2024-05-30T19:38:06,646 Created temporary directory: /tmp/pip-build-tracker-favj_vbk 2024-05-30T19:38:06,648 Initialized build tracking at /tmp/pip-build-tracker-favj_vbk 2024-05-30T19:38:06,648 Created build tracker: /tmp/pip-build-tracker-favj_vbk 2024-05-30T19:38:06,648 Entered build tracker: /tmp/pip-build-tracker-favj_vbk 2024-05-30T19:38:06,649 Created temporary directory: /tmp/pip-wheel-w9310ffg 2024-05-30T19:38:06,653 Created temporary directory: /tmp/pip-ephem-wheel-cache-s0g1y5jk 2024-05-30T19:38:06,676 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-30T19:38:06,680 2 location(s) to search for versions of pyjess: 2024-05-30T19:38:06,680 * https://pypi.org/simple/pyjess/ 2024-05-30T19:38:06,680 * https://www.piwheels.org/simple/pyjess/ 2024-05-30T19:38:06,680 Fetching project page and analyzing links: https://pypi.org/simple/pyjess/ 2024-05-30T19:38:06,681 Getting page https://pypi.org/simple/pyjess/ 2024-05-30T19:38:06,682 Found index url https://pypi.org/simple/ 2024-05-30T19:38:06,735 Fetched page https://pypi.org/simple/pyjess/ as application/vnd.pypi.simple.v1+json 2024-05-30T19:38:06,763 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/f7/30/5e78014d6334257c5769c3404317240f3b33109c3bf0763e2c6846a636af/pyjess-0.1.0-cp310-cp310-macosx_10_12_x86_64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,763 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/4b/a1/ae3808dd9d957f1c67d915fb46ca8979c5387cb7528b1f31c2d4b53de9a5/pyjess-0.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,763 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/9b/8d/15b77c22301389b8b8dcf96ce0ac0f9b0ca9b664bd0426da4bca35a11929/pyjess-0.1.0-cp310-cp310-win_amd64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,763 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/b9/ab/fb9fa464e8d1352a4b11eab0c426a4a33e79f0cb2a7eaa78a052dfa49af5/pyjess-0.1.0-cp311-cp311-macosx_10_12_x86_64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,764 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/c8/6b/e041f9e89157bcf9d01b0e39c12e88e7e6d50b096011e1481f135c71c33a/pyjess-0.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,764 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/5c/1d/3eb3effb9d0b17c5c59cd2b375279251172e95c7b3d6528ab0611b6d748f/pyjess-0.1.0-cp311-cp311-win_amd64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,764 Skipping link: No binaries permitted for pyjess: 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https://files.pythonhosted.org/packages/ff/a9/46445ed8d4c24389b030f60aa0a7ffbccf0fab1b923a21e299920414c2de/pyjess-0.1.0-cp37-cp37m-macosx_10_12_x86_64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,765 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/ab/3d/172e67e4558ef57e7a2dbc32b7fbd4dd52318abde858df216e20ed60ffd6/pyjess-0.1.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,766 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/a2/e7/f678f6c53042afc3d82b1bb9e30500057b77ba535b86890b9e45f970c0bd/pyjess-0.1.0-cp37-cp37m-win_amd64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,766 Skipping link: No binaries permitted for pyjess: 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No binaries permitted for pyjess: https://files.pythonhosted.org/packages/29/81/37698e83c2dce41587a91b147bc30ce2f477a6be35f13a690cc12c071c65/pyjess-0.1.1-cp311-cp311-macosx_10_12_x86_64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,771 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/92/45/f7f8a1ed0ba5382f5585d48bf58526eeb8420f3ec2a3e881c73ec06bb0f9/pyjess-0.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,771 Skipping link: No binaries permitted for pyjess: https://files.pythonhosted.org/packages/6b/88/136ee209f710392529318f9cc6c57ce82d3759a7b4aa561fadf907913b9a/pyjess-0.1.1-cp311-cp311-win_amd64.whl (from https://pypi.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,771 Skipping link: No binaries permitted for pyjess: 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https://www.piwheels.org/simple/pyjess/pyjess-0.1.1-cp39-cp39-linux_armv6l.whl#sha256=fad8b8d6b9fc0e97b8f4e3b3a415848eccd46d20e48c6f8115fb31d8a57c7feb (from https://www.piwheels.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,870 Skipping link: No binaries permitted for pyjess: https://www.piwheels.org/simple/pyjess/pyjess-0.1.1-cp39-cp39-linux_armv7l.whl#sha256=fad8b8d6b9fc0e97b8f4e3b3a415848eccd46d20e48c6f8115fb31d8a57c7feb (from https://www.piwheels.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,870 Skipping link: No binaries permitted for pyjess: https://www.piwheels.org/simple/pyjess/pyjess-0.1.0-cp311-cp311-linux_armv6l.whl#sha256=13f5fa70d82a5119953407d64045630eb94daa1235e792dacb3d24645a3d9927 (from https://www.piwheels.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,870 Skipping link: No binaries permitted for pyjess: https://www.piwheels.org/simple/pyjess/pyjess-0.1.0-cp311-cp311-linux_armv7l.whl#sha256=13f5fa70d82a5119953407d64045630eb94daa1235e792dacb3d24645a3d9927 (from https://www.piwheels.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,871 Skipping link: No binaries permitted for pyjess: https://www.piwheels.org/simple/pyjess/pyjess-0.1.0-cp37-cp37m-linux_armv6l.whl#sha256=2986707bf88e6fd7d09c9e0d646da94bc3c6c6ee931b1281e4a0efd94a2a614c (from https://www.piwheels.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,871 Skipping link: No binaries permitted for pyjess: https://www.piwheels.org/simple/pyjess/pyjess-0.1.0-cp37-cp37m-linux_armv7l.whl#sha256=2986707bf88e6fd7d09c9e0d646da94bc3c6c6ee931b1281e4a0efd94a2a614c (from https://www.piwheels.