2022-06-23T07:08:06,038 Created temporary directory: /tmp/pip-ephem-wheel-cache-cp40lt5s 2022-06-23T07:08:06,043 Created temporary directory: /tmp/pip-build-tracker-z1ocde1i 2022-06-23T07:08:06,044 Initialized build tracking at /tmp/pip-build-tracker-z1ocde1i 2022-06-23T07:08:06,044 Created build tracker: /tmp/pip-build-tracker-z1ocde1i 2022-06-23T07:08:06,045 Entered build tracker: /tmp/pip-build-tracker-z1ocde1i 2022-06-23T07:08:06,046 Created temporary directory: /tmp/pip-wheel-bwylt_px 2022-06-23T07:08:06,116 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-23T07:08:06,129 2 location(s) to search for versions of oxdna-analysis-tools: 2022-06-23T07:08:06,129 * https://pypi.org/simple/oxdna-analysis-tools/ 2022-06-23T07:08:06,129 * https://www.piwheels.org/simple/oxdna-analysis-tools/ 2022-06-23T07:08:06,130 Fetching project page and analyzing links: https://pypi.org/simple/oxdna-analysis-tools/ 2022-06-23T07:08:06,131 Getting page 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https://files.pythonhosted.org/packages/89/ff/395029dea21f844393d989cbb26c614dd86f822bba65d78ed5a7748aca6a/oxDNA_analysis_tools-1.0.1-py3-none-any.whl#sha256=3221408dd47a42b38484906b35d19479588ff4069288f9ce7d7817897da455c7 (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-06-23T07:08:06,288 Found link https://files.pythonhosted.org/packages/df/13/17bfb0a3fd14aa842b566f34308d54529d61ea01fada217af9048971d50c/oxDNA_analysis_tools-1.0.1.tar.gz#sha256=a3e8ae09b1258872561a5559f458a72942879cba8a07a0f24caaec7e409d4cb1 (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6), version: 1.0.1 2022-06-23T07:08:06,289 Skipping link: No binaries permitted for oxdna-analysis-tools: https://files.pythonhosted.org/packages/82/49/f5e696f37f5715a0aeb1ef04eb86660c5659ef4bf2f4fb8903dc7227e118/oxDNA_analysis_tools-1.0.2-py3-none-any.whl#sha256=16719e55b02c4da05c3f2f954c4e5dc43e599213876539e8abff5160cd0caece (from 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(requires-python:>=3.6), version: 1.0.9 2022-06-23T07:08:06,305 Skipping link: No binaries permitted for oxdna-analysis-tools: https://files.pythonhosted.org/packages/67/90/5a0d0aa16863c43c624f37ebb6dce78b9ae4d8f5bd3b3e60963382fbeb3a/oxDNA_analysis_tools-1.0.12-py3-none-any.whl#sha256=292e000a42eb4df44ab0fdc1896d7554a6839ec9adb8bb350dd7017116aec577 (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-06-23T07:08:06,306 Found link https://files.pythonhosted.org/packages/dd/ee/a25cb9abd84882306389318f74d19f3b40bcdaed4caaca0fbf223a228027/oxDNA_analysis_tools-1.0.12.tar.gz#sha256=c837756ed512c604b3356ea1375cc68472eaf28c2497e5449a0a72d60a30542f (from https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6), version: 1.0.12 2022-06-23T07:08:06,306 Skipping link: No binaries permitted for oxdna-analysis-tools: 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https://pypi.org/simple/oxdna-analysis-tools/) (requires-python:>=3.6) 2022-06-23T07:08:06,310 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 2022-06-23T07:08:06,311 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) 2022-06-23T07:08:06,312 Found link 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(requires-python:>=3.6), version: 1.0.16 2022-06-23T07:08:06,315 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 2022-06-23T07:08:06,316 Fetching project page and analyzing links: https://www.piwheels.org/simple/oxdna-analysis-tools/ 2022-06-23T07:08:06,317 Getting page https://www.piwheels.org/simple/oxdna-analysis-tools/ 2022-06-23T07:08:06,319 Found index url https://www.piwheels.org/simple 2022-06-23T07:08:06,539 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-2.0.0-cp37-cp37m-linux_armv7l.whl#sha256=99e35c7514ec7f1fc7d369d8ee629d21b452c3f436e50f45ea48829422fa4799 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.7) 2022-06-23T07:08:06,540 Skipping link: No binaries permitted for oxdna-analysis-tools: https://www.piwheels.org/simple/oxdna-analysis-tools/oxDNA_analysis_tools-2.0.0-cp37-cp37m-linux_armv6l.whl#sha256=99e35c7514ec7f1fc7d369d8ee629d21b452c3f436e50f45ea48829422fa4799 (from https://www.piwheels.org/simple/oxdna-analysis-tools/) (requires-python:>=3.7) 2022-06-23T07:08:06,540 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) 2022-06-23T07:08:06,541 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 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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) 2022-06-23T07:08:06,544 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) 2022-06-23T07:08:06,545 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) 2022-06-23T07:08:06,545 