2022-07-05T18:47:14,276 Created temporary directory: /tmp/pip-ephem-wheel-cache-cy6d6i5w 2022-07-05T18:47:14,282 Created temporary directory: /tmp/pip-build-tracker-mul05tbx 2022-07-05T18:47:14,282 Initialized build tracking at /tmp/pip-build-tracker-mul05tbx 2022-07-05T18:47:14,283 Created build tracker: /tmp/pip-build-tracker-mul05tbx 2022-07-05T18:47:14,283 Entered build tracker: /tmp/pip-build-tracker-mul05tbx 2022-07-05T18:47:14,284 Created temporary directory: /tmp/pip-wheel-3m96n9ty 2022-07-05T18:47:14,357 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-07-05T18:47:14,366 2 location(s) to search for versions of oxdna-analysis-tools: 2022-07-05T18:47:14,366 * https://pypi.org/simple/oxdna-analysis-tools/ 2022-07-05T18:47:14,366 * https://www.piwheels.org/simple/oxdna-analysis-tools/ 2022-07-05T18:47:14,367 Fetching project page and analyzing links: https://pypi.org/simple/oxdna-analysis-tools/ 2022-07-05T18:47:14,368 Getting page 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https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,532 Found link https://files.pythonhosted.org/packages/c5/4b/a8ea03fa1cb45bdb35dc793e20c2eeda48dc72d22ca81e23c873eb5996ad/oxDNA_analysis_tools-1.0.14.tar.gz#sha256=402c516c3256a87ddebe3c4a0032bc2d156568c1c8f3893e83dc0278654cdcf4 (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6), version: 1.0.14 2022-07-05T18:47:14,533 Skipping link: No binaries permitted for oxdna-analysis-tools: https://files.pythonhosted.org/packages/d6/0c/e874c4b2d7bae0b686a4099e4ad43461247caafc6842f4ee6e2a6e7cec9d/oxDNA_analysis_tools-1.0.15-py3-none-any.whl#sha256=ec10af3bc08bc1b0b4f4336828b337a87c3a1ef7e8399d5a666b8b7c861de7dc (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,534 Found link 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(requires-python:>=3.6), version: 1.0.16 2022-07-05T18:47:14,538 Found link https://files.pythonhosted.org/packages/f6/6d/4d84b7745a400f812af281066a7958894b4979d8f6681b44f90c9e7b38d0/oxDNA_analysis_tools-2.0.0.tar.gz#sha256=7cfe7ee4bdd71ad70409e040457889116ee6f02f038d1c972ce1c1366c24798f (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.7), version: 2.0.0 2022-07-05T18:47:14,538 Skipping link: No binaries permitted for oxdna-analysis-tools: https://files.pythonhosted.org/packages/c6/7e/7c3927dfd80ac2c76b3c96f964d4114c82640b36aa5fb73189d28bbf5316/oxDNA_analysis_tools-2.0.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=aedc8a9b9230a157a4b4a0705e28681c9d27645ab2283ee1d733669782ee8440 (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.8) 2022-07-05T18:47:14,540 Found link https://files.pythonhosted.org/packages/7f/c7/ca513a975734a667b486e242809bd330fa8b300f1518c68485067eef9797/oxDNA_analysis_tools-2.0.1.tar.gz#sha256=8a8c14e7de34eecdc5c5d1af0ce23a978e69d013f6d211180c264eb5f2b94fb0 (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.8), version: 2.0.1 2022-07-05T18:47:14,541 Fetching project page and analyzing links: https://www.piwheels.org/simple/oxdna-analysis-tools/ 2022-07-05T18:47:14,541 Getting page https://www.piwheels.org/simple/oxdna-analysis-tools/ 2022-07-05T18:47:14,543 Found index url https://www.piwheels.org/simple 2022-07-05T18:47:14,783 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-2.0.0-cp39-cp39-linux_armv7l.whl#sha256=b0148c981b90045fdb54b70232bd9ac14b30793197bcaf131ecdb6ed60b0cb51 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.7) 2022-07-05T18:47:14,784 Skipping link: No binaries 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(requires-python:>=3.7) 2022-07-05T18:47:14,786 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.16-py3-none-any.whl#sha256=2298f7e6998b9f282e2c9f54a7eb6246019317486620c5d7d05137526545b85f (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,787 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.15-py3-none-any.whl#sha256=4519c26955f1d5841904fac29af8566a989712f1b0fcb3c20fd9408fb4bad6c3 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,787 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.14-py3-none-any.whl#sha256=924b42a78a41f83ca1508c3466e93e1867a0dcadb2d3c960af0ae1f80106484b (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,788 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.13-py3-none-any.whl#sha256=3a83f902a80b3bc811ce9be9c6dc4aaea3e915b03c673e0639d9c4ebf534dcef (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,789 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.12-py3-none-any.whl#sha256=30078964442db3a8fdee670295f4056cb4666ad6fdf1eaf2bc4a80a86d054b2b (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,790 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.9-py3-none-any.whl#sha256=b6d6e0388ab5ef2ddd3a2708a52c81f7bc4b52cf1e8ff7ea877f74738e2677ba (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,790 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.8-py3-none-any.whl#sha256=1283ef9ec8cf833ed1d09f9d032d3d445f65ffd94c9e96836bc093450f0657e8 