpi.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi 2024-06-25T19:26:47,433 copying moleculekit/interactions/cationpi/cationpi.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi 2024-06-25T19:26:47,435 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds 2024-06-25T19:26:47,437 copying moleculekit/interactions/hbonds/hbonds.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds 2024-06-25T19:26:47,456 copying moleculekit/interactions/hbonds/hbonds.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds 2024-06-25T19:26:47,458 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi 2024-06-25T19:26:47,459 copying moleculekit/interactions/pipi/pipi.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi 2024-06-25T19:26:47,482 copying moleculekit/interactions/pipi/pipi.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi 2024-06-25T19:26:47,484 creating build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole 2024-06-25T19:26:47,485 copying moleculekit/interactions/sigmahole/sigmahole.cpp -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole 2024-06-25T19:26:47,506 copying moleculekit/interactions/sigmahole/sigmahole.pyx -> build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole 2024-06-25T19:26:47,519 UPDATING build/lib.linux-armv7l-cpython-39/moleculekit/_version.py 2024-06-25T19:26:47,519 set build/lib.linux-armv7l-cpython-39/moleculekit/_version.py to '1.8.35' 2024-06-25T19:26:47,519 running build_ext 2024-06-25T19:26:47,533 building 'moleculekit.interactions.hbonds' extension 2024-06-25T19:26:47,534 creating build/temp.linux-armv7l-cpython-39 2024-06-25T19:26:47,534 creating build/temp.linux-armv7l-cpython-39/moleculekit 2024-06-25T19:26:47,535 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions 2024-06-25T19:26:47,535 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions/hbonds 2024-06-25T19:26:47,536 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-wy4x1a7g/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 2024-06-25T19:26:47,796 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:26:47,796 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:26:47,796 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:26:47,796 from moleculekit/interactions/hbonds/hbonds.cpp:1265: 2024-06-25T19:26:47,796 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:26:47,796 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:26:47,796 | ^~~~~~~ 2024-06-25T19:26:48,244 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:26:48,245 from moleculekit/interactions/hbonds/hbonds.cpp:1269: 2024-06-25T19:26:48,245 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:26:48,245 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:26:48,245 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:26:48,245 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:27:10,814 moleculekit/interactions/hbonds/hbonds.cpp: In function ‘PyObject* __pyx_pw_11moleculekit_12interactions_6hbonds_1calculate(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’: 2024-06-25T19:27:10,815 moleculekit/interactions/hbonds/hbonds.cpp:21469:52: warning: ‘__pyx_v_d_idx_h’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:27:10,815 21469 | (__pyx_v_results[__pyx_v_f]).push_back(__pyx_v_d_idx_h); 2024-06-25T19:27:10,815 | ^~~~~~~~~~~~~~~ 2024-06-25T19:27:10,815 moleculekit/interactions/hbonds/hbonds.cpp:20486:57: note: ‘__pyx_v_d_idx_h’ was declared here 2024-06-25T19:27:10,815 20486 | __pyx_t_11moleculekit_12interactions_6hbonds_UINT32_t __pyx_v_d_idx_h; 2024-06-25T19:27:10,815 | ^~~~~~~~~~~~~~~ 2024-06-25T19:27:13,939 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 2024-06-25T19:27:14,254 building 'moleculekit.interactions.pipi' extension 2024-06-25T19:27:14,255 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions/pipi 2024-06-25T19:27:14,256 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-wy4x1a7g/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 2024-06-25T19:27:14,488 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:27:14,488 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:27:14,488 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:27:14,489 from moleculekit/interactions/pipi/pipi.cpp:1265: 2024-06-25T19:27:14,489 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:27:14,489 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:27:14,489 | ^~~~~~~ 2024-06-25T19:27:14,957 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:27:14,957 from moleculekit/interactions/pipi/pipi.cpp:1269: 2024-06-25T19:27:14,957 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:27:14,957 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:27:14,958 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:27:14,958 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:27:42,798 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 2024-06-25T19:27:43,122 building 'moleculekit.interactions.cationpi' extension 2024-06-25T19:27:43,122 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions/cationpi 2024-06-25T19:27:43,123 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-wy4x1a7g/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 2024-06-25T19:27:43,353 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:27:43,354 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:27:43,354 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:27:43,354 from moleculekit/interactions/cationpi/cationpi.cpp:1265: 2024-06-25T19:27:43,354 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:27:43,354 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:27:43,354 | ^~~~~~~ 2024-06-25T19:27:43,785 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:27:43,785 from moleculekit/interactions/cationpi/cationpi.cpp:1269: 2024-06-25T19:27:43,785 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:27:43,785 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:27:43,785 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:27:43,785 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:28:11,251 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 2024-06-25T19:28:11,573 building 'moleculekit.interactions.sigmahole' extension 2024-06-25T19:28:11,574 creating build/temp.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole 2024-06-25T19:28:11,575 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-wy4x1a7g/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 2024-06-25T19:28:12,033 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:28:12,034 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:28:12,034 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:28:12,034 from moleculekit/interactions/sigmahole/sigmahole.cpp:1265: 2024-06-25T19:28:12,034 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:28:12,034 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:28:12,034 | ^~~~~~~ 2024-06-25T19:28:12,498 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:28:12,499 from moleculekit/interactions/sigmahole/sigmahole.cpp:1269: 2024-06-25T19:28:12,499 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:28:12,499 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:28:12,499 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:28:12,499 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:28:39,608 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 2024-06-25T19:28:39,925 building 'moleculekit.wrapping' extension 2024-06-25T19:28:39,926 creating build/temp.linux-armv7l-cpython-39/moleculekit/wrapping 2024-06-25T19:28:39,926 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-wy4x1a7g/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 2024-06-25T19:28:40,160 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:28:40,160 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:28:40,160 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:28:40,160 from moleculekit/wrapping/wrapping.cpp:1265: 2024-06-25T19:28:40,161 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:28:40,161 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:28:40,161 | ^~~~~~~ 2024-06-25T19:28:40,601 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:28:40,602 from moleculekit/wrapping/wrapping.cpp:1269: 2024-06-25T19:28:40,602 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:28:40,602 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:28:40,602 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:28:40,602 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:06,012 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 2024-06-25T19:29:06,227 building 'moleculekit.bondguesser_utils' extension 2024-06-25T19:29:06,227 creating build/temp.linux-armv7l-cpython-39/moleculekit/bondguesser_utils 2024-06-25T19:29:06,228 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-wy4x1a7g/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 2024-06-25T19:29:06,469 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:29:06,469 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:29:06,469 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:29:06,470 from moleculekit/bondguesser_utils/bondguesser_utils.cpp:1265: 2024-06-25T19:29:06,470 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:29:06,470 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:29:06,470 | ^~~~~~~ 2024-06-25T19:29:06,906 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:29:06,906 from moleculekit/bondguesser_utils/bondguesser_utils.cpp:1269: 2024-06-25T19:29:06,906 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:29:06,906 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:29:06,906 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:29:06,907 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,011 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)’: 2024-06-25T19:29:08,011 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] 2024-06-25T19:29:08,012 20255 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2024-06-25T19:29:08,012 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-25T19:29:08,012 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] 2024-06-25T19:29:08,013 20267 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2024-06-25T19:29:08,013 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-25T19:29:08,013 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] 2024-06-25T19:29:08,013 20279 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2024-06-25T19:29:08,013 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-25T19:29:08,014 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20318:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,014 20318 | __pyx_t_12 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-25T19:29:08,014 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,015 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20357:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,015 20357 | __pyx_t_12 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-25T19:29:08,015 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,016 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20396:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,016 20396 | __pyx_t_12 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,016 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,017 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20435:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,017 20435 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-25T19:29:08,017 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,018 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20441:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,018 20441 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-25T19:29:08,018 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,019 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20482:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,019 20482 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-25T19:29:08,019 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,020 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20488:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,020 20488 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,020 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,021 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20529:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,021 20529 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-25T19:29:08,021 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,022 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20535:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,022 20535 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,022 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,023 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20576:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,023 20576 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-25T19:29:08,023 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,024 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20629:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,024 20629 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,024 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,025 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20676:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,025 20676 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,025 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,026 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20717:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,026 20717 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-25T19:29:08,026 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,027 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20723:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,027 20723 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-25T19:29:08,027 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,027 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20729:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,028 20729 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,028 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,028 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20776:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,029 20776 | __pyx_t_13 = (__pyx_v_yi < (__pyx_v_yboxes - 1)); 2024-06-25T19:29:08,029 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,029 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20782:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,029 20782 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,030 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,030 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20823:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,030 20823 | __pyx_t_13 = (__pyx_v_xi < (__pyx_v_xboxes - 1)); 2024-06-25T19:29:08,031 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,031 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20835:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,031 20835 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,032 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,033 moleculekit/bondguesser_utils/bondguesser_utils.cpp:20888:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2024-06-25T19:29:08,033 20888 | __pyx_t_13 = (__pyx_v_zi < (__pyx_v_zboxes - 1)); 2024-06-25T19:29:08,033 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,052 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)’: 2024-06-25T19:29:08,053 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] 2024-06-25T19:29:08,053 21510 | __pyx_t_6 = (__pyx_v_boxneigh == __pyx_v_n_boxes); 2024-06-25T19:29:08,053 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:08,054 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] 2024-06-25T19:29:08,054 21547 | __pyx_t_6 = (__pyx_v_boxneigh == __pyx_v_boxidx); 2024-06-25T19:29:08,054 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-06-25T19:29:31,077 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 2024-06-25T19:29:31,373 building 'moleculekit.atomselect_utils' extension 2024-06-25T19:29:31,374 creating build/temp.linux-armv7l-cpython-39/moleculekit/atomselect_utils 2024-06-25T19:29:31,374 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-wy4x1a7g/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 2024-06-25T19:29:31,609 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:29:31,610 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:29:31,610 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:29:31,610 from moleculekit/atomselect_utils/atomselect_utils.cpp:1282: 2024-06-25T19:29:31,610 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:29:31,610 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:29:31,610 | ^~~~~~~ 2024-06-25T19:29:32,063 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:29:32,063 from moleculekit/atomselect_utils/atomselect_utils.cpp:1286: 2024-06-25T19:29:32,063 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:29:32,063 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:29:32,064 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:29:32,064 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:29:33,319 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 >&)’: 2024-06-25T19:29:33,319 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] 2024-06-25T19:29:33,320 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); 2024-06-25T19:29:33,320 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-06-25T19:29:33,325 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 >&)’: 2024-06-25T19:29:33,325 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] 2024-06-25T19:29:33,325 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); 2024-06-25T19:29:33,325 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-25T19:29:33,330 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 >&)’: 2024-06-25T19:29:33,330 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] 2024-06-25T19:29:33,330 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); 2024-06-25T19:29:33,331 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-25T19:30:03,597 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 2024-06-25T19:30:03,928 building 'moleculekit.distance_utils' extension 2024-06-25T19:30:03,928 creating build/temp.linux-armv7l-cpython-39/moleculekit/distance_utils 2024-06-25T19:30:03,929 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-wy4x1a7g/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 2024-06-25T19:30:04,160 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:30:04,161 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:30:04,161 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:30:04,161 from moleculekit/distance_utils/distance_utils.cpp:1265: 2024-06-25T19:30:04,161 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:30:04,161 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:30:04,161 | ^~~~~~~ 2024-06-25T19:30:04,643 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:30:04,644 from moleculekit/distance_utils/distance_utils.cpp:1269: 2024-06-25T19:30:04,644 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:30:04,644 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:30:04,644 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:30:04,644 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:30:05,822 moleculekit/distance_utils/distance_utils.cpp: In function ‘PyObject* __pyx_pf_11moleculekit_14distance_utils_2get_collisions(PyObject*, __Pyx_memviewslice, __Pyx_memviewslice, float)’: 2024-06-25T19:30:05,822 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] 2024-06-25T19:30:05,822 21813 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2024-06-25T19:30:05,822 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-25T19:30:05,823 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] 2024-06-25T19:30:05,823 21825 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2024-06-25T19:30:05,823 | ~~~~~~~~~~^~~~~~~~~~~ 2024-06-25T19:30:38,937 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 2024-06-25T19:30:39,269 building 'moleculekit.occupancy_utils' extension 2024-06-25T19:30:39,270 creating build/temp.linux-armv7l-cpython-39/moleculekit/occupancy_utils 2024-06-25T19:30:39,271 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-wy4x1a7g/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 2024-06-25T19:30:39,504 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:30:39,504 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:30:39,504 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:30:39,504 from moleculekit/occupancy_utils/occupancy_utils.cpp:1265: 2024-06-25T19:30:39,504 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:30:39,504 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:30:39,504 | ^~~~~~~ 2024-06-25T19:30:39,927 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:30:39,927 from moleculekit/occupancy_utils/occupancy_utils.cpp:1269: 2024-06-25T19:30:39,927 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:30:39,927 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:30:39,928 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:30:39,928 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:31:02,439 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 2024-06-25T19:31:02,654 building 'moleculekit.cython_utils' extension 2024-06-25T19:31:02,654 creating build/temp.linux-armv7l-cpython-39/moleculekit/cython_utils 2024-06-25T19:31:02,655 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-wy4x1a7g/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 2024-06-25T19:31:02,887 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:31:02,888 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:31:02,888 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:31:02,888 from moleculekit/cython_utils/cython_utils.cpp:1265: 2024-06-25T19:31:02,888 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:31:02,888 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:31:02,888 | ^~~~~~~ 2024-06-25T19:31:03,318 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ufuncobject.h:4, 2024-06-25T19:31:03,318 from moleculekit/cython_utils/cython_utils.cpp:1269: 2024-06-25T19:31:03,318 /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/npy_math.h: In function ‘npy_longdouble npy_creall(npy_clongdouble)’: 2024-06-25T19:31:03,319 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:31:03,319 405 | return ((longdouble_t *) &z)[0]; 2024-06-25T19:31:03,319 | ~^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:31:28,296 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 2024-06-25T19:31:28,633 building 'moleculekit.xtc' extension 2024-06-25T19:31:28,634 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats 2024-06-25T19:31:28,634 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc 2024-06-25T19:31:28,635 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src 2024-06-25T19:31:28,636 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-wy4x1a7g/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 2024-06-25T19:31:28,873 moleculekit/fileformats/xtc/src/xdrfile.cpp:66:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,874 66 | "OK", 2024-06-25T19:31:28,874 | ^~~~ 2024-06-25T19:31:28,874 moleculekit/fileformats/xtc/src/xdrfile.cpp:67:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,874 67 | "Header", 2024-06-25T19:31:28,874 | ^~~~~~~~ 2024-06-25T19:31:28,875 moleculekit/fileformats/xtc/src/xdrfile.cpp:68:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,875 68 | "String", 2024-06-25T19:31:28,875 | ^~~~~~~~ 2024-06-25T19:31:28,875 moleculekit/fileformats/xtc/src/xdrfile.cpp:69:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,875 69 | "Double", 2024-06-25T19:31:28,875 | ^~~~~~~~ 2024-06-25T19:31:28,876 moleculekit/fileformats/xtc/src/xdrfile.cpp:70:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,876 70 | "Integer", 2024-06-25T19:31:28,876 | ^~~~~~~~~ 2024-06-25T19:31:28,876 moleculekit/fileformats/xtc/src/xdrfile.cpp:71:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,876 71 | "Float", 2024-06-25T19:31:28,876 | ^~~~~~~ 2024-06-25T19:31:28,877 moleculekit/fileformats/xtc/src/xdrfile.cpp:72:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,877 72 | "Unsigned integer", 2024-06-25T19:31:28,877 | ^~~~~~~~~~~~~~~~~~ 2024-06-25T19:31:28,877 moleculekit/fileformats/xtc/src/xdrfile.cpp:73:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,877 73 | "Compressed 3D coordinate", 2024-06-25T19:31:28,877 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:31:28,878 moleculekit/fileformats/xtc/src/xdrfile.cpp:74:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,878 74 | "Closing file", 2024-06-25T19:31:28,878 | ^~~~~~~~~~~~~~ 2024-06-25T19:31:28,878 moleculekit/fileformats/xtc/src/xdrfile.cpp:75:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,878 75 | "Magic number", 2024-06-25T19:31:28,878 | ^~~~~~~~~~~~~~ 2024-06-25T19:31:28,878 moleculekit/fileformats/xtc/src/xdrfile.cpp:76:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,879 76 | "Not enough memory", 2024-06-25T19:31:28,879 | ^~~~~~~~~~~~~~~~~~~ 2024-06-25T19:31:28,879 moleculekit/fileformats/xtc/src/xdrfile.cpp:77:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,879 77 | "End of file", 2024-06-25T19:31:28,879 | ^~~~~~~~~~~~~ 2024-06-25T19:31:28,879 moleculekit/fileformats/xtc/src/xdrfile.cpp:78:2: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2024-06-25T19:31:28,880 78 | "File not found" 2024-06-25T19:31:28,880 | ^~~~~~~~~~~~~~~~ 2024-06-25T19:31:28,888 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofint(int)’: 2024-06-25T19:31:28,888 moleculekit/fileformats/xtc/src/xdrfile.cpp:459:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,888 459 | while (size >= num && num_of_bits < 32) 2024-06-25T19:31:28,888 | ~~~~~^~~~~~ 2024-06-25T19:31:28,889 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofints(int, unsigned int*)’: 2024-06-25T19:31:28,890 moleculekit/fileformats/xtc/src/xdrfile.cpp:505:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:28,890 505 | while (bytes[num_of_bytes] >= num) 2024-06-25T19:31:28,890 | ~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-06-25T19:31:28,892 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘void encodeints(int*, int, int, unsigned int*, unsigned int*)’: 2024-06-25T19:31:28,893 moleculekit/fileformats/xtc/src/xdrfile.cpp:614:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,893 614 | if (num_of_bits >= num_of_bytes * 8) 2024-06-25T19:31:28,893 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-06-25T19:31:28,893 moleculekit/fileformats/xtc/src/xdrfile.cpp:616:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,893 616 | for (i = 0; i < num_of_bytes; i++) 2024-06-25T19:31:28,894 | ~~^~~~~~~~~~~~~~ 2024-06-25T19:31:28,894 moleculekit/fileformats/xtc/src/xdrfile.cpp:624:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,894 624 | for (i = 0; i < num_of_bytes-1; i++) 2024-06-25T19:31:28,894 | ~~^~~~~~~~~~~~~~~~ 2024-06-25T19:31:28,896 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int decodebits(int*, int)’: 2024-06-25T19:31:28,896 moleculekit/fileformats/xtc/src/xdrfile.cpp:664:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:28,896 664 | if (lastbits < num_of_bits) 2024-06-25T19:31:28,896 | ~~~~~~~~~^~~~~~~~~~~~~ 2024-06-25T19:31:28,900 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_decompress_coord_float(float*, int*, float*, XDRFILE*)’: 2024-06-25T19:31:28,900 moleculekit/fileformats/xtc/src/xdrfile.cpp:785:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:28,900 785 | if(size3>xfp->buf1size) 2024-06-25T19:31:28,900 | ~~~~~^~~~~~~~~~~~~~ 2024-06-25T19:31:28,903 moleculekit/fileformats/xtc/src/xdrfile.cpp:842:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:28,903 842 | maxidx = (LASTIDX= size3 ) { return -1; } 2024-06-25T19:31:28,906 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:28,907 moleculekit/fileformats/xtc/src/xdrfile.cpp:935:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,907 935 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:28,907 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:28,907 moleculekit/fileformats/xtc/src/xdrfile.cpp:938:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,908 938 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:28,908 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:28,908 moleculekit/fileformats/xtc/src/xdrfile.cpp:945:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,908 945 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:28,908 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:28,909 moleculekit/fileformats/xtc/src/xdrfile.cpp:948:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,909 948 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:28,909 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:28,909 moleculekit/fileformats/xtc/src/xdrfile.cpp:951:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,910 951 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:28,910 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:28,911 moleculekit/fileformats/xtc/src/xdrfile.cpp:756:17: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-06-25T19:31:28,911 756 | int smallidx, minidx, maxidx; 2024-06-25T19:31:28,911 | ^~~~~~ 2024-06-25T19:31:28,911 moleculekit/fileformats/xtc/src/xdrfile.cpp:759:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-06-25T19:31:28,911 759 | int smallnum, smaller, larger, i, is_smaller, run; 2024-06-25T19:31:28,912 | ^~~~~~ 2024-06-25T19:31:28,912 moleculekit/fileformats/xtc/src/xdrfile.cpp:763:6: warning: unused variable ‘errval’ [-Wunused-variable] 2024-06-25T19:31:28,912 763 | int errval=1; 2024-06-25T19:31:28,912 | ^~~~~~ 2024-06-25T19:31:28,914 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_compress_coord_float(float*, int, float, XDRFILE*)’: 2024-06-25T19:31:28,914 moleculekit/fileformats/xtc/src/xdrfile.cpp:1011:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:28,914 1011 | if(size3>xfp->buf1size) 2024-06-25T19:31:28,914 | ~~~~~^~~~~~~~~~~~~~ 2024-06-25T19:31:28,916 moleculekit/fileformats/xtc/src/xdrfile.cpp:1068:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,916 1068 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-25T19:31:28,916 | ~~~~~~~~^~~~~~~ 2024-06-25T19:31:28,917 moleculekit/fileformats/xtc/src/xdrfile.cpp:1084:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,917 1084 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-25T19:31:28,917 | ~~~~~~~~^~~~~~~ 2024-06-25T19:31:28,917 moleculekit/fileformats/xtc/src/xdrfile.cpp:1098:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,917 