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) 2022-06-23T07:08:06,546 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) 2022-06-23T07:08:06,546 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) 2022-06-23T07:08:06,547 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) 2022-06-23T07:08:06,547 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) 2022-06-23T07:08:06,548 Skipping link: not a file: https://www.piwheels.org/simple/oxdna-analysis-tools/ 2022-06-23T07:08:06,549 Skipping link: not a file: https://pypi.org/simple/oxdna-analysis-tools/ 2022-06-23T07:08:06,599 Given no hashes to check 1 links for project 'oxdna-analysis-tools': discarding no candidates 2022-06-23T07:08:06,640 Collecting oxdna-analysis-tools==2.0.0 2022-06-23T07:08:06,644 Created temporary directory: /tmp/pip-unpack-ge3lhmd8 2022-06-23T07:08:06,743 Downloading oxDNA_analysis_tools-2.0.0.tar.gz (164 kB) 2022-06-23T07:08:07,152 Added oxdna-analysis-tools==2.0.0 from https://files.pythonhosted.org/packages/f6/6d/4d84b7745a400f812af281066a7958894b4979d8f6681b44f90c9e7b38d0/oxDNA_analysis_tools-2.0.0.tar.gz#sha256=7cfe7ee4bdd71ad70409e040457889116ee6f02f038d1c972ce1c1366c24798f to build tracker '/tmp/pip-build-tracker-z1ocde1i' 2022-06-23T07:08:07,165 Created temporary directory: /tmp/pip-build-env-0owoyn19 2022-06-23T07:08:07,185 Created temporary directory: /tmp/pip-standalone-pip-whxzghym 2022-06-23T07:08:09,584 Installing build dependencies: started 2022-06-23T07:08:09,586 Running command pip subprocess to install build dependencies 2022-06-23T07:08:20,792 Using pip 22.1.2 from /tmp/pip-standalone-pip-whxzghym/__env_pip__.zip/pip (python 3.9) 2022-06-23T07:08:22,406 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-23T07:08:26,365 Collecting setuptools>=42 2022-06-23T07:08:26,660 Using cached https://www.piwheels.org/simple/setuptools/setuptools-62.6.0-py3-none-any.whl (1.2 MB) 2022-06-23T07:08:27,357 Collecting wheel 2022-06-23T07:08:27,390 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-06-23T07:08:31,055 Collecting numpy 2022-06-23T07:08:31,094 Downloading https://www.piwheels.org/simple/numpy/numpy-1.23.0-cp39-cp39-linux_armv7l.whl (12.3 MB) 2022-06-23T07:08:33,928 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.3/12.3 MB 4.0 MB/s eta 0:00:00 2022-06-23T07:08:38,514 Collecting Cython 2022-06-23T07:08:39,562 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.30-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-06-23T07:08:47,237 Installing collected packages: wheel, setuptools, numpy, Cython 2022-06-23T07:08:47,534 Creating /tmp/pip-build-env-0owoyn19/overlay/bin 2022-06-23T07:08:47,539 changing mode of /tmp/pip-build-env-0owoyn19/overlay/bin/wheel to 755 2022-06-23T07:09:11,590 changing mode of /tmp/pip-build-env-0owoyn19/overlay/bin/f2py to 755 2022-06-23T07:09:11,595 changing mode of /tmp/pip-build-env-0owoyn19/overlay/bin/f2py3 to 755 2022-06-23T07:09:11,599 changing mode of /tmp/pip-build-env-0owoyn19/overlay/bin/f2py3.9 to 755 2022-06-23T07:09:17,953 changing mode of /tmp/pip-build-env-0owoyn19/overlay/bin/cygdb to 755 2022-06-23T07:09:17,957 changing mode of /tmp/pip-build-env-0owoyn19/overlay/bin/cython to 755 2022-06-23T07:09:17,962 changing mode of /tmp/pip-build-env-0owoyn19/overlay/bin/cythonize to 755 2022-06-23T07:09:18,015 Successfully installed Cython-0.29.30 numpy-1.23.0 setuptools-62.6.0 wheel-0.37.1 2022-06-23T07:09:18,893 Installing build dependencies: finished with status 'done' 2022-06-23T07:09:18,922 Getting requirements to build wheel: started 2022-06-23T07:09:18,924 Running command Getting requirements to build wheel 2022-06-23T07:09:26,080 running egg_info 2022-06-23T07:09:26,675 writing src/oxDNA_analysis_tools.egg-info/PKG-INFO 2022-06-23T07:09:27,299 writing dependency_links to src/oxDNA_analysis_tools.egg-info/dependency_links.txt 2022-06-23T07:09:28,982 writing entry points to src/oxDNA_analysis_tools.egg-info/entry_points.txt 2022-06-23T07:09:30,103 writing requirements to src/oxDNA_analysis_tools.egg-info/requires.txt 2022-06-23T07:09:30,665 writing top-level names to src/oxDNA_analysis_tools.egg-info/top_level.txt 2022-06-23T07:09:31,951 reading manifest file 'src/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-06-23T07:09:31,961 reading manifest template 'MANIFEST.in' 2022-06-23T07:09:31,967 adding license file 'LICENSE' 2022-06-23T07:09:31,978 writing manifest file 'src/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-06-23T07:09:31,983 ################################################################################ 2022-06-23T07:09:31,984 All set up! All scripts in the package can now be run from the command line with 2022-06-23T07:09:31,984 oat 2022-06-23T07:09:31,985 importing functions in your own scripts can be done with 2022-06-23T07:09:31,986 from oxDNA_analysis_tools. import 2022-06-23T07:09:31,986 If you would like to enable autocomplete in Bash, either add 2022-06-23T07:09:31,987 source oat-completion.sh 2022-06-23T07:09:31,988 to your .bashrc or run 2022-06-23T07:09:31,988 cat oat-completion.sh >> ~/.bash_completion 2022-06-23T07:09:31,989 to make autocompletes available to all users. 