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,871 Skipping link: No binaries permitted for pyjess: https://www.piwheels.org/simple/pyjess/pyjess-0.1.0-cp39-cp39-linux_armv6l.whl#sha256=7b40916b8bd3ea61ed8dbb6a4618b9d67b3691d69e88bb9f633600b8d24a6e9c (from https://www.piwheels.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,871 Skipping link: No binaries permitted for pyjess: https://www.piwheels.org/simple/pyjess/pyjess-0.1.0-cp39-cp39-linux_armv7l.whl#sha256=7b40916b8bd3ea61ed8dbb6a4618b9d67b3691d69e88bb9f633600b8d24a6e9c (from https://www.piwheels.org/simple/pyjess/) (requires-python:>=3.5) 2024-05-30T19:38:06,871 Skipping link: not a file: https://www.piwheels.org/simple/pyjess/ 2024-05-30T19:38:06,872 Skipping link: not a file: https://pypi.org/simple/pyjess/ 2024-05-30T19:38:06,888 Given no hashes to check 1 links for project 'pyjess': discarding no candidates 2024-05-30T19:38:06,903 Collecting pyjess==0.2.1 2024-05-30T19:38:06,906 Created temporary directory: /tmp/pip-unpack-2mjphuz8 2024-05-30T19:38:06,949 Downloading pyjess-0.2.1.tar.gz (212 kB) 2024-05-30T19:38:07,160 Added pyjess==0.2.1 from https://files.pythonhosted.org/packages/b4/9c/ab552993cde0526b2f3a7b6b577a60aab372f71f69c8a590edc1190e4736/pyjess-0.2.1.tar.gz to build tracker '/tmp/pip-build-tracker-favj_vbk' 2024-05-30T19:38:07,165 Created temporary directory: /tmp/pip-build-env-giyo1t8b 2024-05-30T19:38:07,175 Installing build dependencies: started 2024-05-30T19:38:07,176 Running command pip subprocess to install build dependencies 2024-05-30T19:38:08,938 Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2024-05-30T19:38:10,454 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-30T19:38:13,512 Collecting setuptools>=46.4 2024-05-30T19:38:13,677 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.0.0-py3-none-any.whl (863 kB) 2024-05-30T19:38:15,059 Collecting cython~=3.0 2024-05-30T19:38:15,099 Using cached https://www.piwheels.org/simple/cython/Cython-3.0.10-cp39-cp39-linux_armv7l.whl (10.7 MB) 2024-05-30T19:38:17,122 Installing collected packages: setuptools, cython 2024-05-30T19:38:22,821 Creating /tmp/pip-build-env-giyo1t8b/overlay/bin 2024-05-30T19:38:22,823 changing mode of /tmp/pip-build-env-giyo1t8b/overlay/bin/cygdb to 755 2024-05-30T19:38:22,826 changing mode of /tmp/pip-build-env-giyo1t8b/overlay/bin/cython to 755 2024-05-30T19:38:22,828 changing mode of /tmp/pip-build-env-giyo1t8b/overlay/bin/cythonize to 755 2024-05-30T19:38:22,849 Successfully installed cython-3.0.10 setuptools-70.0.0 2024-05-30T19:38:23,397 Installing build dependencies: finished with status 'done' 2024-05-30T19:38:23,402 Getting requirements to build wheel: started 2024-05-30T19:38:23,403 Running command Getting requirements to build wheel 2024-05-30T19:38:24,391 Getting requirements to build wheel: finished with status 'done' 2024-05-30T19:38:24,411 Installing backend dependencies: started 2024-05-30T19:38:24,412 Running command pip subprocess to install backend dependencies 2024-05-30T19:38:25,566 Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2024-05-30T19:38:26,392 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-30T19:38:26,898 Collecting wheel 2024-05-30T19:38:26,913 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-05-30T19:38:28,361 Installing collected packages: wheel 2024-05-30T19:38:28,582 Creating /tmp/pip-build-env-giyo1t8b/normal/bin 2024-05-30T19:38:28,584 changing mode of /tmp/pip-build-env-giyo1t8b/normal/bin/wheel to 755 2024-05-30T19:38:28,596 Successfully installed wheel-0.43.0 2024-05-30T19:38:28,981 Installing backend dependencies: finished with status 'done' 2024-05-30T19:38:28,984 Created temporary directory: /tmp/pip-modern-metadata-iovmnu30 2024-05-30T19:38:28,986 Preparing metadata (pyproject.toml): started 2024-05-30T19:38:28,987 Running command Preparing metadata (pyproject.toml) 2024-05-30T19:38:29,883 running dist_info 2024-05-30T19:38:29,891 creating /tmp/pip-modern-metadata-iovmnu30/pyjess.egg-info 2024-05-30T19:38:29,896 writing /tmp/pip-modern-metadata-iovmnu30/pyjess.egg-info/PKG-INFO 2024-05-30T19:38:29,900 writing dependency_links to /tmp/pip-modern-metadata-iovmnu30/pyjess.egg-info/dependency_links.txt 2024-05-30T19:38:29,902 writing top-level names to /tmp/pip-modern-metadata-iovmnu30/pyjess.egg-info/top_level.txt 2024-05-30T19:38:29,904 writing manifest file '/tmp/pip-modern-metadata-iovmnu30/pyjess.egg-info/SOURCES.txt' 2024-05-30T19:38:29,931 reading manifest file '/tmp/pip-modern-metadata-iovmnu30/pyjess.egg-info/SOURCES.txt' 2024-05-30T19:38:29,934 reading manifest template 'MANIFEST.in' 2024-05-30T19:38:29,964 warning: no files found matching '*.pxi' under directory 'pyjess' 2024-05-30T19:38:29,978 warning: no files found matching '*.pxd' under directory 'pyjess' 2024-05-30T19:38:29,985 warning: no files found matching '*.h' under directory 'pyjess' 2024-05-30T19:38:30,003 warning: no files found matching 'LICENSE' under directory 'vendor/jess' 2024-05-30T19:38:30,009 warning: no files found matching 'AUTHORS' under directory 'vendor/jess' 2024-05-30T19:38:30,014 warning: no files found matching 'CHANGELOG' under directory 'vendor/jess' 2024-05-30T19:38:30,032 no previously-included directories found matching 'vendor/sword/vendor' 2024-05-30T19:38:30,052 warning: no files found matching '*.pxi' under directory 'pyjess' 2024-05-30T19:38:30,065 warning: no files found matching '*.pxd' under directory 'pyjess' 2024-05-30T19:38:30,071 warning: no files found matching '*.h' under directory 'pyjess' 2024-05-30T19:38:30,076 warning: no previously-included files matching '*.cpp' found under directory 'pyjess' 2024-05-30T19:38:30,077 warning: no previously-included files matching '*.html' found under directory 'pyjess' 2024-05-30T19:38:30,077 adding license file 'COPYING' 2024-05-30T19:38:30,082 writing manifest file '/tmp/pip-modern-metadata-iovmnu30/pyjess.egg-info/SOURCES.txt' 2024-05-30T19:38:30,083 creating '/tmp/pip-modern-metadata-iovmnu30/pyjess-0.2.1.dist-info' 2024-05-30T19:38:30,261 Preparing metadata (pyproject.toml): finished with status 'done' 2024-05-30T19:38:30,268 Source in /tmp/pip-wheel-w9310ffg/pyjess_31a120e9ea8046c28a3fb65b844a88b2 has version 0.2.1, which satisfies requirement pyjess==0.2.1 from https://files.pythonhosted.org/packages/b4/9c/ab552993cde0526b2f3a7b6b577a60aab372f71f69c8a590edc1190e4736/pyjess-0.2.1.tar.gz 2024-05-30T19:38:30,269 Removed pyjess==0.2.1 from https://files.pythonhosted.org/packages/b4/9c/ab552993cde0526b2f3a7b6b577a60aab372f71f69c8a590edc1190e4736/pyjess-0.2.1.tar.gz from build tracker '/tmp/pip-build-tracker-favj_vbk' 2024-05-30T19:38:30,275 Created temporary directory: /tmp/pip-unpack-epg0uxhw 2024-05-30T19:38:30,276 Created temporary directory: /tmp/pip-unpack-8qkhk261 2024-05-30T19:38:30,279 Building wheels for collected packages: pyjess 2024-05-30T19:38:30,283 Created temporary directory: /tmp/pip-wheel-ceh5w53t 2024-05-30T19:38:30,283 Destination directory: /tmp/pip-wheel-ceh5w53t 2024-05-30T19:38:30,285 Building wheel for pyjess (pyproject.toml): started 2024-05-30T19:38:30,286 Running command Building wheel for pyjess (pyproject.toml) 2024-05-30T19:38:31,216 running bdist_wheel 2024-05-30T19:38:31,248 running build 2024-05-30T19:38:31,249 running build_py 2024-05-30T19:38:31,257 creating build 2024-05-30T19:38:31,257 creating build/lib.linux-armv7l-cpython-39 2024-05-30T19:38:31,258 creating build/lib.linux-armv7l-cpython-39/pyjess 2024-05-30T19:38:31,259 copying pyjess/__init__.py -> build/lib.linux-armv7l-cpython-39/pyjess 2024-05-30T19:38:31,262 creating build/lib.linux-armv7l-cpython-39/pyjess/tests 2024-05-30T19:38:31,263 copying pyjess/tests/test_atom.py -> build/lib.linux-armv7l-cpython-39/pyjess/tests 2024-05-30T19:38:31,265 copying pyjess/tests/test_template_atom.py -> build/lib.linux-armv7l-cpython-39/pyjess/tests 2024-05-30T19:38:31,266 copying pyjess/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyjess/tests 2024-05-30T19:38:31,268 copying pyjess/tests/utils.py -> build/lib.linux-armv7l-cpython-39/pyjess/tests 2024-05-30T19:38:31,270 copying pyjess/tests/test_jess.py -> build/lib.linux-armv7l-cpython-39/pyjess/tests 2024-05-30T19:38:31,272 copying pyjess/tests/test_template.py -> build/lib.linux-armv7l-cpython-39/pyjess/tests 2024-05-30T19:38:31,273 copying pyjess/tests/test_molecule.py -> build/lib.linux-armv7l-cpython-39/pyjess/tests 2024-05-30T19:38:31,275 creating build/lib.linux-armv7l-cpython-39/pyjess/tests/data 2024-05-30T19:38:31,276 copying pyjess/tests/data/__init__.py -> build/lib.linux-armv7l-cpython-39/pyjess/tests/data 2024-05-30T19:38:31,281 copying pyjess/_jess.pyi -> build/lib.linux-armv7l-cpython-39/pyjess 2024-05-30T19:38:31,284 copying pyjess/py.typed -> build/lib.linux-armv7l-cpython-39/pyjess 2024-05-30T19:38:31,285 copying pyjess/tests/data/template_01.qry -> build/lib.linux-armv7l-cpython-39/pyjess/tests/data 2024-05-30T19:38:31,287 copying pyjess/tests/data/1.3.3.tpl -> build/lib.linux-armv7l-cpython-39/pyjess/tests/data 2024-05-30T19:38:31,290 copying pyjess/tests/data/1AMY+1.3.3.txt -> build/lib.linux-armv7l-cpython-39/pyjess/tests/data 2024-05-30T19:38:31,294 copying pyjess/tests/data/pdb1lnb.pdb -> build/lib.linux-armv7l-cpython-39/pyjess/tests/data 2024-05-30T19:38:31,300 copying pyjess/tests/data/1AMY.pdb -> build/lib.linux-armv7l-cpython-39/pyjess/tests/data 2024-05-30T19:38:31,308 copying pyjess/tests/data/template_02.qry -> build/lib.linux-armv7l-cpython-39/pyjess/tests/data 2024-05-30T19:38:31,311 running build_clib 2024-05-30T19:38:31,319 creating build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,320 generating build/temp.linux-armv7l-cpython-39/libjess.a from vendor/jess/src/Annulus.c, vendor/jess/src/Atom.c, vendor/jess/src/Jess.c, vendor/jess/src/Join.c, vendor/jess/src/KdTree.c, vendor/jess/src/Molecule.c, vendor/jess/src/Region.c, vendor/jess/src/Scanner.c, vendor/jess/src/Super.c, vendor/jess/src/TessAtom.c, vendor/jess/src/TessTemplate.c 2024-05-30T19:38:31,320 building jess with unix compiler 2024-05-30T19:38:31,320 generating build/temp.linux-armv7l-cpython-39/Annulus.h from vendor/jess/src/Annulus.h 2024-05-30T19:38:31,321 copying vendor/jess/src/Annulus.h -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,323 generating build/temp.linux-armv7l-cpython-39/Atom.h from vendor/jess/src/Atom.h 2024-05-30T19:38:31,324 patching vendor/jess/src/Atom.h with patches/Atom.h.patch 2024-05-30T19:38:31,326 generating build/temp.linux-armv7l-cpython-39/Jess.h from vendor/jess/src/Jess.h 2024-05-30T19:38:31,327 copying vendor/jess/src/Jess.h -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,329 generating build/temp.linux-armv7l-cpython-39/Join.h from vendor/jess/src/Join.h 2024-05-30T19:38:31,329 copying vendor/jess/src/Join.h -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,331 generating build/temp.linux-armv7l-cpython-39/KdTree.h from vendor/jess/src/KdTree.h 2024-05-30T19:38:31,332 copying vendor/jess/src/KdTree.h -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,333 generating build/temp.linux-armv7l-cpython-39/Molecule.h from vendor/jess/src/Molecule.h 2024-05-30T19:38:31,334 patching vendor/jess/src/Molecule.h with patches/Molecule.h.patch 2024-05-30T19:38:31,336 generating build/temp.linux-armv7l-cpython-39/Region.h from vendor/jess/src/Region.h 2024-05-30T19:38:31,336 copying vendor/jess/src/Region.h -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,338 generating build/temp.linux-armv7l-cpython-39/Scanner.h from vendor/jess/src/Scanner.h 2024-05-30T19:38:31,339 copying vendor/jess/src/Scanner.h -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,341 