1098 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-25T19:31:28,918 | ~~~~~~~~^~~~~~~ 2024-06-25T19:31:28,919 moleculekit/fileformats/xtc/src/xdrfile.cpp:1137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,919 1137 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2024-06-25T19:31:28,919 | ^ 2024-06-25T19:31:28,919 moleculekit/fileformats/xtc/src/xdrfile.cpp:1143:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:28,920 1143 | maxidx = (LASTIDXxfp->buf1size) 2024-06-25T19:31:28,927 | ~~~~~^~~~~~~~~~~~~~ 2024-06-25T19:31:28,928 moleculekit/fileformats/xtc/src/xdrfile.cpp:1377:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:28,929 1377 | maxidx = (LASTIDXxfp->buf1size) { 2024-06-25T19:31:28,934 | ~~~~~^~~~~~~~~~~~~~ 2024-06-25T19:31:28,938 moleculekit/fileformats/xtc/src/xdrfile.cpp:1628:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:28,938 1628 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2024-06-25T19:31:28,938 | ^ 2024-06-25T19:31:28,938 moleculekit/fileformats/xtc/src/xdrfile.cpp:1633:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:28,938 1633 | maxidx = (LASTIDX= num && num_of_bits < 32) 2024-06-25T19:31:53,766 | ~~~~~^~~~~~ 2024-06-25T19:31:53,767 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int sizeofints(int, unsigned int*)’: 2024-06-25T19:31:53,767 moleculekit/fileformats/xtc/src/xdrfile.cpp:505:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:53,767 505 | while (bytes[num_of_bytes] >= num) 2024-06-25T19:31:53,767 | ~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-06-25T19:31:53,770 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘void encodeints(int*, int, int, unsigned int*, unsigned int*)’: 2024-06-25T19:31:53,770 moleculekit/fileformats/xtc/src/xdrfile.cpp:614:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,771 614 | if (num_of_bits >= num_of_bytes * 8) 2024-06-25T19:31:53,771 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-06-25T19:31:53,771 moleculekit/fileformats/xtc/src/xdrfile.cpp:616:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,771 616 | for (i = 0; i < num_of_bytes; i++) 2024-06-25T19:31:53,771 | ~~^~~~~~~~~~~~~~ 2024-06-25T19:31:53,772 moleculekit/fileformats/xtc/src/xdrfile.cpp:624:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,772 624 | for (i = 0; i < num_of_bytes-1; i++) 2024-06-25T19:31:53,772 | ~~^~~~~~~~~~~~~~~~ 2024-06-25T19:31:53,774 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int decodebits(int*, int)’: 2024-06-25T19:31:53,774 moleculekit/fileformats/xtc/src/xdrfile.cpp:664:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:53,774 664 | if (lastbits < num_of_bits) 2024-06-25T19:31:53,774 | ~~~~~~~~~^~~~~~~~~~~~~ 2024-06-25T19:31:53,778 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_decompress_coord_float(float*, int*, float*, XDRFILE*)’: 2024-06-25T19:31:53,778 moleculekit/fileformats/xtc/src/xdrfile.cpp:785:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:53,778 785 | if(size3>xfp->buf1size) 2024-06-25T19:31:53,778 | ~~~~~^~~~~~~~~~~~~~ 2024-06-25T19:31:53,780 moleculekit/fileformats/xtc/src/xdrfile.cpp:842:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:53,781 842 | maxidx = (LASTIDX= size3 ) { return -1; } 2024-06-25T19:31:53,784 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:53,784 moleculekit/fileformats/xtc/src/xdrfile.cpp:935:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,785 935 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:53,785 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:53,785 moleculekit/fileformats/xtc/src/xdrfile.cpp:938:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,785 938 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:53,785 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:53,786 moleculekit/fileformats/xtc/src/xdrfile.cpp:945:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,786 945 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:53,786 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:53,787 moleculekit/fileformats/xtc/src/xdrfile.cpp:948:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,787 948 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:53,787 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:53,787 moleculekit/fileformats/xtc/src/xdrfile.cpp:951:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,787 951 | if(countmjh >= size3 ) { return -1; } 2024-06-25T19:31:53,788 | ~~~~~~~~~^~~~~~~~ 2024-06-25T19:31:53,788 moleculekit/fileformats/xtc/src/xdrfile.cpp:756:17: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-06-25T19:31:53,789 756 | int smallidx, minidx, maxidx; 2024-06-25T19:31:53,789 | ^~~~~~ 2024-06-25T19:31:53,789 moleculekit/fileformats/xtc/src/xdrfile.cpp:759:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-06-25T19:31:53,789 759 | int smallnum, smaller, larger, i, is_smaller, run; 2024-06-25T19:31:53,789 | ^~~~~~ 2024-06-25T19:31:53,789 moleculekit/fileformats/xtc/src/xdrfile.cpp:763:6: warning: unused variable ‘errval’ [-Wunused-variable] 2024-06-25T19:31:53,790 763 | int errval=1; 2024-06-25T19:31:53,790 | ^~~~~~ 2024-06-25T19:31:53,792 moleculekit/fileformats/xtc/src/xdrfile.cpp: In function ‘int xdrfile_compress_coord_float(float*, int, float, XDRFILE*)’: 2024-06-25T19:31:53,793 moleculekit/fileformats/xtc/src/xdrfile.cpp:1011:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:53,793 1011 | if(size3>xfp->buf1size) 2024-06-25T19:31:53,793 | ~~~~~^~~~~~~~~~~~~~ 2024-06-25T19:31:53,795 moleculekit/fileformats/xtc/src/xdrfile.cpp:1068:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,795 1068 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-25T19:31:53,795 | ~~~~~~~~^~~~~~~ 2024-06-25T19:31:53,796 moleculekit/fileformats/xtc/src/xdrfile.cpp:1084:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,797 1084 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-25T19:31:53,797 | ~~~~~~~~^~~~~~~ 2024-06-25T19:31:53,798 moleculekit/fileformats/xtc/src/xdrfile.cpp:1098:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,798 1098 | countmjh++; if( countmjh> size3) { return -1; } 2024-06-25T19:31:53,798 | ~~~~~~~~^~~~~~~ 2024-06-25T19:31:53,800 moleculekit/fileformats/xtc/src/xdrfile.cpp:1137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,800 1137 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2024-06-25T19:31:53,800 | ^ 2024-06-25T19:31:53,801 moleculekit/fileformats/xtc/src/xdrfile.cpp:1143:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:53,801 1143 | maxidx = (LASTIDXxfp->buf1size) 2024-06-25T19:31:53,810 | ~~~~~^~~~~~~~~~~~~~ 2024-06-25T19:31:53,812 moleculekit/fileformats/xtc/src/xdrfile.cpp:1377:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:53,812 1377 | maxidx = (LASTIDXxfp->buf1size) { 2024-06-25T19:31:53,820 | ~~~~~^~~~~~~~~~~~~~ 2024-06-25T19:31:53,824 moleculekit/fileformats/xtc/src/xdrfile.cpp:1628:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:31:53,824 1628 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2024-06-25T19:31:53,825 | ^ 2024-06-25T19:31:53,825 moleculekit/fileformats/xtc/src/xdrfile.cpp:1633:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:31:53,825 1633 | maxidx = (LASTIDX= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; 2024-06-25T19:32:28,371 | ^ 2024-06-25T19:32:28,378 moleculekit/fileformats/xtc/trr.c:12009:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,378 12009 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-25T19:32:28,378 | ^ 2024-06-25T19:32:28,379 moleculekit/fileformats/xtc/trr.c:2485:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,379 2485 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-06-25T19:32:28,379 | ^ 2024-06-25T19:32:28,385 moleculekit/fileformats/xtc/trr.c:10545:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-06-25T19:32:28,385 10545 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-06-25T19:32:28,385 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:32:28,391 moleculekit/fileformats/xtc/trr.c:12003:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,392 12003 | __pyx_t_28 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-06-25T19:32:28,392 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-06-25T19:32:28,399 moleculekit/fileformats/xtc/trr.c:11956:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,399 11956 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; 2024-06-25T19:32:28,399 | ^ 2024-06-25T19:32:28,406 moleculekit/fileformats/xtc/trr.c:11952:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,406 11952 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-25T19:32:28,406 | ^ 2024-06-25T19:32:28,407 moleculekit/fileformats/xtc/trr.c:2485:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,407 2485 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-06-25T19:32:28,407 | ^ 2024-06-25T19:32:28,413 moleculekit/fileformats/xtc/trr.c:10561:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-06-25T19:32:28,413 10561 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-06-25T19:32:28,413 | ^~~~~~~~~~~~~~~~~~~~ 2024-06-25T19:32:28,419 moleculekit/fileformats/xtc/trr.c:11946:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,419 11946 | __pyx_t_28 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-06-25T19:32:28,419 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-06-25T19:32:28,425 moleculekit/fileformats/xtc/trr.c:12345:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,426 12345 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-25T19:32:28,426 | ^ 2024-06-25T19:32:28,433 moleculekit/fileformats/xtc/trr.c:12341:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,433 12341 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-06-25T19:32:28,433 | ^ 2024-06-25T19:32:28,440 moleculekit/fileformats/xtc/trr.c:12186:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,440 12186 | } else if (unlikely(__pyx_t_35 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-25T19:32:28,440 | ^ 2024-06-25T19:32:28,447 moleculekit/fileformats/xtc/trr.c:12182:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,447 12182 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-06-25T19:32:28,448 | ^ 2024-06-25T19:32:28,453 moleculekit/fileformats/xtc/trr.c:12238:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,454 12238 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2024-06-25T19:32:28,454 | ^ 2024-06-25T19:32:28,461 moleculekit/fileformats/xtc/trr.c:12234:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:28,461 12234 | } else if (unlikely(__pyx_t_35 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2024-06-25T19:32:28,461 | ^ 2024-06-25T19:32:34,883 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 2024-06-25T19:32:35,070 building 'moleculekit.dcd' extension 2024-06-25T19:32:35,071 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/dcd 2024-06-25T19:32:35,072 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src 2024-06-25T19:32:35,073 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-wy4x1a7g/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 2024-06-25T19:32:35,408 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:32:35,408 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:32:35,408 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:32:35,408 from moleculekit/fileformats/dcd/dcd.c:1256: 2024-06-25T19:32:35,408 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:32:35,409 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:32:35,409 | ^~~~~~~ 2024-06-25T19:32:36,433 In file included from moleculekit/fileformats/dcd/include/dcdplugin.h:1, 2024-06-25T19:32:36,433 from moleculekit/fileformats/dcd/dcd.c:1262: 2024-06-25T19:32:36,433 moleculekit/fileformats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2024-06-25T19:32:36,433 474 | static int fio_write_str(fio_fd fd, const char *str) { 2024-06-25T19:32:36,433 | ^~~~~~~~~~~~~ 2024-06-25T19:32:36,434 moleculekit/fileformats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2024-06-25T19:32:36,434 470 | static int fio_read_int32(fio_fd fd, int *i) { 2024-06-25T19:32:36,434 | ^~~~~~~~~~~~~~ 2024-06-25T19:32:36,434 moleculekit/fileformats/dcd/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 2024-06-25T19:32:36,434 466 | static int fio_write_int32(fio_fd fd, int i) { 2024-06-25T19:32:36,434 | ^~~~~~~~~~~~~~~ 2024-06-25T19:32:36,434 moleculekit/fileformats/dcd/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2024-06-25T19:32:36,435 457 | static fio_size_t fio_ftell(fio_fd fd) { 2024-06-25T19:32:36,435 | ^~~~~~~~~ 2024-06-25T19:32:36,435 moleculekit/fileformats/dcd/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 2024-06-25T19:32:36,435 450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { 2024-06-25T19:32:36,435 | ^~~~~~~~~ 2024-06-25T19:32:36,435 moleculekit/fileformats/dcd/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 2024-06-25T19:32:36,435 415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { 2024-06-25T19:32:36,435 | ^~~~~~~~~ 2024-06-25T19:32:36,435 moleculekit/fileformats/dcd/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2024-06-25T19:32:36,436 394 | static int fio_fclose(fio_fd fd) { 2024-06-25T19:32:36,436 | ^~~~~~~~~~ 2024-06-25T19:32:36,436 moleculekit/fileformats/dcd/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2024-06-25T19:32:36,436 366 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2024-06-25T19:32:36,436 | ^~~~~~~~ 2024-06-25T19:32:49,067 moleculekit/fileformats/dcd/dcd.c: In function ‘__pyx_pf_11moleculekit_3dcd_17DCDTrajectoryFile_18read’: 2024-06-25T19:32:49,067 moleculekit/fileformats/dcd/dcd.c:1158:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:32:49,068 1158 | #define PyInt_FromLong PyLong_FromLong 2024-06-25T19:32:49,068 | ^~~~~~~~~~~~~~~ 2024-06-25T19:32:49,072 moleculekit/fileformats/dcd/dcd.c:8476:7: note: ‘__pyx_v_i’ was declared here 2024-06-25T19:32:49,072 8476 | int __pyx_v_i; 2024-06-25T19:32:49,073 | ^~~~~~~~~ 2024-06-25T19:32:52,341 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-wy4x1a7g/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 2024-06-25T19:32:52,522 moleculekit/fileformats/dcd/src/dcdplugin.c: In function ‘read_dcdheader’: 2024-06-25T19:32:52,523 moleculekit/fileformats/dcd/src/dcdplugin.c:150:55: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:32:52,523 150 | else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) 2024-06-25T19:32:52,524 | ^~ 2024-06-25T19:32:52,524 moleculekit/fileformats/dcd/src/dcdplugin.c:173:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:32:52,524 173 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) 2024-06-25T19:32:52,524 | ^~ 2024-06-25T19:32:52,525 moleculekit/fileformats/dcd/src/dcdplugin.c:194:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:32:52,525 194 | if (input_integer[0] != dcdcordmagic) 2024-06-25T19:32:52,525 | ^~ 2024-06-25T19:32:52,529 moleculekit/fileformats/dcd/src/dcdplugin.c:409:47: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:32:52,529 409 | if ((input_integer[0] + input_integer[1]) != ((*N) - (*NAMNF)) * 4) 2024-06-25T19:32:52,529 | ^~ 2024-06-25T19:32:52,530 moleculekit/fileformats/dcd/src/dcdplugin.c:428:47: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-06-25T19:32:52,530 428 | if ((input_integer[0] + input_integer[1]) != ((*N) - (*NAMNF)) * 4) 2024-06-25T19:32:52,531 | ^~ 2024-06-25T19:32:52,534 moleculekit/fileformats/dcd/src/dcdplugin.c: In function ‘read_dcdstep’: 2024-06-25T19:32:52,535 moleculekit/fileformats/dcd/src/dcdplugin.c:651:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:32:52,535 651 | if (tmpbuf[i] != sizeof(float) * N) 2024-06-25T19:32:52,535 | ^~ 2024-06-25T19:32:52,536 moleculekit/fileformats/dcd/src/dcdplugin.c:659:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-06-25T19:32:52,536 659 | if ((tmpbuf[2 * i] + tmpbuf[2 * i + 1]) != sizeof(float) * N) 2024-06-25T19:32:52,536 | ^~ 2024-06-25T19:32:52,559 In file included from moleculekit/fileformats/dcd/src/dcdplugin.c:55: 2024-06-25T19:32:52,560 At top level: 2024-06-25T19:32:52,560 moleculekit/fileformats/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2024-06-25T19:32:52,560 96 | static void swap2_aligned(void *v, long ndata) { 2024-06-25T19:32:52,561 | ^~~~~~~~~~~~~ 2024-06-25T19:32:52,561 moleculekit/fileformats/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2024-06-25T19:32:52,561 32 | static void swap2_unaligned(void *v, long ndata) { 2024-06-25T19:32:52,561 | ^~~~~~~~~~~~~~~ 2024-06-25T19:32:52,561 In file included from moleculekit/fileformats/dcd/src/dcdplugin.c:46: 2024-06-25T19:32:52,562 moleculekit/fileformats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2024-06-25T19:32:52,562 474 | static int fio_write_str(fio_fd fd, const char *str) { 2024-06-25T19:32:52,562 | ^~~~~~~~~~~~~ 2024-06-25T19:32:52,562 moleculekit/fileformats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2024-06-25T19:32:52,562 470 | static int fio_read_int32(fio_fd fd, int *i) { 2024-06-25T19:32:52,562 | ^~~~~~~~~~~~~~ 2024-06-25T19:32:53,666 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 2024-06-25T19:32:53,810 building 'moleculekit.binpos' extension 2024-06-25T19:32:53,811 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/binpos 2024-06-25T19:32:53,812 creating build/temp.