2022-06-23T07:09:32,312 Getting requirements to build wheel: finished with status 'done' 2022-06-23T07:09:32,335 Created temporary directory: /tmp/pip-modern-metadata-et89xifx 2022-06-23T07:09:32,341 Preparing metadata (pyproject.toml): started 2022-06-23T07:09:32,343 Running command Preparing metadata (pyproject.toml) 2022-06-23T07:09:38,740 running dist_info 2022-06-23T07:09:39,351 creating /tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info 2022-06-23T07:09:39,992 writing /tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info/PKG-INFO 2022-06-23T07:09:40,547 writing dependency_links to /tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info/dependency_links.txt 2022-06-23T07:09:42,199 writing entry points to /tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info/entry_points.txt 2022-06-23T07:09:43,301 writing requirements to /tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info/requires.txt 2022-06-23T07:09:43,856 writing top-level names to /tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info/top_level.txt 2022-06-23T07:09:43,859 writing manifest file '/tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-06-23T07:09:45,136 reading manifest file '/tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-06-23T07:09:45,139 reading manifest template 'MANIFEST.in' 2022-06-23T07:09:45,145 adding license file 'LICENSE' 2022-06-23T07:09:45,154 writing manifest file '/tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-06-23T07:09:45,157 creating '/tmp/pip-modern-metadata-et89xifx/oxDNA_analysis_tools-2.0.0.dist-info' 2022-06-23T07:09:45,355 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-06-23T07:09:45,371 ################################################################################ 2022-06-23T07:09:45,371 All set up! All scripts in the package can now be run from the command line with 2022-06-23T07:09:45,372 oat 2022-06-23T07:09:45,372 importing functions in your own scripts can be done with 2022-06-23T07:09:45,373 from oxDNA_analysis_tools. import 2022-06-23T07:09:45,373 If you would like to enable autocomplete in Bash, either add 2022-06-23T07:09:45,374 source oat-completion.sh 2022-06-23T07:09:45,374 to your .bashrc or run 2022-06-23T07:09:45,375 cat oat-completion.sh >> ~/.bash_completion 2022-06-23T07:09:45,376 to make autocompletes available to all users. 2022-06-23T07:09:45,706 Preparing metadata (pyproject.toml): finished with status 'done' 2022-06-23T07:09:45,721 Source in /tmp/pip-wheel-bwylt_px/oxdna-analysis-tools_08f9ff4db6414e27b11678f5f3283eb5 has version 2.0.0, which satisfies requirement oxdna-analysis-tools==2.0.0 from https://files.pythonhosted.org/packages/f6/6d/4d84b7745a400f812af281066a7958894b4979d8f6681b44f90c9e7b38d0/oxDNA_analysis_tools-2.0.0.tar.gz#sha256=7cfe7ee4bdd71ad70409e040457889116ee6f02f038d1c972ce1c1366c24798f 2022-06-23T07:09:45,724 Removed oxdna-analysis-tools==2.0.0 from https://files.pythonhosted.org/packages/f6/6d/4d84b7745a400f812af281066a7958894b4979d8f6681b44f90c9e7b38d0/oxDNA_analysis_tools-2.0.0.tar.gz#sha256=7cfe7ee4bdd71ad70409e040457889116ee6f02f038d1c972ce1c1366c24798f from build tracker '/tmp/pip-build-tracker-z1ocde1i' 2022-06-23T07:09:45,739 Created temporary directory: /tmp/pip-unpack-gwlk9_ns 2022-06-23T07:09:45,740 Building wheels for collected packages: oxdna-analysis-tools 2022-06-23T07:09:45,749 Created temporary directory: /tmp/pip-wheel-ya9ily9d 2022-06-23T07:09:45,749 Destination directory: /tmp/pip-wheel-ya9ily9d 2022-06-23T07:09:45,754 Building wheel for oxdna-analysis-tools (pyproject.toml): started 2022-06-23T07:09:45,756 Running command Building wheel for oxdna-analysis-tools (pyproject.toml) 2022-06-23T07:09:51,752 running bdist_wheel 2022-06-23T07:09:52,432 running build 2022-06-23T07:09:52,433 running build_py 2022-06-23T07:09:53,084 creating build 2022-06-23T07:09:53,084 creating build/lib.linux-armv7l-cpython-39 2022-06-23T07:09:53,086 creating build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,088 copying src/oxDNA_analysis_tools/forces2pairs.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,092 copying src/oxDNA_analysis_tools/mean.