generating build/temp.linux-armv7l-cpython-39/Super.h from vendor/jess/src/Super.h 2024-05-30T19:38:31,341 copying vendor/jess/src/Super.h -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,343 generating build/temp.linux-armv7l-cpython-39/Template.h from vendor/jess/src/Template.h 2024-05-30T19:38:31,343 patching vendor/jess/src/Template.h with patches/Template.h.patch 2024-05-30T19:38:31,345 generating build/temp.linux-armv7l-cpython-39/TessAtom.h from vendor/jess/src/TessAtom.h 2024-05-30T19:38:31,346 patching vendor/jess/src/TessAtom.h with patches/TessAtom.h.patch 2024-05-30T19:38:31,348 generating build/temp.linux-armv7l-cpython-39/TessTemplate.h from vendor/jess/src/TessTemplate.h 2024-05-30T19:38:31,348 patching vendor/jess/src/TessTemplate.h with patches/TessTemplate.h.patch 2024-05-30T19:38:31,351 generating build/temp.linux-armv7l-cpython-39/Annulus.c from vendor/jess/src/Annulus.c 2024-05-30T19:38:31,351 copying vendor/jess/src/Annulus.c -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,353 generating build/temp.linux-armv7l-cpython-39/Atom.c from vendor/jess/src/Atom.c 2024-05-30T19:38:31,354 copying vendor/jess/src/Atom.c -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,356 generating build/temp.linux-armv7l-cpython-39/Jess.c from vendor/jess/src/Jess.c 2024-05-30T19:38:31,356 patching vendor/jess/src/Jess.c with patches/Jess.c.patch 2024-05-30T19:38:31,359 generating build/temp.linux-armv7l-cpython-39/Join.c from vendor/jess/src/Join.c 2024-05-30T19:38:31,360 copying vendor/jess/src/Join.c -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,362 generating build/temp.linux-armv7l-cpython-39/KdTree.c from vendor/jess/src/KdTree.c 2024-05-30T19:38:31,362 patching vendor/jess/src/KdTree.c with patches/KdTree.c.patch 2024-05-30T19:38:31,365 generating build/temp.linux-armv7l-cpython-39/Molecule.c from vendor/jess/src/Molecule.c 2024-05-30T19:38:31,365 patching vendor/jess/src/Molecule.c with patches/Molecule.c.patch 2024-05-30T19:38:31,367 generating build/temp.linux-armv7l-cpython-39/Region.c from vendor/jess/src/Region.c 2024-05-30T19:38:31,368 copying vendor/jess/src/Region.c -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,370 generating build/temp.linux-armv7l-cpython-39/Scanner.c from vendor/jess/src/Scanner.c 2024-05-30T19:38:31,371 copying vendor/jess/src/Scanner.c -> build/temp.linux-armv7l-cpython-39 2024-05-30T19:38:31,373 generating build/temp.linux-armv7l-cpython-39/Super.c from vendor/jess/src/Super.c 2024-05-30T19:38:31,373 patching vendor/jess/src/Super.c with patches/Super.c.patch 2024-05-30T19:38:31,376 generating build/temp.linux-armv7l-cpython-39/TessAtom.c from vendor/jess/src/TessAtom.c 2024-05-30T19:38:31,376 patching vendor/jess/src/TessAtom.c with patches/TessAtom.c.patch 2024-05-30T19:38:31,380 generating build/temp.linux-armv7l-cpython-39/TessTemplate.c from vendor/jess/src/TessTemplate.c 2024-05-30T19:38:31,380 patching vendor/jess/src/TessTemplate.c with patches/TessTemplate.c.patch 2024-05-30T19:38:31,397 generating build/temp.linux-armv7l-cpython-39/Annulus.o from build/temp.linux-armv7l-cpython-39/Annulus.c 2024-05-30T19:38:31,398 generating build/temp.linux-armv7l-cpython-39/Atom.o from build/temp.linux-armv7l-cpython-39/Atom.c 2024-05-30T19:38:31,399 generating build/temp.linux-armv7l-cpython-39/Jess.o from build/temp.linux-armv7l-cpython-39/Jess.c 2024-05-30T19:38:31,399 generating build/temp.linux-armv7l-cpython-39/Join.o from build/temp.linux-armv7l-cpython-39/Join.c 2024-05-30T19:38:31,400 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/Annulus.c -o build/temp.linux-armv7l-cpython-39/Annulus.o 2024-05-30T19:38:31,400 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/Atom.c -o build/temp.linux-armv7l-cpython-39/Atom.o 2024-05-30T19:38:31,400 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/Join.c -o build/temp.linux-armv7l-cpython-39/Join.o 2024-05-30T19:38:31,401 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/Jess.c -o build/temp.linux-armv7l-cpython-39/Jess.o 2024-05-30T19:38:31,582 build/temp.linux-armv7l-cpython-39/Annulus.c: In function ‘Annulus_ro’: 2024-05-30T19:38:31,582 build/temp.linux-armv7l-cpython-39/Annulus.c:66:12: warning: unused variable ‘t4’ [-Wunused-variable] 2024-05-30T19:38:31,583 66 | double t3,t4; 2024-05-30T19:38:31,584 | ^~ 2024-05-30T19:38:31,584 build/temp.linux-armv7l-cpython-39/Annulus.c:66:9: warning: unused variable ‘t3’ [-Wunused-variable] 2024-05-30T19:38:31,585 66 | double t3,t4; 2024-05-30T19:38:31,585 | ^~ 2024-05-30T19:38:31,614 build/temp.linux-armv7l-cpython-39/Jess.c: In function ‘JessQuery_next’: 2024-05-30T19:38:31,615 build/temp.linux-armv7l-cpython-39/Jess.c:180:12: warning: variable ‘T’ set but not used [-Wunused-but-set-variable] 2024-05-30T19:38:31,616 180 | Template *T; 2024-05-30T19:38:31,616 | ^ 2024-05-30T19:38:31,672 generating build/temp.linux-armv7l-cpython-39/KdTree.o from build/temp.linux-armv7l-cpython-39/KdTree.c 2024-05-30T19:38:31,676 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/KdTree.c -o build/temp.linux-armv7l-cpython-39/KdTree.o 2024-05-30T19:38:31,697 generating build/temp.linux-armv7l-cpython-39/Molecule.o from build/temp.linux-armv7l-cpython-39/Molecule.c 2024-05-30T19:38:31,698 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/Molecule.c -o build/temp.linux-armv7l-cpython-39/Molecule.o 2024-05-30T19:38:31,728 generating build/temp.linux-armv7l-cpython-39/Region.o from build/temp.linux-armv7l-cpython-39/Region.c 2024-05-30T19:38:31,729 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/Region.c -o build/temp.linux-armv7l-cpython-39/Region.o 2024-05-30T19:38:31,798 generating build/temp.linux-armv7l-cpython-39/Scanner.o from