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,791 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.7-py3-none-any.whl#sha256=f98b328d052365f8a32ef8410ae09dea05cb705511e95eb0393c3f3642c30345 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,791 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.6-py3-none-any.whl#sha256=3e3793c4a59dd64f86e2733487678785a4e2b86e46e2495f1fb14468b859e683 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,792 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.5-py3-none-any.whl#sha256=c2ff7807b831fb3247b3d8f7d21229442ed7dc63a97bb8d3d57016ab2d179e84 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,792 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.4-py3-none-any.whl#sha256=2796c6b7ccce7a9681045e5823ea6d8ba3a768fd645335d6a74f64eb1b183aed (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,793 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.3-py3-none-any.whl#sha256=2d0c7a78c5b92be1d8835f7975ad51b9fe25a3d8b659711ae20c82f37003f36f (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,793 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.2-py3-none-any.whl#sha256=6a6b25f8023f325afd5a76bc15448dc0e660cf2ef82f3c62ca393db17f5984f6 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,794 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.1-py3-none-any.whl#sha256=0ca7f983b569de7181fe802c33f7d89e60f0dd8bc6bdccca11004157f8a15e11 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,794 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-1.0.0-py3-none-any.whl#sha256=c32c816be37a1c53155d220930ed097d981c7cbf0fd9b6d794860b226d93faf8 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-07-05T18:47:14,795 Skipping link: not a file: https://www.piwheels.org/simple/oxdna-analysis-tools/ 2022-07-05T18:47:14,796 Skipping link: not a file: https://pypi.org/simple/oxdna-analysis-tools/ 2022-07-05T18:47:14,845 Given no hashes to check 1 links for project 'oxdna-analysis-tools': discarding no candidates 2022-07-05T18:47:14,887 Collecting oxdna-analysis-tools==2.0.1 2022-07-05T18:47:14,891 Created temporary directory: /tmp/pip-unpack-_y36xjmi 2022-07-05T18:47:15,310 Downloading oxDNA_analysis_tools-2.0.1.tar.gz (165 kB) 2022-07-05T18:47:15,715 Added oxdna-analysis-tools==2.0.1 from https://files.pythonhosted.org/packages/7f/c7/ca513a975734a667b486e242809bd330fa8b300f1518c68485067eef9797/oxDNA_analysis_tools-2.0.1.tar.gz#sha256=8a8c14e7de34eecdc5c5d1af0ce23a978e69d013f6d211180c264eb5f2b94fb0 to build tracker '/tmp/pip-build-tracker-mul05tbx' 2022-07-05T18:47:15,728 Created temporary directory: /tmp/pip-build-env-ylwi7j4z 2022-07-05T18:47:15,750 Created temporary directory: /tmp/pip-standalone-pip-ppdg208w 2022-07-05T18:47:18,086 Installing build dependencies: started 2022-07-05T18:47:18,089 Running command pip subprocess to install build dependencies 2022-07-05T18:47:29,349 Using pip 22.1.2 from /tmp/pip-standalone-pip-ppdg208w/__env_pip__.zip/pip (python 3.9) 2022-07-05T18:47:31,140 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-07-05T18:47:35,109 Collecting setuptools>=42 2022-07-05T18:47:35,394 Using cached https://www.piwheels.org/simple/setuptools/setuptools-63.1.0-py3-none-any.whl (1.2 MB) 2022-07-05T18:47:36,053 Collecting wheel 2022-07-05T18:47:36,087 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-07-05T18:47:39,767 Collecting numpy 2022-07-05T18:47:42,226 Using cached https://www.piwheels.org/simple/numpy/numpy-1.23.0-cp39-cp39-linux_armv7l.whl (12.3 MB) 2022-07-05T18:47:46,985 Collecting Cython 2022-07-05T18:47:48,002 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.30-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-07-05T18:47:56,601 Installing collected packages: wheel, setuptools, numpy, Cython 2022-07-05T18:47:56,894 Creating /tmp/pip-build-env-ylwi7j4z/overlay/bin 2022-07-05T18:47:56,899 changing mode of /tmp/pip-build-env-ylwi7j4z/overlay/bin/wheel to 755 2022-07-05T18:48:20,697 changing mode of /tmp/pip-build-env-ylwi7j4z/overlay/bin/f2py to 755 2022-07-05T18:48:20,702 changing mode of /tmp/pip-build-env-ylwi7j4z/overlay/bin/f2py3 to 755 2022-07-05T18:48:20,706 changing mode of /tmp/pip-build-env-ylwi7j4z/overlay/bin/f2py3.9 to 755 2022-07-05T18:48:26,918 changing mode of /tmp/pip-build-env-ylwi7j4z/overlay/bin/cygdb to 755 2022-07-05T18:48:26,923 changing mode of /tmp/pip-build-env-ylwi7j4z/overlay/bin/cython to 755 2022-07-05T18:48:26,928 changing mode of /tmp/pip-build-env-ylwi7j4z/overlay/bin/cythonize to 755 2022-07-05T18:48:26,981 Successfully installed Cython-0.29.30 numpy-1.23.0 setuptools-63.1.0 wheel-0.37.1 2022-07-05T18:48:27,870 Installing build dependencies: finished with status 'done' 2022-07-05T18:48:27,900 Getting requirements to build wheel: started 2022-07-05T18:48:27,902 Running command Getting requirements to build wheel 2022-07-05T18:48:34,922 running egg_info 2022-07-05T18:48:35,527 writing src/oxDNA_analysis_tools.egg-info/PKG-INFO 2022-07-05T18:48:36,149 writing