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,096 copying src/oxDNA_analysis_tools/anm_parameterize.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,099 copying src/oxDNA_analysis_tools/subset_trajectory.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,103 copying src/oxDNA_analysis_tools/minify.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,106 copying src/oxDNA_analysis_tools/align.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,110 copying src/oxDNA_analysis_tools/backbone_flexibility.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,114 copying src/oxDNA_analysis_tools/distance.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,118 copying src/oxDNA_analysis_tools/centroid.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,122 copying src/oxDNA_analysis_tools/plot_energy.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,125 copying src/oxDNA_analysis_tools/pca.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,129 copying src/oxDNA_analysis_tools/__init__.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,132 copying src/oxDNA_analysis_tools/db_to_force.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,135 copying src/oxDNA_analysis_tools/entry.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,139 copying src/oxDNA_analysis_tools/deviations.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,143 copying src/oxDNA_analysis_tools/bond_analysis.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,147 copying src/oxDNA_analysis_tools/generate_force.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,151 copying src/oxDNA_analysis_tools/config.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,156 copying src/oxDNA_analysis_tools/output_bonds.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,160 copying src/oxDNA_analysis_tools/oxDNA_PDB2.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,165 copying src/oxDNA_analysis_tools/contact_map.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,169 copying src/oxDNA_analysis_tools/duplex_finder.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,174 copying src/oxDNA_analysis_tools/oxDNA_PDB.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,179 copying src/oxDNA_analysis_tools/clustering.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,183 copying src/oxDNA_analysis_tools/duplex_angle_plotter.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,189 copying src/oxDNA_analysis_tools/multidimensional_scaling_mean.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,193 copying src/oxDNA_analysis_tools/superimpose.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools 2022-06-23T07:09:53,198 creating build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-06-23T07:09:53,200 copying src/oxDNA_analysis_tools/external_force_utils/forces.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-06-23T07:09:53,205 copying src/oxDNA_analysis_tools/external_force_utils/__init__.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-06-23T07:09:53,209 copying src/oxDNA_analysis_tools/external_force_utils/exclude_force.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-06-23T07:09:53,213 copying src/oxDNA_analysis_tools/external_force_utils/force_reader.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/external_force_utils 2022-06-23T07:09:53,219 creating build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,221 copying src/oxDNA_analysis_tools/UTILS/RyeReader.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,226 copying src/oxDNA_analysis_tools/UTILS/base.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,234 copying src/oxDNA_analysis_tools/UTILS/pdb.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,239 copying src/oxDNA_analysis_tools/UTILS/data_structures.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,243 copying src/oxDNA_analysis_tools/UTILS/chunksize.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,248 copying src/oxDNA_analysis_tools/UTILS/readers.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,251 copying src/oxDNA_analysis_tools/UTILS/oat_multiprocesser.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,254 copying src/oxDNA_analysis_tools/UTILS/__init__.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,257 copying src/oxDNA_analysis_tools/UTILS/protein_to_pdb.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,262 copying src/oxDNA_analysis_tools/UTILS/utils.