build/temp.linux-armv7l-cpython-39/Scanner.c 2024-05-30T19:38:31,799 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/Scanner.c -o build/temp.linux-armv7l-cpython-39/Scanner.o 2024-05-30T19:38:31,806 build/temp.linux-armv7l-cpython-39/KdTree.c: In function ‘KdTree_create’: 2024-05-30T19:38:31,807 build/temp.linux-armv7l-cpython-39/KdTree.c:137:8: warning: unused variable ‘j’ [-Wunused-variable] 2024-05-30T19:38:31,807 137 | int i,j; 2024-05-30T19:38:31,807 | ^ 2024-05-30T19:38:31,808 build/temp.linux-armv7l-cpython-39/KdTree.c: In function ‘KdTree_free’: 2024-05-30T19:38:31,808 build/temp.linux-armv7l-cpython-39/KdTree.c:166:6: warning: unused variable ‘i’ [-Wunused-variable] 2024-05-30T19:38:31,808 166 | int i; 2024-05-30T19:38:31,809 | ^ 2024-05-30T19:38:31,815 At top level: 2024-05-30T19:38:31,815 build/temp.linux-armv7l-cpython-39/KdTree.c:120:12: warning: ‘imin’ defined but not used [-Wunused-function] 2024-05-30T19:38:31,815 120 | static int imin(int x, int y) 2024-05-30T19:38:31,816 | ^~~~ 2024-05-30T19:38:31,925 build/temp.linux-armv7l-cpython-39/Scanner.c: In function ‘Scanner_create’: 2024-05-30T19:38:31,925 build/temp.linux-armv7l-cpython-39/Scanner.c:82:6: warning: unused variable ‘m’ [-Wunused-variable] 2024-05-30T19:38:31,926 82 | int m; 2024-05-30T19:38:31,926 | ^ 2024-05-30T19:38:31,969 generating build/temp.linux-armv7l-cpython-39/Super.o from build/temp.linux-armv7l-cpython-39/Super.c 2024-05-30T19:38:31,970 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/Super.c -o build/temp.linux-armv7l-cpython-39/Super.o 2024-05-30T19:38:31,997 generating build/temp.linux-armv7l-cpython-39/TessAtom.o from build/temp.linux-armv7l-cpython-39/TessAtom.c 2024-05-30T19:38:31,998 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/TessAtom.c -o build/temp.linux-armv7l-cpython-39/TessAtom.o 2024-05-30T19:38:32,113 generating build/temp.linux-armv7l-cpython-39/TessTemplate.o from build/temp.linux-armv7l-cpython-39/TessTemplate.c 2024-05-30T19:38:32,114 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 -D_GNU_SOURCE=1 -Ivendor/jess -Ibuild/temp.linux-armv7l-cpython-39 -c build/temp.linux-armv7l-cpython-39/TessTemplate.c -o build/temp.linux-armv7l-cpython-39/TessTemplate.o 2024-05-30T19:38:32,146 build/temp.linux-armv7l-cpython-39/Super.c: In function ‘Superposition_compute’: 2024-05-30T19:38:32,147 build/temp.linux-armv7l-cpython-39/Super.c:146:13: warning: unused variable ‘tst’ [-Wunused-variable] 2024-05-30T19:38:32,147 146 | double tmp,tst; 2024-05-30T19:38:32,147 | ^~~ 2024-05-30T19:38:32,147 build/temp.linux-armv7l-cpython-39/Super.c:146:9: warning: unused variable ‘tmp’ [-Wunused-variable] 2024-05-30T19:38:32,148 146 | double tmp,tst; 2024-05-30T19:38:32,148 | ^~~ 2024-05-30T19:38:32,148 build/temp.linux-armv7l-cpython-39/Super.c:143:9: warning: unused variable ‘v’ [-Wunused-variable] 2024-05-30T19:38:32,148 143 | double v[3]; 2024-05-30T19:38:32,149 | ^ 2024-05-30T19:38:32,151 build/temp.linux-armv7l-cpython-39/Super.c: In function ‘superpose’: 2024-05-30T19:38:32,152 build/temp.linux-armv7l-cpython-39/Super.c:412:9: warning: unused variable ‘Q’ [-Wunused-variable] 2024-05-30T19:38:32,152 412 | double Q[9]; 2024-05-30T19:38:32,153 | ^ 2024-05-30T19:38:32,296 build/temp.linux-armv7l-cpython-39/TessTemplate.c: In function ‘TessTemplate_check’: 2024-05-30T19:38:32,297 build/temp.linux-armv7l-cpython-39/TessTemplate.c:85:16: warning: unused variable ‘f’ [-Wunused-variable] 2024-05-30T19:38:32,297 85 | int a,b,c,d,e,f; 2024-05-30T19:38:32,298 | ^ 2024-05-30T19:38:32,298 build/temp.linux-armv7l-cpython-39/TessTemplate.c:85:14: warning: unused variable ‘e’ [-Wunused-variable] 2024-05-30T19:38:32,298 85 | int a,b,c,d,e,f; 2024-05-30T19:38:32,298 | ^ 2024-05-30T19:38:32,334 build/temp.linux-armv7l-cpython-39/TessAtom.c: In function ‘TessAtom_create’: 2024-05-30T19:38:32,335 build/temp.linux-armv7l-cpython-39/TessAtom.c:165:2: warning: ‘strncpy’ output may be truncated copying 4 bytes from a string of length 4 [-Wstringop-truncation] 2024-05-30T19:38:32,335 165 | strncpy(A->name[0],a.name,4); 2024-05-30T19:38:32,335 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T19:38:32,336 build/temp.linux-armv7l-cpython-39/TessAtom.c:166:2: warning: ‘strncpy’ output may be truncated copying 3 bytes from a string of length 3 [-Wstringop-truncation] 2024-05-30T19:38:32,336 166 | strncpy(A->resName[0],a.resName,3); 2024-05-30T19:38:32,336 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T19:38:32,842 generating build/temp.linux-armv7l-cpython-39/libjess.a from build/temp.linux-armv7l-cpython-39/Annulus.o, build/temp.linux-armv7l-cpython-39/Atom.o, build/temp.linux-armv7l-cpython-39/Jess.o, build/temp.linux-armv7l-cpython-39/Join.o, build/temp.linux-armv7l-cpython-39/KdTree.o, build/temp.linux-armv7l-cpython-39/Molecule.o, build/temp.linux-armv7l-cpython-39/Region.o, build/temp.linux-armv7l-cpython-39/Scanner.o, build/temp.linux-armv7l-cpython-39/Super.o, build/temp.linux-armv7l-cpython-39/TessAtom.o, build/temp.linux-armv7l-cpython-39/TessTemplate.o 2024-05-30T19:38:32,844 arm-linux-gnueabihf-gcc-ar rcs build/temp.linux-armv7l-cpython-39/libjess.a build/temp.linux-armv7l-cpython-39/Annulus.o build/temp.linux-armv7l-cpython-39/Atom.o build/temp.linux-armv7l-cpython-39/Jess.o build/temp.linux-armv7l-cpython-39/Join.o build/temp.linux-armv7l-cpython-39/KdTree.o build/temp.linux-armv7l-cpython-39/Molecule.o build/temp.linux-armv7l-cpython-39/Region.o build/temp.linux-armv7l-cpython-39/Scanner.o build/temp.linux-armv7l-cpython-39/Super.o build/temp.linux-armv7l-cpython-39/TessAtom.o build/temp.linux-armv7l-cpython-39/TessTemplate.o 2024-05-30T19:38:32,876 running build_ext 2024-05-30T19:38:36,368 Compiling pyjess/_jess.pyx because it changed. 