dependency_links to src/oxDNA_analysis_tools.egg-info/dependency_links.txt 2022-07-05T18:48:37,837 writing entry points to src/oxDNA_analysis_tools.egg-info/entry_points.txt 2022-07-05T18:48:38,969 writing requirements to src/oxDNA_analysis_tools.egg-info/requires.txt 2022-07-05T18:48:39,528 writing top-level names to src/oxDNA_analysis_tools.egg-info/top_level.txt 2022-07-05T18:48:40,825 reading manifest file 'src/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-07-05T18:48:40,834 reading manifest template 'MANIFEST.in' 2022-07-05T18:48:40,840 adding license file 'LICENSE' 2022-07-05T18:48:40,851 writing manifest file 'src/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-07-05T18:48:40,856 ################################################################################ 2022-07-05T18:48:40,857 All set up! All scripts in the package can now be run from the command line with 2022-07-05T18:48:40,857 oat 2022-07-05T18:48:40,858 importing functions in your own scripts can be done with 2022-07-05T18:48:40,859 from oxDNA_analysis_tools. import 2022-07-05T18:48:40,860 If you would like to enable autocomplete in Bash, either add 2022-07-05T18:48:40,861 source oat-completion.sh 2022-07-05T18:48:40,862 to your .bashrc or run 2022-07-05T18:48:40,863 cat oat-completion.sh >> ~/.bash_completion 2022-07-05T18:48:40,864 to make autocompletes available to all users. 2022-07-05T18:48:41,181 Getting requirements to build wheel: finished with status 'done' 2022-07-05T18:48:41,207 Created temporary directory: /tmp/pip-modern-metadata-wi18a68w 2022-07-05T18:48:41,213 Preparing metadata (pyproject.toml): started 2022-07-05T18:48:41,215 Running command Preparing metadata (pyproject.toml) 2022-07-05T18:48:47,718 running dist_info 2022-07-05T18:48:48,347 creating /tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info 2022-07-05T18:48:49,004 writing /tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info/PKG-INFO 2022-07-05T18:48:49,571 writing dependency_links to /tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info/dependency_links.txt 2022-07-05T18:48:51,259 writing entry points to /tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info/entry_points.txt 2022-07-05T18:48:52,391 writing requirements to /tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info/requires.txt 2022-07-05T18:48:52,956 writing top-level names to /tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info/top_level.txt 2022-07-05T18:48:52,959 writing manifest file '/tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-07-05T18:48:54,256 reading manifest file '/tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-07-05T18:48:54,260 reading manifest template 'MANIFEST.in' 2022-07-05T18:48:54,267 adding license file 'LICENSE' 2022-07-05T18:48:54,276 writing manifest file '/tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-07-05T18:48:54,280 creating '/tmp/pip-modern-metadata-wi18a68w/oxDNA_analysis_tools-2.0.1.dist-info' 2022-07-05T18:48:54,482 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-07-05T18:48:54,497 ################################################################################ 2022-07-05T18:48:54,498 All set up! All scripts in the package can now be run from the command line with 2022-07-05T18:48:54,499 oat 2022-07-05T18:48:54,500 importing functions in your own scripts can be done with 2022-07-05T18:48:54,501 from oxDNA_analysis_tools. import 2022-07-05T18:48:54,502 If you would like to enable autocomplete in Bash, either add 2022-07-05T18:48:54,503 source oat-completion.sh 2022-07-05T18:48:54,503 to your .bashrc or run 2022-07-05T18:48:54,504 cat oat-completion.sh >> ~/.bash_completion 2022-07-05T18:48:54,505 to make autocompletes available to all users. 2022-07-05T18:48:54,831 Preparing metadata (pyproject.toml): finished with status 'done' 2022-07-05T18:48:54,847 Source in /tmp/pip-wheel-3m96n9ty/oxdna-analysis-tools_d070873c0947466ab6deff95f10cb8b6 has version 2.0.1, which satisfies requirement oxdna-analysis-tools==2.0.1 from https://files.pythonhosted.org/packages/7f/c7/ca513a975734a667b486e242809bd330fa8b300f1518c68485067eef9797/oxDNA_analysis_tools-2.0.1.tar.gz#sha256=8a8c14e7de34eecdc5c5d1af0ce23a978e69d013f6d211180c264eb5f2b94fb0 2022-07-05T18:48:54,849 Removed oxdna-analysis-tools==2.0.1 from https://files.pythonhosted.org/packages/7f/c7/ca513a975734a667b486e242809bd330fa8b300f1518c68485067eef9797/oxDNA_analysis_tools-2.0.1.tar.gz#sha256=8a8c14e7de34eecdc5c5d1af0ce23a978e69d013f6d211180c264eb5f2b94fb0 from build tracker '/tmp/pip-build-tracker-mul05tbx' 2022-07-05T18:48:54,864 Created temporary directory: /tmp/pip-unpack-2_4xk3ai 2022-07-05T18:48:54,865 Building wheels for collected packages: oxdna-analysis-tools 2022-07-05T18:48:54,875 Created temporary directory: /tmp/pip-wheel-f_6yb79t 2022-07-05T18:48:54,875 Destination directory: /tmp/pip-wheel-f_6yb79t 2022-07-05T18:48:54,881 Building wheel for oxdna-analysis-tools (pyproject.toml): started 2022-07-05T18:48:54,883 Running command Building wheel for oxdna-analysis-tools (pyproject.toml) 2022-07-05T18:49:00,827 running bdist_wheel 2022-07-05T18:49:01,511 running build 2022-07-05T18:49:01,512 running build_py 2022-07-05T18:49:02,169 creating build 2022-07-05T18:49:02,170 creating build/lib.linux-armv7l-cpython-39 2022-07-05T18:49:02,171 creating build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,173 copying src/oxDNA_analysis_tools/subset_trajectory.