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,265 copying src/oxDNA_analysis_tools/UTILS/geom.py -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:53,269 running egg_info 2022-06-23T07:09:54,475 writing src/oxDNA_analysis_tools.egg-info/PKG-INFO 2022-06-23T07:09:55,033 writing dependency_links to src/oxDNA_analysis_tools.egg-info/dependency_links.txt 2022-06-23T07:09:56,690 writing entry points to src/oxDNA_analysis_tools.egg-info/entry_points.txt 2022-06-23T07:09:57,795 writing requirements to src/oxDNA_analysis_tools.egg-info/requires.txt 2022-06-23T07:09:58,349 writing top-level names to src/oxDNA_analysis_tools.egg-info/top_level.txt 2022-06-23T07:09:58,397 reading manifest file 'src/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-06-23T07:09:58,403 reading manifest template 'MANIFEST.in' 2022-06-23T07:09:58,408 adding license file 'LICENSE' 2022-06-23T07:09:58,419 writing manifest file 'src/oxDNA_analysis_tools.egg-info/SOURCES.txt' 2022-06-23T07:09:58,424 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: !! 2022-06-23T07:09:58,425 ############################ 2022-06-23T07:09:58,425 # Package would be ignored # 2022-06-23T07:09:58,425 ############################ 2022-06-23T07:09:58,426 Python recognizes 'oxDNA_analysis_tools.cython_utils' as an importable package, however it is 2022-06-23T07:09:58,426 included in the distribution as "data". 2022-06-23T07:09:58,426 This behavior is likely to change in future versions of setuptools (and 2022-06-23T07:09:58,427 therefore is considered deprecated). 2022-06-23T07:09:58,427 Please make sure that 'oxDNA_analysis_tools.cython_utils' is included as a package by using 2022-06-23T07:09:58,428 setuptools' `packages` configuration field or the proper discovery methods. 2022-06-23T07:09:58,428 You can read more about "package discovery" and "data files" on setuptools 2022-06-23T07:09:58,429 documentation page. 2022-06-23T07:09:58,430 !! 2022-06-23T07:09:58,430 check.warn(importable) 2022-06-23T07:09:58,431 creating build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/cython_utils 2022-06-23T07:09:58,431 copying src/oxDNA_analysis_tools/cython_utils/get_confs.c -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/cython_utils 2022-06-23T07:09:58,449 copying src/oxDNA_analysis_tools/cython_utils/get_confs.pyx -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/cython_utils 2022-06-23T07:09:58,453 copying src/oxDNA_analysis_tools/UTILS/dd12_na.pdb -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:58,460 copying src/oxDNA_analysis_tools/UTILS/model.h -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:58,465 copying src/oxDNA_analysis_tools/UTILS/rna_model.h -> build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS 2022-06-23T07:09:58,479 running build_ext 2022-06-23T07:09:58,491 building 'oxDNA_analysis_tools.UTILS.get_confs' extension 2022-06-23T07:09:58,492 creating build/temp.linux-armv7l-cpython-39 2022-06-23T07:09:58,493 creating build/temp.linux-armv7l-cpython-39/src 2022-06-23T07:09:58,494 creating build/temp.linux-armv7l-cpython-39/src/oxDNA_analysis_tools 2022-06-23T07:09:58,495 creating build/temp.linux-armv7l-cpython-39/src/oxDNA_analysis_tools/cython_utils 2022-06-23T07:09:58,497 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 2022-06-23T07:09:59,367 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-23T07:09:59,368 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-23T07:09:59,368 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-23T07:09:59,369 from src/oxDNA_analysis_tools/cython_utils/get_confs.c:711: 2022-06-23T07:09:59,369 /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] 2022-06-23T07:09:59,369 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-23T07:09:59,370 | ^~~~~~~ 2022-06-23T07:09:59,510 src/oxDNA_analysis_tools/cython_utils/get_confs.c: In function ‘__pyx_pf_20oxDNA_analysis_tools_5UTILS_9get_confs_cget_confs’: 2022-06-23T07:09:59,513 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] 2022-06-23T07:09:59,513 2357 | (void)(fread(__pyx_v_chunk, __pyx_v_chunk_size, 1, __pyx_v_traj_file)); 2022-06-23T07:09:59,513 | ^~~~~~~~~~~~~ 2022-06-23T07:09:59,514 In file included from /usr/include/python3.9/Python.h:25, 2022-06-23T07:09:59,514 from src/oxDNA_analysis_tools/cython_utils/get_confs.c:19: 2022-06-23T07:09:59,514 /usr/include/stdio.h:646:39: note: expected ‘void * restrict’ but argument is of type ‘const char *’ 2022-06-23T07:09:59,515 646 | extern size_t fread (void *__restrict __ptr, size_t __size, 2022-06-23T07:09:59,515 | ~~~~~~~~~~~~~~~~~^~~~~ 2022-06-23T07:09:59,524 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] 2022-06-23T07:09:59,525 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) 2022-06-23T07:09:59,525 | ^~~~~~~~~~~~~ 2022-06-23T07:09:59,526 