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src 2024-06-25T19:32:53,813 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-wy4x1a7g/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 2024-06-25T19:32:54,147 In file included from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarraytypes.h:1909, 2024-06-25T19:32:54,147 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/ndarrayobject.h:12, 2024-06-25T19:32:54,147 from /tmp/pip-build-env-wy4x1a7g/overlay/lib/python3.9/site-packages/numpy/_core/include/numpy/arrayobject.h:5, 2024-06-25T19:32:54,148 from moleculekit/fileformats/binpos/binpos.c:1256: 2024-06-25T19:32:54,148 /tmp/pip-build-env-wy4x1a7g/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] 2024-06-25T19:32:54,148 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-06-25T19:32:54,148 | ^~~~~~~ 2024-06-25T19:33:07,575 moleculekit/fileformats/binpos/binpos.c: In function ‘__pyx_pw_11moleculekit_6binpos_20BINPOSTrajectoryFile_7_read’: 2024-06-25T19:33:07,580 moleculekit/fileformats/binpos/binpos.c:8499:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:33:07,581 8499 | if (__pyx_t_1) { 2024-06-25T19:33:07,581 | ^ 2024-06-25T19:33:07,585 moleculekit/fileformats/binpos/binpos.c:7976:7: note: ‘__pyx_v_status’ was declared here 2024-06-25T19:33:07,586 7976 | int __pyx_v_status; 2024-06-25T19:33:07,586 | ^~~~~~~~~~~~~~ 2024-06-25T19:33:07,587 moleculekit/fileformats/binpos/binpos.c:1158:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-06-25T19:33:07,587 1158 | #define PyInt_FromLong PyLong_FromLong 2024-06-25T19:33:07,587 | ^~~~~~~~~~~~~~~ 2024-06-25T19:33:07,592 moleculekit/fileformats/binpos/binpos.c:7973:7: note: ‘__pyx_v_i’ was declared here 2024-06-25T19:33:07,592 7973 | int __pyx_v_i; 2024-06-25T19:33:07,592 | ^~~~~~~~~ 2024-06-25T19:33:09,829 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-wy4x1a7g/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 2024-06-25T19:33:10,128 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 2024-06-25T19:33:10,264 building 'moleculekit.tmalign' extension 2024-06-25T19:33:10,265 creating build/temp.linux-armv7l-cpython-39/moleculekit/tmalign 2024-06-25T19:33:10,266 creating build/temp.linux-armv7l-cpython-39/moleculekit/tmalign/src 2024-06-25T19:33:10,268 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-wy4x1a7g/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 2024-06-25T19:33:39,675 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-wy4x1a7g/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 2024-06-25T19:33:58,109 In file included from /usr/include/c++/10/vector:72, 2024-06-25T19:33:58,109 from moleculekit/tmalign/tmalign_util.cpp:1280: 2024-06-25T19:33:58,109 /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]’: 2024-06-25T19:33:58,109 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-06-25T19:33:58,110 426 | vector<_Tp, _Alloc>:: 2024-06-25T19:33:58,110 | ^~~~~~~~~~~~~~~~~~~ 2024-06-25T19:33:58,689 In file included from /usr/include/c++/10/vector:67, 2024-06-25T19:33:58,689 from moleculekit/tmalign/tmalign_util.cpp:1280: 2024-06-25T19:33:58,690 /usr/include/c++/10/bits/stl_vector.h: In function ‘PyObject* __pyx_pw_11moleculekit_7tmalign_1tmalign(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’: 2024-06-25T19:33:58,690 /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 2024-06-25T19:33:58,690 1198 | _M_realloc_insert(end(), __x); 2024-06-25T19:33:58,690 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-25T19:33:58,690 /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 2024-06-25T19:33:58,690 1198 | _M_realloc_insert(end(), __x); 2024-06-25T19:33:58,691 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-25T19:33:58,691 /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 2024-06-25T19:33:58,691 1198 | _M_realloc_insert(end(), __x); 2024-06-25T19:33:58,692 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-06-25T19:34:01,108 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 2024-06-25T19:34:01,551 UPDATING build/lib.linux-armv7l-cpython-39/moleculekit/_version.py 2024-06-25T19:34:01,551 set build/lib.linux-armv7l-cpython-39/moleculekit/_version.py to '1.8.35' 2024-06-25T19:34:01,551 installing to build/bdist.linux-armv7l/wheel 2024-06-25T19:34:01,551 running install 2024-06-25T19:34:01,577 running install_lib 2024-06-25T19:34:01,584 creating build/bdist.linux-armv7l 2024-06-25T19:34:01,585 creating build/bdist.linux-armv7l/wheel 2024-06-25T19:34:01,587 creating build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,589 copying build/lib.linux-armv7l-cpython-39/moleculekit/xtc.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,613 creating build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-06-25T19:34:01,614 copying build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils/distance_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-06-25T19:34:01,638 copying build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils/distance_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/distance_utils 2024-06-25T19:34:01,641 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-06-25T19:34:01,642 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/tmalign_util.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-06-25T19:34:01,667 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/tmalign_util.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-06-25T19:34:01,669 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign/include 2024-06-25T19:34:01,670 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/include/TMAlign.h -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign/include 2024-06-25T19:34:01,672 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/tmalignlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign 2024-06-25T19:34:01,674 creating build/bdist.linux-armv7l/wheel/moleculekit/tmalign/src 2024-06-25T19:34:01,675 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign/src/TMAlign.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/tmalign/src 2024-06-25T19:34:01,682 copying build/lib.linux-armv7l-cpython-39/moleculekit/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,683 copying build/lib.linux-armv7l-cpython-39/moleculekit/vmdviewer.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,686 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-06-25T19:34:01,687 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-06-25T19:34:01,688 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/netcdf.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-06-25T19:34:01,692 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-06-25T19:34:01,693 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/binposlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-06-25T19:34:01,695 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-06-25T19:34:01,696 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include/molfile_plugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-06-25T19:34:01,699 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include/binposplugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-06-25T19:34:01,701 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/include/largefiles.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/include 2024-06-25T19:34:01,703 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/binpos.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-06-25T19:34:01,722 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/binpos.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos 2024-06-25T19:34:01,725 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/src 2024-06-25T19:34:01,726 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/binpos/src/binposplugin.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/binpos/src 2024-06-25T19:34:01,728 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/utils.py -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats 2024-06-25T19:34:01,731 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-25T19:34:01,732 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/trr.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-25T19:34:01,734 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/trr.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-25T19:34:01,761 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/xdrlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-25T19:34:01,762 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/xtc.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-25T19:34:01,765 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-25T19:34:01,766 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-25T19:34:01,768 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xdr_seek.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-25T19:34:01,769 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-25T19:34:01,771 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xtc.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-25T19:34:01,773 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/trr_header.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-25T19:34:01,775 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/include 2024-06-25T19:34:01,777 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/xtclib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-25T19:34:01,779 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/trrlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-25T19:34:01,781 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-25T19:34:01,782 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdr_seek.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-25T19:34:01,784 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-25T19:34:01,788 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-25T19:34:01,790 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-25T19:34:01,795 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/src/xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc/src 2024-06-25T19:34:01,797 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/xtc/xtc.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/xtc 2024-06-25T19:34:01,826 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-06-25T19:34:01,827 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/dcdlib.pxd -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-06-25T19:34:01,829 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/dcd.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-06-25T19:34:01,832 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-25T19:34:01,833 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/dcdplugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-25T19:34:01,835 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/molfile_plugin.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-25T19:34:01,838 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/largefiles.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-25T19:34:01,840 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/fastio.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-25T19:34:01,843 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/include/endianswap.h -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/include 2024-06-25T19:34:01,846 creating build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/src 2024-06-25T19:34:01,847 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/src/dcdplugin.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd/src 2024-06-25T19:34:01,850 copying build/lib.linux-armv7l-cpython-39/moleculekit/fileformats/dcd/dcd.c -> build/bdist.linux-armv7l/wheel/moleculekit/fileformats/dcd 2024-06-25T19:34:01,865 copying build/lib.linux-armv7l-cpython-39/moleculekit/distance_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,899 copying build/lib.linux-armv7l-cpython-39/moleculekit/rcsb.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,902 creating build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-06-25T19:34:01,903 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils/atomselect_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-06-25T19:34:01,927 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils/atomselect_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect_utils 2024-06-25T19:34:01,930 copying build/lib.linux-armv7l-cpython-39/moleculekit/rdkitintegration.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,933 copying build/lib.linux-armv7l-cpython-39/moleculekit/distance.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,935 copying build/lib.linux-armv7l-cpython-39/moleculekit/align.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:01,938 creating build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,939 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metrictmscore.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,941 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,943 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricdihedral.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,946 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricrmsd.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,949 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/projection.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,952 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metriccoordinate.