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,178 copying src/oxDNA_analysis_tools/align.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,182 copying src/oxDNA_analysis_tools/clustering.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,186 copying src/oxDNA_analysis_tools/distance.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,190 copying src/oxDNA_analysis_tools/config.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,194 copying src/oxDNA_analysis_tools/generate_force.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,198 copying src/oxDNA_analysis_tools/forces2pairs.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,201 copying src/oxDNA_analysis_tools/db_to_force.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,204 copying src/oxDNA_analysis_tools/oxDNA_PDB.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,209 copying src/oxDNA_analysis_tools/deviations.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,213 copying src/oxDNA_analysis_tools/entry.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,216 copying src/oxDNA_analysis_tools/contact_map.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,220 copying src/oxDNA_analysis_tools/minify.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,223 copying src/oxDNA_analysis_tools/superimpose.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,226 copying src/oxDNA_analysis_tools/duplex_finder.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,230 copying src/oxDNA_analysis_tools/duplex_angle_plotter.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,235 copying src/oxDNA_analysis_tools/__init__.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,237 copying src/oxDNA_analysis_tools/bond_analysis.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,241 copying src/oxDNA_analysis_tools/mean.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,245 copying src/oxDNA_analysis_tools/output_bonds.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,250 copying src/oxDNA_analysis_tools/centroid.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,254 copying src/oxDNA_analysis_tools/backbone_flexibility.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,257 copying src/oxDNA_analysis_tools/multidimensional_scaling_mean.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,262 copying src/oxDNA_analysis_tools/anm_parameterize.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,265 copying src/oxDNA_analysis_tools/plot_energy.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,269 copying src/oxDNA_analysis_tools/pca.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,273 copying src/oxDNA_analysis_tools/oxDNA_PDB2.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-07-05T18:49:02,279 creating build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,281 copying src/oxDNA_analysis_tools/UTILS/data_structures.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,285 copying src/oxDNA_analysis_tools/UTILS/pdb.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,289 copying src/oxDNA_analysis_tools/UTILS/geom.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,293 copying src/oxDNA_analysis_tools/UTILS/oat_multiprocesser.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,296 copying src/oxDNA_analysis_tools/UTILS/protein_to_pdb.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,301 copying src/oxDNA_analysis_tools/UTILS/__init__.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,303 copying src/oxDNA_analysis_tools/UTILS/RyeReader.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,308 copying src/oxDNA_analysis_tools/UTILS/base.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,317 copying src/oxDNA_analysis_tools/UTILS/chunksize.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,320 copying src/oxDNA_analysis_tools/UTILS/readers.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,324 copying src/oxDNA_analysis_tools/UTILS/utils.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:02,328 creating build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:02,330 copying src/oxDNA_analysis_tools/external_force_utils/forces.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:02,335 copying src/oxDNA_analysis_tools/external_force_utils/force_reader.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:02,339 copying src/oxDNA_analysis_tools/external_force_utils/exclude_force.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:02,342 copying src/oxDNA_analysis_tools/external_force_utils/__init__.