src/oxDNA_analysis_tools/cython_utils/get_confs.c:1732:78: note: expected ‘char *’ but argument is of type ‘const char *’ 2022-06-23T07:09:59,526 1732 | static PyObject *__pyx_f_20oxDNA_analysis_tools_5UTILS_9get_confs_parse_conf(char *, int, int, int); /*proto*/ 2022-06-23T07:09:59,526 | ^~~~~~ 2022-06-23T07:09:59,529 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] 2022-06-23T07:09:59,530 2482 | free(__pyx_v_chunk); 2022-06-23T07:09:59,530 | ^~~~~~~~~~~~~ 2022-06-23T07:09:59,530 In file included from /usr/include/python3.9/Python.h:34, 2022-06-23T07:09:59,531 from src/oxDNA_analysis_tools/cython_utils/get_confs.c:19: 2022-06-23T07:09:59,531 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2022-06-23T07:09:59,531 565 | extern void free (void *__ptr) __THROW; 2022-06-23T07:09:59,532 | ~~~~~~^~~~~ 2022-06-23T07:09:59,551 src/oxDNA_analysis_tools/cython_utils/get_confs.c: In function ‘__pyx_f_20oxDNA_analysis_tools_5UTILS_9get_confs_parse_conf’: 2022-06-23T07:09:59,554 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] 2022-06-23T07:09:59,555 2799 | __pyx_v_ptr = strtok(__pyx_v_ptr, ((char const *)"t = ")); 2022-06-23T07:09:59,555 | ^~~~~~~~~~~ 2022-06-23T07:09:59,555 In file included from /usr/include/python3.9/Python.h:30, 2022-06-23T07:09:59,556 from src/oxDNA_analysis_tools/cython_utils/get_confs.c:19: 2022-06-23T07:09:59,556 /usr/include/string.h:336:39: note: expected ‘char * restrict’ but argument is of type ‘const char *’ 2022-06-23T07:09:59,556 336 | extern char *strtok (char *__restrict __s, const char *__restrict __delim) 2022-06-23T07:09:59,557 | ~~~~~~~~~~~~~~~~~^~~ 2022-06-23T07:10:09,095 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 2022-06-23T07:10:10,563 installing to build/bdist.linux-armv7l/wheel 2022-06-23T07:10:10,563 running install 2022-06-23T07:10:10,626 running install_lib 2022-06-23T07:10:11,214 creating build/bdist.linux-armv7l 2022-06-23T07:10:11,215 creating build/bdist.linux-armv7l/wheel 2022-06-23T07:10:11,219 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,221 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/forces2pairs.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,225 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/mean.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,231 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/external_force_utils 2022-06-23T07:10:11,232 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 2022-06-23T07:10:11,237 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 2022-06-23T07:10:11,240 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 2022-06-23T07:10:11,244 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 2022-06-23T07:10:11,248 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/anm_parameterize.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,251 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/subset_trajectory.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,255 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/minify.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,259 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/align.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,264 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/backbone_flexibility.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,268 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/distance.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,274 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,276 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/rna_model.h -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,283 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/RyeReader.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,288 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/base.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,296 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/pdb.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,301 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/data_structures.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,305 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/chunksize.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,308 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/model.h -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,312 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/readers.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,316 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/oat_multiprocesser.