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,954 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricsecondarystructure.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,957 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricsphericalcoordinate.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,959 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricplumed2.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,962 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricdistance.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,965 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricshell.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,968 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricsasa.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,970 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/util.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,973 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricgyration.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,975 copying build/lib.linux-armv7l-cpython-39/moleculekit/projections/metricfluctuation.py -> build/bdist.linux-armv7l/wheel/moleculekit/projections 2024-06-25T19:34:01,979 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-25T19:34:01,980 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-25T19:34:01,982 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/interactions.py -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-25T19:34:01,985 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-25T19:34:02,015 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-25T19:34:02,039 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-06-25T19:34:02,040 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi/cationpi.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-06-25T19:34:02,043 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/cationpi/cationpi.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/cationpi 2024-06-25T19:34:02,068 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-25T19:34:02,094 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-06-25T19:34:02,095 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi/pipi.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-06-25T19:34:02,097 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/pipi/pipi.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/pipi 2024-06-25T19:34:02,122 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-06-25T19:34:02,123 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds/hbonds.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-06-25T19:34:02,142 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds/hbonds.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/hbonds 2024-06-25T19:34:02,145 creating build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-06-25T19:34:02,146 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole/sigmahole.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-06-25T19:34:02,166 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/sigmahole/sigmahole.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/interactions/sigmahole 2024-06-25T19:34:02,169 copying build/lib.linux-armv7l-cpython-39/moleculekit/interactions/hbonds.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit/interactions 2024-06-25T19:34:02,189 copying build/lib.linux-armv7l-cpython-39/moleculekit/dcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,206 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,240 copying build/lib.linux-armv7l-cpython-39/moleculekit/viewer.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,242 copying build/lib.linux-armv7l-cpython-39/moleculekit/home.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,244 creating build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-25T19:34:02,245 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/smallmolcdp.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-25T19:34:02,248 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-25T19:34:02,250 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/test_smallmol.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-25T19:34:02,253 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/test_smallmollib.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-25T19:34:02,255 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/smallmollib.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-25T19:34:02,257 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/smallmol.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-25T19:34:02,261 creating build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-25T19:34:02,262 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-25T19:34:02,263 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools/test_tools.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-25T19:34:02,266 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools/clustering.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-25T19:34:02,268 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/tools/restrainedembed.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol/tools 2024-06-25T19:34:02,270 copying build/lib.linux-armv7l-cpython-39/moleculekit/smallmol/util.py -> build/bdist.linux-armv7l/wheel/moleculekit/smallmol 2024-06-25T19:34:02,273 copying build/lib.linux-armv7l-cpython-39/moleculekit/_version.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,274 copying build/lib.linux-armv7l-cpython-39/moleculekit/pymolgraphics.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,276 copying build/lib.linux-armv7l-cpython-39/moleculekit/opm.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,278 copying build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,296 copying build/lib.linux-armv7l-cpython-39/moleculekit/config.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,298 creating build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-06-25T19:34:02,299 copying build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils/cython_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-06-25T19:34:02,302 copying build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils/cython_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/cython_utils 2024-06-25T19:34:02,323 copying build/lib.linux-armv7l-cpython-39/moleculekit/version.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,325 copying build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,327 copying build/lib.linux-armv7l-cpython-39/moleculekit/readers.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,331 copying build/lib.linux-armv7l-cpython-39/moleculekit/writers.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,334 creating build/bdist.linux-armv7l/wheel/moleculekit/share 2024-06-25T19:34:02,335 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/opm_sequences.json -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-06-25T19:34:02,542 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/ALA.cif -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-06-25T19:34:02,545 creating build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr 2024-06-25T19:34:02,550 creating build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,551 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ONL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,554 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4PQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,557 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/004.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,559 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PRK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,562 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BB8.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,564 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,567 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/OCY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,569 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PCA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,571 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NLE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,574 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DAH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,577 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TRO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,579 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/03Y.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,581 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IIL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,584 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/D4P.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,586 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HOX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,588 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BTK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,591 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/KYN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,593 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/004.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,595 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,597 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/D4P.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,600 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GNC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,602 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LMQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,604 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,605 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NAL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,607 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,609 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/OCY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,611 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NZC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,613 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DPP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,614 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HTR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,616 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HHK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,617 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PRK.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,619 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLZ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,621 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ORM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,623 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,624 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,626 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0A1.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,628 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4PH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,629 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DPP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,631 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ME0.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,633 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4PQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,634 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LYZ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,636 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/SEP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,638 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CGU.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,639 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4IN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,641 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PCA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,643 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/YCM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,645 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,646 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/5JP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,648 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ABA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,650 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/FGL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,652 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NCY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,653 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DA2.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,655 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4PH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,657 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BCS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,659 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,660 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LYZ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,662 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/P1L.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,664 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HLU.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,666 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ESC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,667 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IGL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,669 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HQA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,671 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GHG.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,673 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,674 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/YCM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,676 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,678 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,680 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HYP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,681 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0BN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,683 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/AHP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,685 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IML.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,687 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ORM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,688 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CCS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,690 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/5JP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,692 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/M3L.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,693 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,695 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ABA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,697 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/P1L.