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:02,344 running egg_info 2022-07-05T18:49:03,554 writing src/oxDNA_analysis_tools.egg-info/PKG-INFO 2022-07-05T18:49:04,119 writing dependency_links to src/oxDNA_analysis_tools.egg-info/dependency_links.txt 2022-07-05T18:49:05,779 writing entry points to src/oxDNA_analysis_tools.egg-info/entry_points.txt 2022-07-05T18:49:06,891 writing requirements to src/oxDNA_analysis_tools.egg-info/requires.txt 2022-07-05T18:49:07,445 writing top-level names to src/oxDNA_analysis_tools.egg-info/top_level.txt 2022-07-05T18:49:07,495 reading manifest file 'src/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-07-05T18:49:07,502 reading manifest template 'MANIFEST.in' 2022-07-05T18:49:07,507 adding license file 'LICENSE' 2022-07-05T18:49:07,518 writing manifest file 'src/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-07-05T18:49:07,523 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-07-05T18:49:07,524 ############################ 2022-07-05T18:49:07,524 # Package would be ignored # 2022-07-05T18:49:07,525 ############################ 2022-07-05T18:49:07,525 Python recognizes 'oxDNA_analysis_tools.cython_utils' as an importable package, however it is 2022-07-05T18:49:07,525 included in the distribution as "data". 2022-07-05T18:49:07,526 This behavior is likely to change in future versions of setuptools (and 2022-07-05T18:49:07,526 therefore is considered deprecated). 2022-07-05T18:49:07,526 Please make sure that 'oxDNA_analysis_tools.cython_utils' is included as a package by using 2022-07-05T18:49:07,527 setuptools' `packages` configuration field or the proper discovery methods. 2022-07-05T18:49:07,527 You can read more about "package discovery" and "data files" on setuptools 2022-07-05T18:49:07,528 documentation page. 2022-07-05T18:49:07,529 !! 2022-07-05T18:49:07,529 check.warn(importable) 2022-07-05T18:49:07,530 creating build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/cython_utils 2022-07-05T18:49:07,530 copying src/oxDNA_analysis_tools/cython_utils/get_confs.c -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/cython_utils 2022-07-05T18:49:07,555 copying src/oxDNA_analysis_tools/cython_utils/get_confs.pyx -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/cython_utils 2022-07-05T18:49:07,559 copying src/oxDNA_analysis_tools/UTILS/dd12_na.pdb -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:07,567 copying src/oxDNA_analysis_tools/UTILS/model.h -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:07,572 copying src/oxDNA_analysis_tools/UTILS/rna_model.h -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:07,589 running build_ext 2022-07-05T18:49:07,601 building 'oxDNA_analysis_tools.UTILS.get_confs' extension 2022-07-05T18:49:07,603 creating build/temp.linux-armv7l-cpython-39 2022-07-05T18:49:07,603 creating build/temp.linux-armv7l-cpython-39/src 2022-07-05T18:49:07,604 creating build/temp.linux-armv7l-cpython-39/src/oxDNA_analysis_tools 2022-07-05T18:49:07,605 creating build/temp.linux-armv7l-cpython-39/src/oxDNA_analysis_tools/cython_utils 2022-07-05T18:49:07,607 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c src/oxDNA_analysis_tools/cython_utils/get_confs.c -o build/temp.linux-armv7l-cpython-39/src/oxDNA_analysis_tools/cython_utils/get_confs.o 2022-07-05T18:49:08,418 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-07-05T18:49:08,418 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-07-05T18:49:08,419 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-07-05T18:49:08,419 from src/oxDNA_analysis_tools/cython_utils/get_confs.c:711: 2022-07-05T18:49:08,419 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-07-05T18:49:08,420 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-07-05T18:49:08,420 | ^~~~~~~ 2022-07-05T18:49:08,569 src/oxDNA_analysis_tools/cython_utils/get_confs.c: In function ‘__pyx_pf_20oxDNA_analysis_tools_5UTILS_9get_confs_cget_confs’: 2022-07-05T18:49:08,571 src/oxDNA_analysis_tools/cython_utils/get_confs.c:2357:16: warning: passing argument 1 of ‘fread’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2022-07-05T18:49:08,572 2357 | (void)(fread(__pyx_v_chunk, __pyx_v_chunk_size, 1, __pyx_v_traj_file)); 2022-07-05T18:49:08,572 | ^~~~~~~~~~~~~ 2022-07-05T18:49:08,573 In file included from /usr/include/python3.9/Python.h:25, 2022-07-05T18:49:08,573 from src/oxDNA_analysis_tools/cython_utils/get_confs.c:19: 2022-07-05T18:49:08,573 /usr/include/stdio.h:646:39: note: expected ‘void * restrict’ but argument is of type ‘const char *’ 2022-07-05T18:49:08,574 646 | extern size_t fread (void *__restrict __ptr, size_t __size, 2022-07-05T18:49:08,574 | ~~~~~~~~~~~~~~~~~^~~~~ 2022-07-05T18:49:08,583 src/oxDNA_analysis_tools/cython_utils/get_confs.c:2442:77: warning: passing argument 1 of ‘__pyx_f_20oxDNA_analysis_tools_5UTILS_9get_confs_parse_conf’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2022-07-05T18:49:08,584 2442 | __pyx_t_4 = __pyx_f_20oxDNA_analysis_tools_5UTILS_9get_confs_parse_conf(__pyx_v_chunk, (__pyx_v_conf_starts[__pyx_t_9]), (__pyx_v_sizes[__pyx_t_13]), __pyx_v_nbases); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 50, __pyx_L1_error) 2022-07-05T18:49:08,584 | ^~~~~~~~~~~~~ 2022-07-05T18:49:08,585 src/oxDNA_analysis_tools/cython_utils/get_confs.c:1732:78: note: expected ‘char *’ but argument is of type ‘const char *’ 2022-07-05T18:49:08,585 1732 | static PyObject *__pyx_f_20oxDNA_analysis_tools_5UTILS_9get_confs_parse_conf(char *, int, int, int); /*proto*/ 2022-07-05T18:49:08,585 | ^~~~~~ 2022-07-05T18:49:08,588 src/oxDNA_analysis_tools/cython_utils/get_confs.c:2482:8: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2022-07-05T18:49:08,589 2482 | free(__pyx_v_chunk); 2022-07-05T18:49:08,589 | ^~~~~~~~~~~~~ 2022-07-05T18:49:08,589 In file included from /usr/include/python3.9/Python.h:34, 2022-07-05T18:49:08,590 from src/oxDNA_analysis_tools/cython_utils/get_confs.c:19: 2022-07-05T18:49:08,590 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2022-07-05T18:49:08,590 565 | extern void free (void *__ptr) __THROW; 2022-07-05T18:49:08,591 | ~~~~~~^~~~~ 2022-07-05T18:49:08,611 src/oxDNA_analysis_tools/cython_utils/get_confs.c: In function ‘__pyx_f_20oxDNA_analysis_tools_5UTILS_9get_confs_parse_conf’: 2022-07-05T18:49:08,613 src/oxDNA_analysis_tools/cython_utils/get_confs.c:2799:24: warning: passing argument 1 of ‘strtok’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2022-07-05T18:49:08,614 2799 | __pyx_v_ptr = strtok(__pyx_v_ptr, ((char const *)"t = ")); 2022-07-05T18:49:08,614 | ^~~~~~~~~~~ 2022-07-05T18:49:08,615 In file included from /usr/include/python3.9/Python.h:30, 2022-07-05T18:49:08,615 from src/oxDNA_analysis_tools/cython_utils/get_confs.c:19: 2022-07-05T18:49:08,615 /usr/include/string.h:336:39: note: expected ‘char * restrict’ but argument is of type ‘const char *’ 2022-07-05T18:49:08,615 336 | extern char *strtok (char *__restrict __s, const char *__restrict __delim) 2022-07-05T18:49:08,616 | ~~~~~~~~~~~~~~~~~^~~ 2022-07-05T18:49:18,118 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/src/oxDNA_analysis_tools/cython_utils/get_confs.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/get_confs.cpython-39-arm-linux-gnueabihf.so 2022-07-05T18:49:19,587 installing to build/bdist.linux-armv7l/wheel 2022-07-05T18:49:19,588 running install 2022-07-05T18:49:19,651 running install_lib 2022-07-05T18:49:20,237 creating build/bdist.linux-armv7l 2022-07-05T18:49:20,238 creating build/bdist.linux-armv7l/wheel 2022-07-05T18:49:20,242 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,244 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/subset_trajectory.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,249 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/align.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,253 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/clustering.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,258 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/distance.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,262 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/config.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,266 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/generate_force.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,270 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/forces2pairs.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,273 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/db_to_force.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,276 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/oxDNA_PDB.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,280 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/deviations.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,284 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/entry.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,288 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/contact_map.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,292 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/minify.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,296 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,298 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/dd12_na.pdb -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,306 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/get_confs.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,329 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/model.h -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,333 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/data_structures.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,336 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/pdb.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,341 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/geom.