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,319 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/__init__.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,322 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/protein_to_pdb.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,326 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/dd12_na.pdb -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,334 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/utils.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,338 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 2022-06-23T07:10:11,356 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/UTILS/geom.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/UTILS 2022-06-23T07:10:11,361 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/centroid.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,365 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/plot_energy.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,368 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/pca.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,373 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/__init__.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,376 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/db_to_force.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,379 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/entry.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,382 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/deviations.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,386 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/bond_analysis.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,391 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/generate_force.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,394 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/config.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,398 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/output_bonds.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,403 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools/cython_utils 2022-06-23T07:10:11,405 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 2022-06-23T07:10:11,409 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 2022-06-23T07:10:11,429 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/oxDNA_PDB2.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,432 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/contact_map.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,436 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/duplex_finder.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,440 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/oxDNA_PDB.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,445 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/clustering.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,449 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/duplex_angle_plotter.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,454 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/multidimensional_scaling_mean.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,458 copying build/lib.linux-armv7l-cpython-39/oxDNA_analysis_tools/superimpose.py -> build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools 2022-06-23T07:10:11,461 running install_egg_info 2022-06-23T07:10:12,058 Copying src/oxDNA_analysis_tools.egg-info to build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools-2.0.0-py3.9.egg-info 2022-06-23T07:10:12,086 running install_scripts 2022-06-23T07:10:12,222 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-06-23T07:10:12,274 creating build/bdist.linux-armv7l/wheel/oxDNA_analysis_tools-2.0.0.dist-info/WHEEL 2022-06-23T07:10:12,279 creating '/tmp/pip-wheel-ya9ily9d/tmpq4afm_v6/oxDNA_analysis_tools-2.0.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-06-23T07:10:12,284 adding 'oxDNA_analysis_tools/__init__.py' 2022-06-23T07:10:12,288 adding 'oxDNA_analysis_tools/align.py' 2022-06-23T07:10:12,291 adding 'oxDNA_analysis_tools/anm_parameterize.py' 2022-06-23T07:10:12,294 adding 'oxDNA_analysis_tools/backbone_flexibility.py' 2022-06-23T07:10:12,297 adding 'oxDNA_analysis_tools/bond_analysis.py' 2022-06-23T07:10:12,301 adding 'oxDNA_analysis_tools/centroid.py' 2022-06-23T07:10:12,305 adding 'oxDNA_analysis_tools/clustering.py' 2022-06-23T07:10:12,308 adding 'oxDNA_analysis_tools/config.py' 2022-06-23T07:10:12,311 adding 'oxDNA_analysis_tools/contact_map.py' 2022-06-23T07:10:12,313 adding 'oxDNA_analysis_tools/db_to_force.py' 