2024-05-30T19:38:36,368 [1/1] Cythonizing pyjess/_jess.pyx 2024-05-30T19:38:36,368 building pyjess._jess with unix compiler for platform linux-armv7l 2024-05-30T19:38:36,369 checking whether `PyInterpreterState_GetID` is available 2024-05-30T19:38:36,370 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/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/have_getid.c -o build/temp.linux-armv7l-cpython-39/have_getid.o -Werror=implicit-function-declaration 2024-05-30T19:38:36,673 yes 2024-05-30T19:38:36,679 building 'pyjess._jess' extension 2024-05-30T19:38:36,680 creating build/temp.linux-armv7l-cpython-39/pyjess 2024-05-30T19:38:36,681 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 -DCYTHON_WITHOUT_ASSERTIONS=1 -DHAS_PYINTERPRETERSTATE_GETID=1 -Ipyjess -Iinclude -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c pyjess/_jess.c -o build/temp.linux-armv7l-cpython-39/pyjess/_jess.o 2024-05-30T19:38:37,086 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_8Molecule_10__len__’: 2024-05-30T19:38:37,090 pyjess/_jess.c:6816:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,090 6816 | int __pyx_t_1; 2024-05-30T19:38:37,090 | ^~~~~~~~~ 2024-05-30T19:38:37,098 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_8Molecule_14__sizeof__’: 2024-05-30T19:38:37,102 pyjess/_jess.c:7175:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,102 7175 | int __pyx_t_1; 2024-05-30T19:38:37,102 | ^~~~~~~~~ 2024-05-30T19:38:37,208 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_6serial___get__’: 2024-05-30T19:38:37,213 pyjess/_jess.c:10343:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,214 10343 | int __pyx_t_1; 2024-05-30T19:38:37,214 | ^~~~~~~~~ 2024-05-30T19:38:37,216 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_6altloc___get__’: 2024-05-30T19:38:37,221 pyjess/_jess.c:10433:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,221 10433 | int __pyx_t_1; 2024-05-30T19:38:37,221 | ^~~~~~~~~ 2024-05-30T19:38:37,224 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_4name___get__’: 2024-05-30T19:38:37,229 pyjess/_jess.c:10528:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,229 10528 | int __pyx_t_1; 2024-05-30T19:38:37,229 | ^~~~~~~~~ 2024-05-30T19:38:37,232 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_12residue_name___get__’: 2024-05-30T19:38:37,237 pyjess/_jess.c:10648:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,237 10648 | int __pyx_t_1; 2024-05-30T19:38:37,237 | ^~~~~~~~~ 2024-05-30T19:38:37,239 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_14residue_number___get__’: 2024-05-30T19:38:37,244 pyjess/_jess.c:10768:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,244 10768 | int __pyx_t_1; 2024-05-30T19:38:37,245 | ^~~~~~~~~ 2024-05-30T19:38:37,247 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_7segment___get__’: 2024-05-30T19:38:37,252 pyjess/_jess.c:10858:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,253 10858 | int __pyx_t_1; 2024-05-30T19:38:37,253 | ^~~~~~~~~ 2024-05-30T19:38:37,255 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_7element___get__’: 2024-05-30T19:38:37,261 pyjess/_jess.c:10978:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,261 10978 | int __pyx_t_1; 2024-05-30T19:38:37,261 | ^~~~~~~~~ 2024-05-30T19:38:37,263 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_14insertion_code___get__’: 2024-05-30T19:38:37,268 pyjess/_jess.c:11098:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,269 11098 | int __pyx_t_1; 2024-05-30T19:38:37,269 | ^~~~~~~~~ 2024-05-30T19:38:37,273 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_8chain_id___get__’: 2024-05-30T19:38:37,278 pyjess/_jess.c:11193:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,278 11193 | int __pyx_t_1; 2024-05-30T19:38:37,278 | ^~~~~~~~~ 2024-05-30T19:38:37,280 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_9occupancy___get__’: 2024-05-30T19:38:37,286 pyjess/_jess.c:11353:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,286 11353 | int __pyx_t_1; 2024-05-30T19:38:37,286 | ^~~~~~~~~ 2024-05-30T19:38:37,288 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_18temperature_factor___get__’: 2024-05-30T19:38:37,293 pyjess/_jess.c:11443:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,293 11443 | int __pyx_t_1; 2024-05-30T19:38:37,294 | ^~~~~~~~~ 2024-05-30T19:38:37,295 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_6charge___get__’: 2024-05-30T19:38:37,301 pyjess/_jess.c:11533:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,301 11533 | int __pyx_t_1; 2024-05-30T19:38:37,301 | ^~~~~~~~~ 2024-05-30T19:38:37,303 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_1x___get__’: 2024-05-30T19:38:37,309 pyjess/_jess.c:11623:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,309 11623 | int __pyx_t_1; 2024-05-30T19:38:37,309 | ^~~~~~~~~ 2024-05-30T19:38:37,311 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_1y___get__’: 2024-05-30T19:38:37,316 pyjess/_jess.c:11713:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,317 11713 | int __pyx_t_1; 2024-05-30T19:38:37,317 | ^~~~~~~~~ 2024-05-30T19:38:37,318 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_4Atom_1z___get__’: 2024-05-30T19:38:37,324 pyjess/_jess.c:11803:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,324 11803 | int __pyx_t_1; 2024-05-30T19:38:37,324 | ^~~~~~~~~ 2024-05-30T19:38:37,425 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_10match_mode___get__’: 2024-05-30T19:38:37,432 pyjess/_jess.c:14531:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,432 14531 | int __pyx_t_1; 2024-05-30T19:38:37,432 | ^~~~~~~~~ 2024-05-30T19:38:37,434 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_14residue_number___get__’: 2024-05-30T19:38:37,441 