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,345 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/rna_model.h -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,351 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/oat_multiprocesser.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,354 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/protein_to_pdb.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,358 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/__init__.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,361 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/RyeReader.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,365 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/base.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,373 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/chunksize.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,377 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/readers.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,380 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/utils.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-07-05T18:49:20,385 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/cython_utils 2022-07-05T18:49:20,386 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/cython_utils/get_confs.pyx -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/cython_utils 2022-07-05T18:49:20,390 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/cython_utils/get_confs.c -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/cython_utils 2022-07-05T18:49:20,410 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/superimpose.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,414 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/duplex_finder.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,418 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/duplex_angle_plotter.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,423 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/__init__.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,426 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/bond_analysis.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,430 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/mean.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,434 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/output_bonds.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,437 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/centroid.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,441 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/backbone_flexibility.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,445 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/multidimensional_scaling_mean.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,450 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:20,451 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils/forces.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:20,455 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils/force_reader.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:20,458 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils/exclude_force.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:20,461 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils/__init__.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/external_force_utils 2022-07-05T18:49:20,464 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/anm_parameterize.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,467 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/plot_energy.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,470 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/pca.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,474 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/oxDNA_PDB2.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-07-05T18:49:20,477 running install_egg_info 2022-07-05T18:49:21,082 Copying src/oxDNA_analysis_tools.egg-info to build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools-2.0.1-py3.9.egg-info 2022-07-05T18:49:21,109 running install_scripts 2022-07-05T18:49:21,245 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-07-05T18:49:21,298 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools-2.0.1.dist-info/WHEEL 2022-07-05T18:49:21,303 creating '/tmp/pip-wheel-f_6yb79t/tmpqtyis7e6/oxDNA_analysis_tools-2.0.