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,699 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2MR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,701 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,703 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MVA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,704 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BCS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,706 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/YNM.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,708 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/M3L.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,710 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2AS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,712 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,713 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2ML.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,715 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/AA4.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,717 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/03Y.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,719 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IML.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,720 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DA2.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,722 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEN.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,724 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0A1.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,725 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TYQ.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,727 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/1MH.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,729 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,730 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2MR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,732 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MMO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,734 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2AS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,736 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,737 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HPE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,739 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BB8.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,741 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2ML.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,743 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MMO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,744 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TPO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,746 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HLX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,747 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/APD.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,756 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/APD.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,757 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LMQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,759 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HTR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,761 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TPO.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,763 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSS.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,764 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NAL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,766 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HHK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,768 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLZ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,770 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,771 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NVA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,773 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DAB.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,775 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ESC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,777 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TY2.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,778 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/BTK.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,780 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HOX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,782 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IIL.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,784 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/LME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,786 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/IGL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,787 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/FGL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,789 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GNC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,791 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HLX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,793 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HQA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,794 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NLE.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,796 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2GX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,797 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ME0.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,799 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/1MH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,800 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HLU.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,802 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TYQ.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,804 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,806 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/OMX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,808 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/AHP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,809 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ONL.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,811 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TY2.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,813 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CGU.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,815 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALC.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,817 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/.gitkeep -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,818 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/I2M.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,819 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HPE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,821 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/4IN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,823 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/2GX.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,825 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/ALY.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,826 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/I2M.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,828 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NVA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,829 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0BN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,831 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0AF.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,833 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CSS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,835 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/0AF.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,836 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/AA4.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,838 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GME.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,840 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NZC.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,842 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DAH.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,843 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,845 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MME.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,847 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,848 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PTR.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,850 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MEA.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,852 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/YNM.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,854 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MLE.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,856 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/GHG.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,857 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/PTR.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,859 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/HYP.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,861 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/NCY.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,863 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/SEP.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,864 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/OMX.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,866 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/KYN.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,867 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/CCS.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,869 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/TRO.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,871 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/DAB.xml -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,872 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/pdb2pqr/residues/MVA.dat -> build/bdist.linux-armv7l/wheel/moleculekit/share/pdb2pqr/residues 2024-06-25T19:34:02,874 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/backbone.cif -> build/bdist.linux-armv7l/wheel/moleculekit/share 2024-06-25T19:34:02,876 creating build/bdist.linux-armv7l/wheel/moleculekit/share/atomselect 2024-06-25T19:34:02,877 copying build/lib.linux-armv7l-cpython-39/moleculekit/share/atomselect/atomselect.json -> build/bdist.linux-armv7l/wheel/moleculekit/share/atomselect 2024-06-25T19:34:02,879 creating build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-06-25T19:34:02,880 copying build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils/bondguesser_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-06-25T19:34:02,898 copying build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils/bondguesser_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/bondguesser_utils 2024-06-25T19:34:02,901 creating build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-06-25T19:34:02,902 copying build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils/occupancy_utils.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-06-25T19:34:02,904 copying build/lib.linux-armv7l-cpython-39/moleculekit/occupancy_utils/occupancy_utils.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/occupancy_utils 2024-06-25T19:34:02,923 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx 2024-06-25T19:34:02,925 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-25T19:34:02,926 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-25T19:34:02,927 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader/PdbxReader.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-25T19:34:02,930 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader/PdbxContainers.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-25T19:34:02,933 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/reader/PdbxParser.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/reader 2024-06-25T19:34:02,935 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx 2024-06-25T19:34:02,937 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-06-25T19:34:02,938 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-06-25T19:34:02,939 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/writer/PdbxWriter.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/writer 2024-06-25T19:34:02,941 creating build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-25T19:34:02,942 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests/PdbxReadWriteTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-25T19:34:02,944 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests/PdbxWriterTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-25T19:34:02,946 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-25T19:34:02,948 copying build/lib.linux-armv7l-cpython-39/moleculekit/pdbx/tests/PdbxReaderTests.py -> build/bdist.linux-armv7l/wheel/moleculekit/pdbx/tests 2024-06-25T19:34:02,950 creating build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,951 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/hhblitsprofile.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,953 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/moleculechecks.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,955 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/voxeldescriptors.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,958 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,959 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/sequencestructuralalignment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,961 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/modelling.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,964 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/docking.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,966 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/graphalignment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,968 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/preparation.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,971 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/atomtyper.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,973 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/detect.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,976 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/crystalpacking.