pyjess/_jess.c:14621:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,441 14621 | int __pyx_t_1; 2024-05-30T19:38:37,441 | ^~~~~~~~~ 2024-05-30T19:38:37,445 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_8chain_id___get__’: 2024-05-30T19:38:37,452 pyjess/_jess.c:14713:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,453 14713 | int __pyx_t_1; 2024-05-30T19:38:37,453 | ^~~~~~~~~ 2024-05-30T19:38:37,454 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_1x___get__’: 2024-05-30T19:38:37,462 pyjess/_jess.c:14893:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,462 14893 | int __pyx_t_1; 2024-05-30T19:38:37,462 | ^~~~~~~~~ 2024-05-30T19:38:37,464 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_1y___get__’: 2024-05-30T19:38:37,471 pyjess/_jess.c:14983:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,471 14983 | int __pyx_t_1; 2024-05-30T19:38:37,471 | ^~~~~~~~~ 2024-05-30T19:38:37,473 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_1z___get__’: 2024-05-30T19:38:37,480 pyjess/_jess.c:15073:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,481 15073 | int __pyx_t_1; 2024-05-30T19:38:37,481 | ^~~~~~~~~ 2024-05-30T19:38:37,484 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_10atom_names___get__’: 2024-05-30T19:38:37,492 pyjess/_jess.c:15165:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,492 15165 | int __pyx_t_1; 2024-05-30T19:38:37,492 | ^~~~~~~~~ 2024-05-30T19:38:37,498 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_13residue_names___get__’: 2024-05-30T19:38:37,505 pyjess/_jess.c:15336:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,505 15336 | int __pyx_t_1; 2024-05-30T19:38:37,506 | ^~~~~~~~~ 2024-05-30T19:38:37,507 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_12TemplateAtom_15distance_weight___get__’: 2024-05-30T19:38:37,515 pyjess/_jess.c:15505:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,515 15505 | int __pyx_t_1; 2024-05-30T19:38:37,515 | ^~~~~~~~~ 2024-05-30T19:38:37,571 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_8Template_10__len__’: 2024-05-30T19:38:37,580 pyjess/_jess.c:17706:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,580 17706 | int __pyx_t_1; 2024-05-30T19:38:37,580 | ^~~~~~~~~ 2024-05-30T19:38:37,590 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_8Template_14__sizeof__’: 2024-05-30T19:38:37,599 pyjess/_jess.c:18133:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-30T19:38:37,599 18133 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2024-05-30T19:38:37,599 | ^ 2024-05-30T19:38:37,611 pyjess/_jess.c:18070:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,611 18070 | int __pyx_t_1; 2024-05-30T19:38:37,611 | ^~~~~~~~~ 2024-05-30T19:38:37,615 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_8Template_9dimension___get__’: 2024-05-30T19:38:37,624 pyjess/_jess.c:18376:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,624 18376 | int __pyx_t_1; 2024-05-30T19:38:37,625 | ^~~~~~~~~ 2024-05-30T19:38:37,683 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_3Hit_11determinant___get__’: 2024-05-30T19:38:37,693 pyjess/_jess.c:20399:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,693 20399 | int __pyx_t_1; 2024-05-30T19:38:37,693 | ^~~~~~~~~ 2024-05-30T19:38:37,695 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_3Hit_10log_evalue___get__’: 2024-05-30T19:38:37,705 pyjess/_jess.c:20540:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,705 20540 | int __pyx_t_1; 2024-05-30T19:38:37,706 | ^~~~~~~~~ 2024-05-30T19:38:37,707 pyjess/_jess.c: In function ‘__pyx_pf_6pyjess_5_jess_3Hit_6evalue___get__’: 2024-05-30T19:38:37,718 pyjess/_jess.c:20641:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-05-30T19:38:37,718 20641 | int __pyx_t_1; 2024-05-30T19:38:37,718 | ^~~~~~~~~ 2024-05-30T19:38:37,724 pyjess/_jess.c: In function ‘__pyx_f_6pyjess_5_jess_3Hit_atoms’: 2024-05-30T19:38:37,734 pyjess/_jess.c:20749:7: warning: unused variable ‘__pyx_t_7’ [-Wunused-variable] 2024-05-30T19:38:37,735 20749 | int __pyx_t_7; 2024-05-30T19:38:37,735 | ^~~~~~~~~ 2024-05-30T19:39:11,575 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/pyjess/_jess.o build/temp.linux-armv7l-cpython-39/libjess.a -L/usr/lib -Lbuild/temp.linux-armv7l-cpython-39 -ljess -ljess -o build/lib.linux-armv7l-cpython-39/pyjess/_jess.cpython-39-arm-linux-gnueabihf.so 2024-05-30T19:39:11,808 installing to build/bdist.linux-armv7l/wheel 2024-05-30T19:39:11,808 running install 2024-05-30T19:39:11,835 running install_lib 2024-05-30T19:39:11,843 creating build/bdist.linux-armv7l 2024-05-30T19:39:11,844 creating build/bdist.linux-armv7l/wheel 2024-05-30T19:39:11,845 creating build/bdist.linux-armv7l/wheel/pyjess 2024-05-30T19:39:11,846 copying build/lib.linux-armv7l-cpython-39/pyjess/py.typed -> build/bdist.linux-armv7l/wheel/pyjess 2024-05-30T19:39:11,848 copying build/lib.linux-armv7l-cpython-39/pyjess/__init__.py -> build/bdist.linux-armv7l/wheel/pyjess 2024-05-30T19:39:11,849 copying build/lib.linux-armv7l-cpython-39/pyjess/_jess.pyi -> build/bdist.linux-armv7l/wheel/pyjess 2024-05-30T19:39:11,852 copying build/lib.linux-armv7l-cpython-39/pyjess/_jess.