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-07-05T18:49:21,308 adding 'oxDNA_analysis_tools/__init__.py' 2022-07-05T18:49:21,312 adding 'oxDNA_analysis_tools/align.py' 2022-07-05T18:49:21,315 adding 'oxDNA_analysis_tools/anm_parameterize.py' 2022-07-05T18:49:21,318 adding 'oxDNA_analysis_tools/backbone_flexibility.py' 2022-07-05T18:49:21,321 adding 'oxDNA_analysis_tools/bond_analysis.py' 2022-07-05T18:49:21,325 adding 'oxDNA_analysis_tools/centroid.py' 2022-07-05T18:49:21,329 adding 'oxDNA_analysis_tools/clustering.py' 2022-07-05T18:49:21,332 adding 'oxDNA_analysis_tools/config.py' 2022-07-05T18:49:21,335 adding 'oxDNA_analysis_tools/contact_map.py' 2022-07-05T18:49:21,337 adding 'oxDNA_analysis_tools/db_to_force.py' 2022-07-05T18:49:21,341 adding 'oxDNA_analysis_tools/deviations.py' 2022-07-05T18:49:21,346 adding 'oxDNA_analysis_tools/distance.py' 2022-07-05T18:49:21,350 adding 'oxDNA_analysis_tools/duplex_angle_plotter.py' 2022-07-05T18:49:21,354 adding 'oxDNA_analysis_tools/duplex_finder.py' 2022-07-05T18:49:21,357 adding 'oxDNA_analysis_tools/entry.py' 2022-07-05T18:49:21,359 adding 'oxDNA_analysis_tools/forces2pairs.py' 2022-07-05T18:49:21,362 adding 'oxDNA_analysis_tools/generate_force.py' 2022-07-05T18:49:21,365 adding 'oxDNA_analysis_tools/mean.py' 2022-07-05T18:49:21,369 adding 'oxDNA_analysis_tools/minify.py' 2022-07-05T18:49:21,372 adding 'oxDNA_analysis_tools/multidimensional_scaling_mean.py' 2022-07-05T18:49:21,375 adding 'oxDNA_analysis_tools/output_bonds.py' 2022-07-05T18:49:21,380 adding 'oxDNA_analysis_tools/oxDNA_PDB.py' 2022-07-05T18:49:21,383 adding 'oxDNA_analysis_tools/oxDNA_PDB2.py' 2022-07-05T18:49:21,387 adding 'oxDNA_analysis_tools/pca.py' 2022-07-05T18:49:21,391 adding 'oxDNA_analysis_tools/plot_energy.py' 2022-07-05T18:49:21,394 adding 'oxDNA_analysis_tools/subset_trajectory.py' 2022-07-05T18:49:21,396 adding 'oxDNA_analysis_tools/superimpose.py' 2022-07-05T18:49:21,402 adding 'oxDNA_analysis_tools/UTILS/RyeReader.py' 2022-07-05T18:49:21,405 adding 'oxDNA_analysis_tools/UTILS/__init__.py' 2022-07-05T18:49:21,424 adding 'oxDNA_analysis_tools/UTILS/base.py' 2022-07-05T18:49:21,427 adding 'oxDNA_analysis_tools/UTILS/chunksize.py' 2022-07-05T18:49:21,430 adding 'oxDNA_analysis_tools/UTILS/data_structures.py' 2022-07-05T18:49:21,449 adding 'oxDNA_analysis_tools/UTILS/dd12_na.pdb' 2022-07-05T18:49:21,453 adding 'oxDNA_analysis_tools/UTILS/geom.py' 2022-07-05T18:49:21,598 adding 'oxDNA_analysis_tools/UTILS/get_confs.cpython-39-arm-linux-gnueabihf.so' 2022-07-05T18:49:21,606 adding 'oxDNA_analysis_tools/UTILS/model.h' 2022-07-05T18:49:21,609 adding 'oxDNA_analysis_tools/UTILS/oat_multiprocesser.py' 2022-07-05T18:49:21,613 adding 'oxDNA_analysis_tools/UTILS/pdb.py' 2022-07-05T18:49:21,617 adding 'oxDNA_analysis_tools/UTILS/protein_to_pdb.py' 2022-07-05T18:49:21,621 adding 'oxDNA_analysis_tools/UTILS/readers.py' 2022-07-05T18:49:21,630 adding 'oxDNA_analysis_tools/UTILS/rna_model.h' 2022-07-05T18:49:21,633 adding 'oxDNA_analysis_tools/UTILS/utils.py' 2022-07-05T18:49:21,694 adding 'oxDNA_analysis_tools/cython_utils/get_confs.c' 2022-07-05T18:49:21,703 adding 'oxDNA_analysis_tools/cython_utils/get_confs.pyx' 2022-07-05T18:49:21,707 adding 'oxDNA_analysis_tools/external_force_utils/__init__.py' 2022-07-05T18:49:21,709 adding 'oxDNA_analysis_tools/external_force_utils/exclude_force.py' 2022-07-05T18:49:21,712 adding 'oxDNA_analysis_tools/external_force_utils/force_reader.py' 2022-07-05T18:49:21,714 adding 'oxDNA_analysis_tools/external_force_utils/forces.py' 2022-07-05T18:49:21,731 adding 'oxDNA_analysis_tools-2.0.1.dist-info/LICENSE' 2022-07-05T18:49:21,738 adding 'oxDNA_analysis_tools-2.0.1.dist-info/METADATA' 2022-07-05T18:49:21,740 adding 'oxDNA_analysis_tools-2.0.1.dist-info/WHEEL' 2022-07-05T18:49:21,742 adding 'oxDNA_analysis_tools-2.0.1.dist-info/entry_points.txt' 2022-07-05T18:49:21,743 adding 'oxDNA_analysis_tools-2.0.1.dist-info/top_level.txt' 2022-07-05T18:49:21,746 adding 'oxDNA_analysis_tools-2.0.1.dist-info/RECORD' 2022-07-05T18:49:21,768 removing build/bdist.linux-armv7l/wheel 2022-07-05T18:49:21,803 ################################################################################ 2022-07-05T18:49:21,803 All set up! All scripts in the package can now be run from the command line with 2022-07-05T18:49:21,804 oat 2022-07-05T18:49:21,805 importing functions in your own scripts can be done with 2022-07-05T18:49:21,805 from oxDNA_analysis_tools. import 2022-07-05T18:49:21,806 If you would like to enable autocomplete in Bash, either add 2022-07-05T18:49:21,806 source oat-completion.sh 2022-07-05T18:49:21,807 to your .bashrc or run 2022-07-05T18:49:21,808 cat oat-completion.sh >> ~/.bash_completion 2022-07-05T18:49:21,808 to make autocompletes available to all users. 2022-07-05T18:49:22,203 Building wheel for oxdna-analysis-tools (pyproject.toml): finished with status 'done' 2022-07-05T18:49:22,231 Created wheel for oxdna-analysis-tools: filename=oxDNA_analysis_tools-2.0.1-cp39-cp39-linux_armv7l.whl size=289943 sha256=f7d6de160cc9acc24c6c9622374e866141bbcbf4a4ddf702206ba3b5a963b859 2022-07-05T18:49:22,233 Stored in directory: /tmp/pip-ephem-wheel-cache-cy6d6i5w/wheels/4d/b8/26/7325ddc5b3d66dc137bcf946bea66751604c995e3ed52dfcc9 2022-07-05T18:49:22,265 Successfully built oxdna-analysis-tools 2022-07-05T18:49:22,300 Removed build tracker: '/tmp/pip-build-tracker-mul05tbx'