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,978 creating build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-06-25T19:34:02,979 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-06-25T19:34:02,981 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/obabel_tools/obabel_cli.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools/obabel_tools 2024-06-25T19:34:02,983 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/preparation_customres.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,986 copying build/lib.linux-armv7l-cpython-39/moleculekit/tools/autosegment.py -> build/bdist.linux-armv7l/wheel/moleculekit/tools 2024-06-25T19:34:02,988 copying build/lib.linux-armv7l-cpython-39/moleculekit/molecule.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:02,992 copying build/lib.linux-armv7l-cpython-39/moleculekit/binpos.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,007 creating build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-06-25T19:34:03,008 copying build/lib.linux-armv7l-cpython-39/moleculekit/ply/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-06-25T19:34:03,010 copying build/lib.linux-armv7l-cpython-39/moleculekit/ply/yacc.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-06-25T19:34:03,014 copying build/lib.linux-armv7l-cpython-39/moleculekit/ply/lex.py -> build/bdist.linux-armv7l/wheel/moleculekit/ply 2024-06-25T19:34:03,017 copying build/lib.linux-armv7l-cpython-39/moleculekit/wrapping.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,083 copying build/lib.linux-armv7l-cpython-39/moleculekit/util.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,086 copying build/lib.linux-armv7l-cpython-39/moleculekit/vmdgraphics.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,088 copying build/lib.linux-armv7l-cpython-39/moleculekit/logging.ini -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,090 copying build/lib.linux-armv7l-cpython-39/moleculekit/periodictable.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,093 creating build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-06-25T19:34:03,093 copying build/lib.linux-armv7l-cpython-39/moleculekit/wrapping/wrapping.cpp -> build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-06-25T19:34:03,115 copying build/lib.linux-armv7l-cpython-39/moleculekit/wrapping/wrapping.pyx -> build/bdist.linux-armv7l/wheel/moleculekit/wrapping 2024-06-25T19:34:03,117 copying build/lib.linux-armv7l-cpython-39/moleculekit/vmd_wrapper -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,119 copying build/lib.linux-armv7l-cpython-39/moleculekit/tmalign.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,184 copying build/lib.linux-armv7l-cpython-39/moleculekit/dihedral.py -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,185 copying build/lib.linux-armv7l-cpython-39/moleculekit/trr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,210 creating build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-25T19:34:03,211 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect/languageparser.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-25T19:34:03,214 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect/__init__.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-25T19:34:03,216 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect/analyze.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-25T19:34:03,218 copying build/lib.linux-armv7l-cpython-39/moleculekit/atomselect/atomselect.py -> build/bdist.linux-armv7l/wheel/moleculekit/atomselect 2024-06-25T19:34:03,221 copying build/lib.linux-armv7l-cpython-39/moleculekit/bondguesser_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,244 copying build/lib.linux-armv7l-cpython-39/moleculekit/cython_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/moleculekit 2024-06-25T19:34:03,264 running install_egg_info 2024-06-25T19:34:03,270 Copying moleculekit.egg-info to build/bdist.linux-armv7l/wheel/moleculekit-1.8.35-py3.9.egg-info 2024-06-25T19:34:03,283 running install_scripts 2024-06-25T19:34:03,341 creating build/bdist.linux-armv7l/wheel/moleculekit-1.8.35.dist-info/WHEEL 2024-06-25T19:34:03,345 creating '/tmp/pip-wheel-er1hivg0/.tmp-o8t2jfpk/moleculekit-1.8.35-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-06-25T19:34:03,350 adding 'moleculekit/__init__.py' 2024-06-25T19:34:03,352 adding 'moleculekit/_version.py' 2024-06-25T19:34:03,354 adding 'moleculekit/align.py' 2024-06-25T19:34:03,688 adding 'moleculekit/atomselect_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:03,850 adding 'moleculekit/binpos.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:03,857 adding 'moleculekit/bondguesser.py' 2024-06-25T19:34:04,100 adding 'moleculekit/bondguesser_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:04,109 adding 'moleculekit/config.py' 2024-06-25T19:34:04,369 adding 'moleculekit/cython_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:04,541 adding 'moleculekit/dcd.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:04,547 adding 'moleculekit/dihedral.py' 2024-06-25T19:34:04,548 adding 'moleculekit/distance.py' 2024-06-25T19:34:04,877 adding 'moleculekit/distance_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:04,889 adding 'moleculekit/home.py' 2024-06-25T19:34:04,890 adding 'moleculekit/logging.ini' 2024-06-25T19:34:04,904 adding 'moleculekit/molecule.py' 2024-06-25T19:34:05,131 adding 'moleculekit/occupancy_utils.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:05,139 adding 'moleculekit/opm.py' 2024-06-25T19:34:05,143 adding 'moleculekit/periodictable.py' 2024-06-25T19:34:05,144 adding 'moleculekit/pymolgraphics.py' 2024-06-25T19:34:05,146 adding 'moleculekit/rcsb.py' 2024-06-25T19:34:05,147 adding 'moleculekit/rdkitintegration.py' 2024-06-25T19:34:05,161 adding 'moleculekit/readers.py' 2024-06-25T19:34:05,767 adding 'moleculekit/tmalign.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:06,078 adding 'moleculekit/trr.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:06,090 adding 'moleculekit/util.py' 2024-06-25T19:34:06,092 adding 'moleculekit/version.py' 2024-06-25T19:34:06,093 adding 'moleculekit/viewer.py' 2024-06-25T19:34:06,095 adding 'moleculekit/vmd_wrapper' 2024-06-25T19:34:06,096 adding 'moleculekit/vmdgraphics.py' 2024-06-25T19:34:06,098 adding 'moleculekit/vmdviewer.py' 2024-06-25T19:34:06,365 adding 'moleculekit/wrapping.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:06,380 adding 'moleculekit/writers.py' 2024-06-25T19:34:06,647 adding 'moleculekit/xtc.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:06,657 adding 'moleculekit/atomselect/__init__.py' 2024-06-25T19:34:06,659 adding 'moleculekit/atomselect/analyze.py' 2024-06-25T19:34:06,661 adding 'moleculekit/atomselect/atomselect.py' 2024-06-25T19:34:06,663 adding 'moleculekit/atomselect/languageparser.py' 2024-06-25T19:34:06,770 adding 'moleculekit/atomselect_utils/atomselect_utils.cpp' 2024-06-25T19:34:06,781 adding 'moleculekit/atomselect_utils/atomselect_utils.pyx' 2024-06-25T19:34:06,874 adding 'moleculekit/bondguesser_utils/bondguesser_utils.cpp' 2024-06-25T19:34:06,883 adding 'moleculekit/bondguesser_utils/bondguesser_utils.pyx' 2024-06-25T19:34:06,974 adding 'moleculekit/cython_utils/cython_utils.cpp' 2024-06-25T19:34:06,982 adding 'moleculekit/cython_utils/cython_utils.pyx' 2024-06-25T19:34:07,086 adding 'moleculekit/distance_utils/distance_utils.cpp' 2024-06-25T19:34:07,097 adding 'moleculekit/distance_utils/distance_utils.pyx' 2024-06-25T19:34:07,099 adding 'moleculekit/fileformats/__init__.py' 2024-06-25T19:34:07,104 adding 'moleculekit/fileformats/netcdf.py' 2024-06-25T19:34:07,106 adding 'moleculekit/fileformats/utils.py' 2024-06-25T19:34:07,168 adding 'moleculekit/fileformats/binpos/binpos.c' 2024-06-25T19:34:07,176 adding 'moleculekit/fileformats/binpos/binpos.pyx' 2024-06-25T19:34:07,177 adding 'moleculekit/fileformats/binpos/binposlib.pxd' 2024-06-25T19:34:07,179 adding 'moleculekit/fileformats/binpos/include/binposplugin.h' 2024-06-25T19:34:07,180 adding 'moleculekit/fileformats/binpos/include/largefiles.h' 2024-06-25T19:34:07,185 adding 'moleculekit/fileformats/binpos/include/molfile_plugin.h' 2024-06-25T19:34:07,187 adding 'moleculekit/fileformats/binpos/src/binposplugin.c' 2024-06-25T19:34:07,252 adding 'moleculekit/fileformats/dcd/dcd.c' 2024-06-25T19:34:07,260 adding 'moleculekit/fileformats/dcd/dcd.pyx' 2024-06-25T19:34:07,261 adding 'moleculekit/fileformats/dcd/dcdlib.pxd' 2024-06-25T19:34:07,263 adding 'moleculekit/fileformats/dcd/include/dcdplugin.h' 2024-06-25T19:34:07,264 adding 'moleculekit/fileformats/dcd/include/endianswap.h' 2024-06-25T19:34:07,266 adding 'moleculekit/fileformats/dcd/include/fastio.h' 2024-06-25T19:34:07,268 adding 'moleculekit/fileformats/dcd/include/largefiles.h' 2024-06-25T19:34:07,273 adding 'moleculekit/fileformats/dcd/include/molfile_plugin.h' 2024-06-25T19:34:07,278 adding 'moleculekit/fileformats/dcd/src/dcdplugin.c' 2024-06-25T19:34:07,375 adding 'moleculekit/fileformats/xtc/trr.c' 2024-06-25T19:34:07,386 adding 'moleculekit/fileformats/xtc/trr.pyx' 2024-06-25T19:34:07,388 adding 'moleculekit/fileformats/xtc/trrlib.pxd' 2024-06-25T19:34:07,389 adding 'moleculekit/fileformats/xtc/xdrlib.pxd' 2024-06-25T19:34:07,479 adding 'moleculekit/fileformats/xtc/xtc.cpp' 2024-06-25T19:34:07,488 adding 'moleculekit/fileformats/xtc/xtc.pyx' 2024-06-25T19:34:07,489 adding 'moleculekit/fileformats/xtc/xtclib.pxd' 2024-06-25T19:34:07,492 adding 'moleculekit/fileformats/xtc/include/trr_header.h' 2024-06-25T19:34:07,493 adding 'moleculekit/fileformats/xtc/include/xdr_seek.h' 2024-06-25T19:34:07,496 adding 'moleculekit/fileformats/xtc/include/xdrfile.h' 2024-06-25T19:34:07,497 adding 'moleculekit/fileformats/xtc/include/xdrfile_trr.h' 2024-06-25T19:34:07,498 adding 'moleculekit/fileformats/xtc/include/xdrfile_xtc.h' 2024-06-25T19:34:07,500 adding 'moleculekit/fileformats/xtc/include/xtc.h' 2024-06-25T19:34:07,502 adding 'moleculekit/fileformats/xtc/src/xdr_seek.c' 2024-06-25T19:34:07,508 adding 'moleculekit/fileformats/xtc/src/xdrfile.cpp' 2024-06-25T19:34:07,511 adding 'moleculekit/fileformats/xtc/src/xdrfile_trr.c' 2024-06-25T19:34:07,512 adding 'moleculekit/fileformats/xtc/src/xdrfile_xtc.cpp' 2024-06-25T19:34:07,514 adding 'moleculekit/fileformats/xtc/src/xtc.cpp' 2024-06-25T19:34:07,517 adding 'moleculekit/interactions/__init__.py' 2024-06-25T19:34:07,801 adding 'moleculekit/interactions/cationpi.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:08,072 adding 'moleculekit/interactions/hbonds.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:08,084 adding 'moleculekit/interactions/interactions.py' 2024-06-25T19:34:08,367 adding 'moleculekit/interactions/pipi.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:08,656 adding 'moleculekit/interactions/sigmahole.cpython-39-arm-linux-gnueabihf.so' 2024-06-25T19:34:08,758 adding 'moleculekit/interactions/cationpi/cationpi.cpp' 2024-06-25T19:34:08,767 adding 'moleculekit/interactions/cationpi/cationpi.pyx' 2024-06-25T19:34:08,860 adding 'moleculekit/interactions/hbonds/hbonds.cpp' 2024-06-25T19:34:08,869 adding 'moleculekit/interactions/hbonds/hbonds.pyx' 2024-06-25T19:34:08,962 adding 'moleculekit/interactions/pipi/pipi.cpp' 2024-06-25T19:34:08,972 adding 'moleculekit/interactions/pipi/pipi.pyx' 2024-06-25T19:34:09,065 adding 'moleculekit/interactions/sigmahole/sigmahole.cpp' 2024-06-25T19:34:09,075 adding 'moleculekit/interactions/sigmahole/sigmahole.pyx' 2024-06-25T19:34:09,165 adding 'moleculekit/occupancy_utils/occupancy_utils.cpp' 2024-06-25T19:34:09,174 adding 'moleculekit/occupancy_utils/occupancy_utils.pyx' 2024-06-25T19:34:09,175 adding 'moleculekit/pdbx/__init__.py' 2024-06-25T19:34:09,179 adding 'moleculekit/pdbx/reader/PdbxContainers.py' 2024-06-25T19:34:09,182 adding 'moleculekit/pdbx/reader/PdbxParser.py' 2024-06-25T19:34:09,184 adding 'moleculekit/pdbx/reader/PdbxReader.py' 2024-06-25T19:34:09,185 adding 'moleculekit/pdbx/reader/__init__.py' 2024-06-25T19:34:09,187 adding 'moleculekit/pdbx/tests/PdbxReadWriteTests.py' 2024-06-25T19:34:09,189 adding 'moleculekit/pdbx/tests/PdbxReaderTests.py' 2024-06-25T19:34:09,190 adding 'moleculekit/pdbx/tests/PdbxWriterTests.py' 2024-06-25T19:34:09,192 adding 'moleculekit/pdbx/tests/__init__.py' 2024-06-25T19:34:09,194 adding 'moleculekit/pdbx/writer/PdbxWriter.py' 2024-06-25T19:34:09,195 adding 'moleculekit/pdbx/writer/__init__.py' 2024-06-25T19:34:09,197 adding 'moleculekit/ply/__init__.py' 2024-06-25T19:34:09,201 adding 'moleculekit/ply/lex.py' 2024-06-25T19:34:09,213 adding 'moleculekit/ply/yacc.py' 2024-06-25T19:34:09,215 adding 'moleculekit/projections/__init__.py' 2024-06-25T19:34:09,217 adding 'moleculekit/projections/metriccoordinate.py' 2024-06-25T19:34:09,221 adding 'moleculekit/projections/metricdihedral.py' 2024-06-25T19:34:09,225 adding 'moleculekit/projections/metricdistance.py' 2024-06-25T19:34:09,227 adding 'moleculekit/projections/metricfluctuation.py' 2024-06-25T19:34:09,228 adding 'moleculekit/projections/metricgyration.py' 2024-06-25T19:34:09,232 adding 'moleculekit/projections/metricplumed2.py' 2024-06-25T19:34:09,234 adding 'moleculekit/projections/metricrmsd.py' 2024-06-25T19:34:09,236 adding 'moleculekit/projections/metricsasa.py' 2024-06-25T19:34:09,238 adding 'moleculekit/projections/metricsecondarystructure.py' 2024-06-25T19:34:09,240 adding 'moleculekit/projections/metricshell.py' 2024-06-25T19:34:09,241 adding 'moleculekit/projections/metricsphericalcoordinate.py' 2024-06-25T19:34:09,243 adding 'moleculekit/projections/metrictmscore.py' 2024-06-25T19:34:09,244 adding 'moleculekit/projections/projection.py' 2024-06-25T19:34:09,246 adding 'moleculekit/projections/util.py' 2024-06-25T19:34:09,248 adding 'moleculekit/share/ALA.cif' 2024-06-25T19:34:09,249 adding 'moleculekit/share/backbone.cif' 2024-06-25T19:34:10,556 adding 'moleculekit/share/opm_sequences.json' 2024-06-25T19:34:10,641 adding 'moleculekit/share/atomselect/atomselect.json' 2024-06-25T19:34:10,646 adding 'moleculekit/share/pdb2pqr/residues/.gitkeep' 2024-06-25T19:34:10,647 adding 'moleculekit/share/pdb2pqr/residues/004.dat' 2024-06-25T19:34:10,648 adding 'moleculekit/share/pdb2pqr/residues/004.xml' 2024-06-25T19:34:10,649 adding 'moleculekit/share/pdb2pqr/residues/03Y.dat' 2024-06-25T19:34:10,651 adding 'moleculekit/share/pdb2pqr/residues/03Y.xml' 2024-06-25T19:34:10,652 adding 'moleculekit/share/pdb2pqr/residues/0A1.dat' 2024-06-25T19:34:10,653 adding 'moleculekit/share/pdb2pqr/residues/0A1.xml' 2024-06-25T19:34:10,654 adding 'moleculekit/share/pdb2pqr/residues/0AF.dat' 2024-06-25T19:34:10,656 adding 'moleculekit/share/pdb2pqr/residues/0AF.xml' 2024-06-25T19:34:10,657 adding 'moleculekit/share/pdb2pqr/residues/0BN.dat' 2024-06-25T19:34:10,658 adding 'moleculekit/share/pdb2pqr/residues/0BN.xml' 2024-06-25T19:34:10,659 adding 'moleculekit/share/pdb2pqr/residues/1MH.dat' 2024-06-25T19:34:10,661 adding 'moleculekit/share/pdb2pqr/residues/1MH.xml' 2024-06-25T19:34:10,662 adding 'moleculekit/share/pdb2pqr/residues/2AS.dat' 2024-06-25T19:34:10,663 adding 'moleculekit/share/pdb2pqr/residues/2AS.xml' 2024-06-25T19:34:10,664 adding 'moleculekit/share/pdb2pqr/residues/2GX.dat' 2024-06-25T19:34:10,665 adding 'moleculekit/share/pdb2pqr/residues/2GX.xml' 2024-06-25T19:34:10,667 adding 