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pyjess 2024-05-30T19:39:11,880 creating build/bdist.linux-armv7l/wheel/pyjess/tests 2024-05-30T19:39:11,881 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/test_atom.py -> build/bdist.linux-armv7l/wheel/pyjess/tests 2024-05-30T19:39:11,883 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/test_template_atom.py -> build/bdist.linux-armv7l/wheel/pyjess/tests 2024-05-30T19:39:11,884 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyjess/tests 2024-05-30T19:39:11,886 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/utils.py -> build/bdist.linux-armv7l/wheel/pyjess/tests 2024-05-30T19:39:11,888 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/test_jess.py -> build/bdist.linux-armv7l/wheel/pyjess/tests 2024-05-30T19:39:11,890 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/test_template.py -> build/bdist.linux-armv7l/wheel/pyjess/tests 2024-05-30T19:39:11,892 creating build/bdist.linux-armv7l/wheel/pyjess/tests/data 2024-05-30T19:39:11,893 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/data/template_01.qry -> build/bdist.linux-armv7l/wheel/pyjess/tests/data 2024-05-30T19:39:11,895 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/data/1.3.3.tpl -> build/bdist.linux-armv7l/wheel/pyjess/tests/data 2024-05-30T19:39:11,897 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/data/1AMY+1.3.3.txt -> build/bdist.linux-armv7l/wheel/pyjess/tests/data 2024-05-30T19:39:11,901 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/data/__init__.py -> build/bdist.linux-armv7l/wheel/pyjess/tests/data 2024-05-30T19:39:11,903 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/data/pdb1lnb.pdb -> build/bdist.linux-armv7l/wheel/pyjess/tests/data 2024-05-30T19:39:11,911 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/data/1AMY.pdb -> build/bdist.linux-armv7l/wheel/pyjess/tests/data 2024-05-30T19:39:11,920 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/data/template_02.qry -> build/bdist.linux-armv7l/wheel/pyjess/tests/data 2024-05-30T19:39:11,921 copying build/lib.linux-armv7l-cpython-39/pyjess/tests/test_molecule.py -> build/bdist.linux-armv7l/wheel/pyjess/tests 2024-05-30T19:39:11,923 running install_egg_info 2024-05-30T19:39:11,934 running egg_info 2024-05-30T19:39:11,939 writing pyjess.egg-info/PKG-INFO 2024-05-30T19:39:11,942 writing dependency_links to pyjess.egg-info/dependency_links.txt 2024-05-30T19:39:11,945 writing top-level names to pyjess.egg-info/top_level.txt 2024-05-30T19:39:11,961 reading manifest file 'pyjess.egg-info/SOURCES.txt' 2024-05-30T19:39:11,968 reading manifest template 'MANIFEST.in' 2024-05-30T19:39:12,007 warning: no files found matching '*.pxi' under directory 'pyjess' 2024-05-30T19:39:12,025 warning: no files found matching '*.pxd' under directory 'pyjess' 2024-05-30T19:39:12,034 warning: no files found matching '*.h' under directory 'pyjess' 2024-05-30T19:39:12,056 warning: no files found matching 'LICENSE' under directory 'vendor/jess' 2024-05-30T19:39:12,062 warning: no files found matching 'AUTHORS' under directory 'vendor/jess' 2024-05-30T19:39:12,069 warning: no files found matching 'CHANGELOG' under directory 'vendor/jess' 2024-05-30T19:39:12,089 no previously-included directories found matching 'vendor/sword/vendor' 2024-05-30T19:39:12,109 warning: no files found matching '*.pxi' under directory 'pyjess' 2024-05-30T19:39:12,122 warning: no files found matching '*.pxd' under directory 'pyjess' 2024-05-30T19:39:12,129 warning: no files found matching '*.h' under directory 'pyjess' 2024-05-30T19:39:12,134 warning: no previously-included files matching '*.cpp' found under directory 'pyjess' 2024-05-30T19:39:12,135 warning: no previously-included files matching '*.html' found under directory 'pyjess' 2024-05-30T19:39:12,135 adding license file 'COPYING' 2024-05-30T19:39:12,141 writing manifest file 'pyjess.egg-info/SOURCES.txt' 2024-05-30T19:39:12,143 Copying pyjess.egg-info to build/bdist.linux-armv7l/wheel/pyjess-0.2.1-py3.9.egg-info 2024-05-30T19:39:12,153 running install_scripts 2024-05-30T19:39:12,204 creating build/bdist.linux-armv7l/wheel/pyjess-0.2.1.dist-info/WHEEL 2024-05-30T19:39:12,207 creating '/tmp/pip-wheel-ceh5w53t/.tmp-2ssqruc0/pyjess-0.2.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-30T19:39:12,209 adding 'pyjess/__init__.py' 2024-05-30T19:39:12,525 adding 'pyjess/_jess.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T19:39:12,536 adding 'pyjess/_jess.pyi' 2024-05-30T19:39:12,537 adding 'pyjess/py.typed' 2024-05-30T19:39:12,539 adding 'pyjess/tests/__init__.py' 2024-05-30T19:39:12,540 adding 'pyjess/tests/test_atom.py' 2024-05-30T19:39:12,542 adding 'pyjess/tests/test_jess.py' 2024-05-30T19:39:12,543 adding 'pyjess/tests/test_molecule.py' 2024-05-30T19:39:12,544 adding 'pyjess/tests/test_template.py' 2024-05-30T19:39:12,546 adding 'pyjess/tests/test_template_atom.py' 2024-05-30T19:39:12,547 adding 'pyjess/tests/utils.py' 2024-05-30T19:39:12,549 adding 'pyjess/tests/data/1.3.3.tpl' 2024-05-30T19:39:12,561 adding 'pyjess/tests/data/1AMY+1.3.3.txt' 2024-05-30T19:39:12,615 adding 'pyjess/tests/data/1AMY.pdb' 2024-05-30T19:39:12,618 adding 'pyjess/tests/data/__init__.py' 2024-05-30T19:39:12,661 adding 'pyjess/tests/data/pdb1lnb.pdb' 2024-05-30T19:39:12,664 adding 'pyjess/tests/data/template_01.qry' 2024-05-30T19:39:12,665 adding 'pyjess/tests/data/template_02.qry' 2024-05-30T19:39:12,668 adding 'pyjess-0.2.1.dist-info/COPYING' 2024-05-30T19:39:12,669 adding 'pyjess-0.2.1.dist-info/METADATA' 2024-05-30T19:39:12,670 adding 'pyjess-0.2.1.dist-info/WHEEL' 2024-05-30T19:39:12,671 adding 'pyjess-0.2.1.dist-info/top_level.txt' 2024-05-30T19:39:12,672 adding 'pyjess-0.2.1.dist-info/RECORD' 2024-05-30T19:39:12,681 removing build/bdist.linux-armv7l/wheel 2024-05-30T19:39:12,980 Building wheel for pyjess (pyproject.toml): finished with status 'done' 2024-05-30T19:39:13,000 Created wheel for pyjess: filename=pyjess-0.2.1-cp39-cp39-linux_armv7l.whl size=758803 sha256=9583e5c2a7e25b648afa290e2f2a47d96cfb51962a46a34a5c843b06cf95854c 2024-05-30T19:39:13,001 Stored in directory: /tmp/pip-ephem-wheel-cache-s0g1y5jk/wheels/a2/1b/a5/fc20d9b23054ce99fb49ee91266fd796ad246a65374e230467 2024-05-30T19:39:13,014 Successfully built pyjess 2024-05-30T19:39:13,035 Removed build tracker: '/tmp/pip-build-tracker-favj_vbk'