'moleculekit/share/pdb2pqr/residues/2ML.dat' 2024-06-25T19:34:10,668 adding 'moleculekit/share/pdb2pqr/residues/2ML.xml' 2024-06-25T19:34:10,669 adding 'moleculekit/share/pdb2pqr/residues/2MR.dat' 2024-06-25T19:34:10,670 adding 'moleculekit/share/pdb2pqr/residues/2MR.xml' 2024-06-25T19:34:10,672 adding 'moleculekit/share/pdb2pqr/residues/4IN.dat' 2024-06-25T19:34:10,673 adding 'moleculekit/share/pdb2pqr/residues/4IN.xml' 2024-06-25T19:34:10,674 adding 'moleculekit/share/pdb2pqr/residues/4PH.dat' 2024-06-25T19:34:10,675 adding 'moleculekit/share/pdb2pqr/residues/4PH.xml' 2024-06-25T19:34:10,677 adding 'moleculekit/share/pdb2pqr/residues/4PQ.dat' 2024-06-25T19:34:10,678 adding 'moleculekit/share/pdb2pqr/residues/4PQ.xml' 2024-06-25T19:34:10,679 adding 'moleculekit/share/pdb2pqr/residues/5JP.dat' 2024-06-25T19:34:10,680 adding 'moleculekit/share/pdb2pqr/residues/5JP.xml' 2024-06-25T19:34:10,681 adding 'moleculekit/share/pdb2pqr/residues/AA4.dat' 2024-06-25T19:34:10,683 adding 'moleculekit/share/pdb2pqr/residues/AA4.xml' 2024-06-25T19:34:10,684 adding 'moleculekit/share/pdb2pqr/residues/ABA.dat' 2024-06-25T19:34:10,685 adding 'moleculekit/share/pdb2pqr/residues/ABA.xml' 2024-06-25T19:34:10,686 adding 'moleculekit/share/pdb2pqr/residues/AHP.dat' 2024-06-25T19:34:10,687 adding 'moleculekit/share/pdb2pqr/residues/AHP.xml' 2024-06-25T19:34:10,689 adding 'moleculekit/share/pdb2pqr/residues/ALC.dat' 2024-06-25T19:34:10,690 adding 'moleculekit/share/pdb2pqr/residues/ALC.xml' 2024-06-25T19:34:10,691 adding 'moleculekit/share/pdb2pqr/residues/ALN.dat' 2024-06-25T19:34:10,693 adding 'moleculekit/share/pdb2pqr/residues/ALN.xml' 2024-06-25T19:34:10,694 adding 'moleculekit/share/pdb2pqr/residues/ALY.dat' 2024-06-25T19:34:10,695 adding 'moleculekit/share/pdb2pqr/residues/ALY.xml' 2024-06-25T19:34:10,696 adding 'moleculekit/share/pdb2pqr/residues/APD.dat' 2024-06-25T19:34:10,698 adding 'moleculekit/share/pdb2pqr/residues/APD.xml' 2024-06-25T19:34:10,699 adding 'moleculekit/share/pdb2pqr/residues/BB8.dat' 2024-06-25T19:34:10,700 adding 'moleculekit/share/pdb2pqr/residues/BB8.xml' 2024-06-25T19:34:10,701 adding 'moleculekit/share/pdb2pqr/residues/BCS.dat' 2024-06-25T19:34:10,702 adding 'moleculekit/share/pdb2pqr/residues/BCS.xml' 2024-06-25T19:34:10,704 adding 'moleculekit/share/pdb2pqr/residues/BTK.dat' 2024-06-25T19:34:10,705 adding 'moleculekit/share/pdb2pqr/residues/BTK.xml' 2024-06-25T19:34:10,706 adding 'moleculekit/share/pdb2pqr/residues/CCS.dat' 2024-06-25T19:34:10,707 adding 'moleculekit/share/pdb2pqr/residues/CCS.xml' 2024-06-25T19:34:10,709 adding 'moleculekit/share/pdb2pqr/residues/CGU.dat' 2024-06-25T19:34:10,710 adding 'moleculekit/share/pdb2pqr/residues/CGU.xml' 2024-06-25T19:34:10,711 adding 'moleculekit/share/pdb2pqr/residues/CSA.dat' 2024-06-25T19:34:10,712 adding 'moleculekit/share/pdb2pqr/residues/CSA.xml' 2024-06-25T19:34:10,713 adding 'moleculekit/share/pdb2pqr/residues/CSO.dat' 2024-06-25T19:34:10,715 adding 'moleculekit/share/pdb2pqr/residues/CSO.xml' 2024-06-25T19:34:10,716 adding 'moleculekit/share/pdb2pqr/residues/CSP.dat' 2024-06-25T19:34:10,717 adding 'moleculekit/share/pdb2pqr/residues/CSP.xml' 2024-06-25T19:34:10,718 adding 'moleculekit/share/pdb2pqr/residues/CSS.dat' 2024-06-25T19:34:10,719 adding 'moleculekit/share/pdb2pqr/residues/CSS.xml' 2024-06-25T19:34:10,721 adding 'moleculekit/share/pdb2pqr/residues/D4P.dat' 2024-06-25T19:34:10,722 adding 'moleculekit/share/pdb2pqr/residues/D4P.xml' 2024-06-25T19:34:10,723 adding 'moleculekit/share/pdb2pqr/residues/DA2.dat' 2024-06-25T19:34:10,724 adding 'moleculekit/share/pdb2pqr/residues/DA2.xml' 2024-06-25T19:34:10,726 adding 'moleculekit/share/pdb2pqr/residues/DAB.dat' 2024-06-25T19:34:10,727 adding 'moleculekit/share/pdb2pqr/residues/DAB.xml' 2024-06-25T19:34:10,728 adding 'moleculekit/share/pdb2pqr/residues/DAH.dat' 2024-06-25T19:34:10,729 adding 'moleculekit/share/pdb2pqr/residues/DAH.xml' 2024-06-25T19:34:10,730 adding 'moleculekit/share/pdb2pqr/residues/DPP.dat' 2024-06-25T19:34:10,732 adding 'moleculekit/share/pdb2pqr/residues/DPP.xml' 2024-06-25T19:34:10,733 adding 'moleculekit/share/pdb2pqr/residues/ESC.dat' 2024-06-25T19:34:10,734 adding 'moleculekit/share/pdb2pqr/residues/ESC.xml' 2024-06-25T19:34:10,735 adding 'moleculekit/share/pdb2pqr/residues/FGL.dat' 2024-06-25T19:34:10,736 adding 'moleculekit/share/pdb2pqr/residues/FGL.xml' 2024-06-25T19:34:10,738 adding 'moleculekit/share/pdb2pqr/residues/GHG.dat' 2024-06-25T19:34:10,739 adding 'moleculekit/share/pdb2pqr/residues/GHG.xml' 2024-06-25T19:34:10,740 adding 'moleculekit/share/pdb2pqr/residues/GME.dat' 2024-06-25T19:34:10,741 adding 'moleculekit/share/pdb2pqr/residues/GME.xml' 2024-06-25T19:34:10,742 adding 'moleculekit/share/pdb2pqr/residues/GNC.dat' 2024-06-25T19:34:10,744 adding 'moleculekit/share/pdb2pqr/residues/GNC.xml' 2024-06-25T19:34:10,745 adding 'moleculekit/share/pdb2pqr/residues/HHK.dat' 2024-06-25T19:34:10,746 adding 'moleculekit/share/pdb2pqr/residues/HHK.xml' 2024-06-25T19:34:10,747 adding 'moleculekit/share/pdb2pqr/residues/HLU.dat' 2024-06-25T19:34:10,749 adding 'moleculekit/share/pdb2pqr/residues/HLU.xml' 2024-06-25T19:34:10,750 adding 'moleculekit/share/pdb2pqr/residues/HLX.dat' 2024-06-25T19:34:10,751 adding 'moleculekit/share/pdb2pqr/residues/HLX.xml' 2024-06-25T19:34:10,753 adding 'moleculekit/share/pdb2pqr/residues/HOX.dat' 2024-06-25T19:34:10,754 adding 'moleculekit/share/pdb2pqr/residues/HOX.xml' 2024-06-25T19:34:10,755 adding 'moleculekit/share/pdb2pqr/residues/HPE.dat' 2024-06-25T19:34:10,756 adding 'moleculekit/share/pdb2pqr/residues/HPE.xml' 2024-06-25T19:34:10,757 adding 'moleculekit/share/pdb2pqr/residues/HQA.dat' 2024-06-25T19:34:10,759 adding 'moleculekit/share/pdb2pqr/residues/HQA.xml' 2024-06-25T19:34:10,760 adding 'moleculekit/share/pdb2pqr/residues/HTR.dat' 2024-06-25T19:34:10,761 adding 'moleculekit/share/pdb2pqr/residues/HTR.xml' 2024-06-25T19:34:10,762 adding 'moleculekit/share/pdb2pqr/residues/HYP.dat' 2024-06-25T19:34:10,764 adding 'moleculekit/share/pdb2pqr/residues/HYP.xml' 2024-06-25T19:34:10,765 adding 'moleculekit/share/pdb2pqr/residues/I2M.dat' 2024-06-25T19:34:10,766 adding 'moleculekit/share/pdb2pqr/residues/I2M.xml' 2024-06-25T19:34:10,767 adding 'moleculekit/share/pdb2pqr/residues/IGL.dat' 2024-06-25T19:34:10,769 adding 'moleculekit/share/pdb2pqr/residues/IGL.xml' 2024-06-25T19:34:10,770 adding 'moleculekit/share/pdb2pqr/residues/IIL.dat' 2024-06-25T19:34:10,771 adding 'moleculekit/share/pdb2pqr/residues/IIL.xml' 2024-06-25T19:34:10,772 adding 'moleculekit/share/pdb2pqr/residues/IML.dat' 2024-06-25T19:34:10,774 adding 'moleculekit/share/pdb2pqr/residues/IML.xml' 2024-06-25T19:34:10,775 adding 'moleculekit/share/pdb2pqr/residues/KYN.dat' 2024-06-25T19:34:10,776 adding 'moleculekit/share/pdb2pqr/residues/KYN.xml' 2024-06-25T19:34:10,777 adding 'moleculekit/share/pdb2pqr/residues/LME.dat' 2024-06-25T19:34:10,778 adding 'moleculekit/share/pdb2pqr/residues/LME.xml' 2024-06-25T19:34:10,779 adding 'moleculekit/share/pdb2pqr/residues/LMQ.dat' 2024-06-25T19:34:10,781 adding 'moleculekit/share/pdb2pqr/residues/LMQ.xml' 2024-06-25T19:34:10,782 adding 'moleculekit/share/pdb2pqr/residues/LYZ.dat' 2024-06-25T19:34:10,783 adding 'moleculekit/share/pdb2pqr/residues/LYZ.xml' 2024-06-25T19:34:10,785 adding 'moleculekit/share/pdb2pqr/residues/M3L.dat' 2024-06-25T19:34:10,786 adding 'moleculekit/share/pdb2pqr/residues/M3L.xml' 2024-06-25T19:34:10,787 adding 'moleculekit/share/pdb2pqr/residues/ME0.dat' 2024-06-25T19:34:10,788 adding 'moleculekit/share/pdb2pqr/residues/ME0.xml' 2024-06-25T19:34:10,790 adding 'moleculekit/share/pdb2pqr/residues/MEA.dat' 2024-06-25T19:34:10,791 adding 'moleculekit/share/pdb2pqr/residues/MEA.xml' 2024-06-25T19:34:10,792 adding 'moleculekit/share/pdb2pqr/residues/MEN.dat' 2024-06-25T19:34:10,793 adding 'moleculekit/share/pdb2pqr/residues/MEN.xml' 2024-06-25T19:34:10,794 adding 'moleculekit/share/pdb2pqr/residues/MEQ.dat' 2024-06-25T19:34:10,796 adding 'moleculekit/share/pdb2pqr/residues/MEQ.xml' 2024-06-25T19:34:10,797 adding 'moleculekit/share/pdb2pqr/residues/MLE.dat' 2024-06-25T19:34:10,798 adding 'moleculekit/share/pdb2pqr/residues/MLE.xml' 2024-06-25T19:34:10,799 adding 'moleculekit/share/pdb2pqr/residues/MLY.dat' 2024-06-25T19:34:10,801 adding 'moleculekit/share/pdb2pqr/residues/MLY.xml' 2024-06-25T19:34:10,802 adding 'moleculekit/share/pdb2pqr/residues/MLZ.dat' 2024-06-25T19:34:10,803 adding 'moleculekit/share/pdb2pqr/residues/MLZ.xml' 2024-06-25T19:34:10,804 adding 'moleculekit/share/pdb2pqr/residues/MME.dat' 2024-06-25T19:34:10,806 adding 'moleculekit/share/pdb2pqr/residues/MME.xml' 2024-06-25T19:34:10,807 adding 'moleculekit/share/pdb2pqr/residues/MMO.dat' 2024-06-25T19:34:10,808 adding 'moleculekit/share/pdb2pqr/residues/MMO.xml' 2024-06-25T19:34:10,809 adding 'moleculekit/share/pdb2pqr/residues/MVA.dat' 2024-06-25T19:34:10,810 adding 'moleculekit/share/pdb2pqr/residues/MVA.xml' 2024-06-25T19:34:10,812 adding 'moleculekit/share/pdb2pqr/residues/NAL.dat' 2024-06-25T19:34:10,813 adding 'moleculekit/share/pdb2pqr/residues/NAL.xml' 2024-06-25T19:34:10,814 adding 'moleculekit/share/pdb2pqr/residues/NCY.dat' 2024-06-25T19:34:10,815 adding 'moleculekit/share/pdb2pqr/residues/NCY.xml' 2024-06-25T19:34:10,817 adding 'moleculekit/share/pdb2pqr/residues/NLE.dat' 2024-06-25T19:34:10,818 adding 'moleculekit/share/pdb2pqr/residues/NLE.xml' 2024-06-25T19:34:10,819 adding 'moleculekit/share/pdb2pqr/residues/NVA.dat' 2024-06-25T19:34:10,820 adding 'moleculekit/share/pdb2pqr/residues/NVA.xml' 2024-06-25T19:34:10,822 adding 'moleculekit/share/pdb2pqr/residues/NZC.dat' 2024-06-25T19:34:10,823 adding 'moleculekit/share/pdb2pqr/residues/NZC.xml' 2024-06-25T19:34:10,824 adding 'moleculekit/share/pdb2pqr/residues/OCY.dat' 2024-06-25T19:34:10,825 adding 'moleculekit/share/pdb2pqr/residues/OCY.xml' 2024-06-25T19:34:10,826 adding 'moleculekit/share/pdb2pqr/residues/OMX.dat' 2024-06-25T19:34:10,828 adding 'moleculekit/share/pdb2pqr/residues/OMX.xml' 2024-06-25T19:34:10,829 adding 'moleculekit/share/pdb2pqr/residues/ONL.dat' 2024-06-25T19:34:10,830 adding 'moleculekit/share/pdb2pqr/residues/ONL.xml' 2024-06-25T19:34:10,831 adding 'moleculekit/share/pdb2pqr/residues/ORM.dat' 2024-06-25T19:34:10,832 adding 'moleculekit/share/pdb2pqr/residues/ORM.xml' 2024-06-25T19:34:10,834 adding 'moleculekit/share/pdb2pqr/residues/P1L.dat' 2024-06-25T19:34:10,835 adding 'moleculekit/share/pdb2pqr/residues/P1L.xml' 2024-06-25T19:34:10,836 adding 'moleculekit/share/pdb2pqr/residues/PCA.dat' 2024-06-25T19:34:10,838 adding 'moleculekit/share/pdb2pqr/residues/PCA.xml' 2024-06-25T19:34:10,839 adding 'moleculekit/share/pdb2pqr/residues/PRK.dat' 2024-06-25T19:34:10,840 adding 'moleculekit/share/pdb2pqr/residues/PRK.xml' 2024-06-25T19:34:10,841 adding 'moleculekit/share/pdb2pqr/residues/PTR.dat' 2024-06-25T19:34:10,843 adding 'moleculekit/share/pdb2pqr/residues/PTR.xml' 2024-06-25T19:34:10,844 adding 'moleculekit/share/pdb2pqr/residues/SEP.dat' 2024-06-25T19:34:10,845 adding 'moleculekit/share/pdb2pqr/residues/SEP.xml' 2024-06-25T19:34:10,846 adding 'moleculekit/share/pdb2pqr/residues/TPO.dat' 2024-06-25T19:34:10,847 adding 'moleculekit/share/pdb2pqr/residues/TPO.xml' 2024-06-25T19:34:10,849 adding 'moleculekit/share/pdb2pqr/residues/TRO.dat' 2024-06-25T19:34:10,850 adding 'moleculekit/share/pdb2pqr/residues/TRO.xml' 2024-06-25T19:34:10,851 adding 'moleculekit/share/pdb2pqr/residues/TY2.dat' 2024-06-25T19:34:10,852 adding 'moleculekit/share/pdb2pqr/residues/TY2.xml' 2024-06-25T19:34:10,854 adding 'moleculekit/share/pdb2pqr/residues/TYQ.dat' 2024-06-25T19:34:10,855 adding 'moleculekit/share/pdb2pqr/residues/TYQ.xml' 2024-06-25T19:34:10,856 adding 'moleculekit/share/pdb2pqr/residues/YCM.dat' 2024-06-25T19:34:10,857 adding 'moleculekit/share/pdb2pqr/residues/YCM.xml' 2024-06-25T19:34:10,858 adding 'moleculekit/share/pdb2pqr/residues/YNM.dat' 2024-06-25T19:34:10,860 adding 'moleculekit/share/pdb2pqr/residues/YNM.xml' 2024-06-25T19:34:10,862 adding 'moleculekit/smallmol/__init__.py' 2024-06-25T19:34:10,867 adding 'moleculekit/smallmol/smallmol.py' 2024-06-25T19:34:10,869 adding 'moleculekit/smallmol/smallmolcdp.py' 2024-06-25T19:34:10,871 adding 'moleculekit/smallmol/smallmollib.py' 2024-06-25T19:34:10,873 adding 'moleculekit/smallmol/test_smallmol.py' 2024-06-25T19:34:10,874 adding 'moleculekit/smallmol/test_smallmollib.py' 2024-06-25T19:34:10,876 adding 'moleculekit/smallmol/util.py' 2024-06-25T19:34:10,878 adding 'moleculekit/smallmol/tools/__init__.py' 2024-06-25T19:34:10,880 adding 'moleculekit/smallmol/tools/clustering.py' 2024-06-25T19:34:10,881 adding 'moleculekit/smallmol/tools/restrainedembed.py' 2024-06-25T19:34:10,883 adding 'moleculekit/smallmol/tools/test_tools.py' 2024-06-25T19:34:10,974 adding 'moleculekit/tmalign/tmalign_util.cpp' 2024-06-25T19:34:10,983 adding 'moleculekit/tmalign/tmalign_util.pyx' 2024-06-25T19:34:10,984 adding 'moleculekit/tmalign/tmalignlib.pxd' 2024-06-25T19:34:10,986 adding 'moleculekit/tmalign/include/TMAlign.h' 2024-06-25T19:34:11,003 adding 'moleculekit/tmalign/src/TMAlign.cpp' 2024-06-25T19:34:11,006 adding 'moleculekit/tools/__init__.py' 2024-06-25T19:34:11,009 adding 'moleculekit/tools/atomtyper.py' 2024-06-25T19:34:11,011 adding 'moleculekit/tools/autosegment.py' 2024-06-25T19:34:11,013 adding 'moleculekit/tools/crystalpacking.py' 2024-06-25T19:34:11,016 adding 'moleculekit/tools/detect.py' 2024-06-25T19:34:11,018 adding 'moleculekit/tools/docking.py' 2024-06-25T19:34:11,020 adding 'moleculekit/tools/graphalignment.py' 2024-06-25T19:34:11,022 adding 'moleculekit/tools/hhblitsprofile.py' 2024-06-25T19:34:11,023 adding 'moleculekit/tools/modelling.py' 2024-06-25T19:34:11,025 adding 'moleculekit/tools/moleculechecks.py' 2024-06-25T19:34:11,031 adding 'moleculekit/tools/preparation.py' 2024-06-25T19:34:11,034 adding 'moleculekit/tools/preparation_customres.py' 2024-06-25T19:34:11,036 adding 'moleculekit/tools/sequencestructuralalignment.py' 2024-06-25T19:34:11,039 adding 'moleculekit/tools/voxeldescriptors.py' 2024-06-25T19:34:11,041 adding 'moleculekit/tools/obabel_tools/__init__.py' 2024-06-25T19:34:11,042 adding 'moleculekit/tools/obabel_tools/obabel_cli.py' 2024-06-25T19:34:11,135 adding 'moleculekit/wrapping/wrapping.cpp' 2024-06-25T19:34:11,145 adding 'moleculekit/wrapping/wrapping.pyx' 2024-06-25T19:34:11,147 adding 'moleculekit-1.8.35.dist-info/LICENSE' 2024-06-25T19:34:11,148 adding 'moleculekit-1.8.35.dist-info/METADATA' 2024-06-25T19:34:11,149 adding 'moleculekit-1.8.35.dist-info/WHEEL' 2024-06-25T19:34:11,150 adding 'moleculekit-1.8.35.dist-info/top_level.txt' 2024-06-25T19:34:11,156 adding 'moleculekit-1.8.35.dist-info/RECORD' 2024-06-25T19:34:11,308 removing build/bdist.linux-armv7l/wheel 2024-06-25T19:34:11,584 Building wheel for moleculekit (pyproject.toml): finished with status 'done' 2024-06-25T19:34:11,943 Created wheel for moleculekit: filename=moleculekit-1.8.35-cp39-cp39-linux_armv7l.whl size=14926482 sha256=bc4488b38699175360d9d00251d83750b68be24b494759299c9703344259af9a 2024-06-25T19:34:11,944 Stored in directory: /tmp/pip-ephem-wheel-cache-8tfom4rk/wheels/6e/f2/90/4a99840f4b4ab8e8bbe9f87a5b313dc1e89196b3d64bb45f4a 2024-06-25T19:34:11,971 Successfully built moleculekit 2024-06-25T19:34:12,346 Removed build tracker: '/tmp/pip-build-tracker-i2at1th5'