2022-06-23T07:10:12,317 adding 'oxDNA_analysis_tools/deviations.py' 2022-06-23T07:10:12,321 adding 'oxDNA_analysis_tools/distance.py' 2022-06-23T07:10:12,326 adding 'oxDNA_analysis_tools/duplex_angle_plotter.py' 2022-06-23T07:10:12,330 adding 'oxDNA_analysis_tools/duplex_finder.py' 2022-06-23T07:10:12,332 adding 'oxDNA_analysis_tools/entry.py' 2022-06-23T07:10:12,334 adding 'oxDNA_analysis_tools/forces2pairs.py' 2022-06-23T07:10:12,337 adding 'oxDNA_analysis_tools/generate_force.py' 2022-06-23T07:10:12,341 adding 'oxDNA_analysis_tools/mean.py' 2022-06-23T07:10:12,344 adding 'oxDNA_analysis_tools/minify.py' 2022-06-23T07:10:12,348 adding 'oxDNA_analysis_tools/multidimensional_scaling_mean.py' 2022-06-23T07:10:12,351 adding 'oxDNA_analysis_tools/output_bonds.py' 2022-06-23T07:10:12,355 adding 'oxDNA_analysis_tools/oxDNA_PDB.py' 2022-06-23T07:10:12,359 adding 'oxDNA_analysis_tools/oxDNA_PDB2.py' 2022-06-23T07:10:12,363 adding 'oxDNA_analysis_tools/pca.py' 2022-06-23T07:10:12,366 adding 'oxDNA_analysis_tools/plot_energy.py' 2022-06-23T07:10:12,369 adding 'oxDNA_analysis_tools/subset_trajectory.py' 2022-06-23T07:10:12,372 adding 'oxDNA_analysis_tools/superimpose.py' 2022-06-23T07:10:12,378 adding 'oxDNA_analysis_tools/UTILS/RyeReader.py' 2022-06-23T07:10:12,380 adding 'oxDNA_analysis_tools/UTILS/__init__.py' 2022-06-23T07:10:12,399 adding 'oxDNA_analysis_tools/UTILS/base.py' 2022-06-23T07:10:12,402 adding 'oxDNA_analysis_tools/UTILS/chunksize.py' 2022-06-23T07:10:12,405 adding 'oxDNA_analysis_tools/UTILS/data_structures.py' 2022-06-23T07:10:12,424 adding 'oxDNA_analysis_tools/UTILS/dd12_na.pdb' 2022-06-23T07:10:12,428 adding 'oxDNA_analysis_tools/UTILS/geom.py' 2022-06-23T07:10:12,576 adding 'oxDNA_analysis_tools/UTILS/get_confs.cpython-39-arm-linux-gnueabihf.so' 2022-06-23T07:10:12,584 adding 'oxDNA_analysis_tools/UTILS/model.h' 2022-06-23T07:10:12,587 adding 'oxDNA_analysis_tools/UTILS/oat_multiprocesser.py' 2022-06-23T07:10:12,591 adding 'oxDNA_analysis_tools/UTILS/pdb.py' 2022-06-23T07:10:12,595 adding 'oxDNA_analysis_tools/UTILS/protein_to_pdb.py' 2022-06-23T07:10:12,598 adding 'oxDNA_analysis_tools/UTILS/readers.py' 2022-06-23T07:10:12,608 adding 'oxDNA_analysis_tools/UTILS/rna_model.h' 2022-06-23T07:10:12,611 adding 'oxDNA_analysis_tools/UTILS/utils.py' 2022-06-23T07:10:12,673 adding 'oxDNA_analysis_tools/cython_utils/get_confs.c' 2022-06-23T07:10:12,682 adding 'oxDNA_analysis_tools/cython_utils/get_confs.pyx' 2022-06-23T07:10:12,685 adding 'oxDNA_analysis_tools/external_force_utils/__init__.py' 2022-06-23T07:10:12,688 adding 'oxDNA_analysis_tools/external_force_utils/exclude_force.py' 2022-06-23T07:10:12,690 adding 'oxDNA_analysis_tools/external_force_utils/force_reader.py' 2022-06-23T07:10:12,693 adding 'oxDNA_analysis_tools/external_force_utils/forces.py' 2022-06-23T07:10:12,710 adding 'oxDNA_analysis_tools-2.0.0.dist-info/LICENSE' 2022-06-23T07:10:12,717 adding 'oxDNA_analysis_tools-2.0.0.dist-info/METADATA' 2022-06-23T07:10:12,719 adding 'oxDNA_analysis_tools-2.0.0.dist-info/WHEEL' 2022-06-23T07:10:12,721 adding 'oxDNA_analysis_tools-2.0.0.dist-info/entry_points.txt' 2022-06-23T07:10:12,723 adding 'oxDNA_analysis_tools-2.0.0.dist-info/top_level.txt' 2022-06-23T07:10:12,725 adding 'oxDNA_analysis_tools-2.0.0.dist-info/RECORD' 2022-06-23T07:10:12,743 removing build/bdist.linux-armv7l/wheel 2022-06-23T07:10:12,778 ################################################################################ 2022-06-23T07:10:12,779 All set up! All scripts in the package can now be run from the command line with 2022-06-23T07:10:12,779 oat 2022-06-23T07:10:12,780 importing functions in your own scripts can be done with 2022-06-23T07:10:12,781 from oxDNA_analysis_tools. import 2022-06-23T07:10:12,781 If you would like to enable autocomplete in Bash, either add 2022-06-23T07:10:12,782 source oat-completion.sh 2022-06-23T07:10:12,782 to your .bashrc or run 2022-06-23T07:10:12,783 cat oat-completion.sh >> ~/.bash_completion 2022-06-23T07:10:12,784 to make autocompletes available to all users. 2022-06-23T07:10:13,165 Building wheel for oxdna-analysis-tools (pyproject.toml): finished with status 'done' 2022-06-23T07:10:13,191 Created wheel for oxdna-analysis-tools: filename=oxDNA_analysis_tools-2.0.0-cp39-cp39-linux_armv7l.whl size=289694 sha256=b0148c981b90045fdb54b70232bd9ac14b30793197bcaf131ecdb6ed60b0cb51 2022-06-23T07:10:13,194 Stored in directory: /tmp/pip-ephem-wheel-cache-cp40lt5s/wheels/20/eb/96/354f38df4b758116156ac122c02cddb0eaa9960d85bf8b4d46 2022-06-23T07:10:13,224 Successfully built oxdna-analysis-tools 2022-06-23T07:10:13,251 Removed build tracker: '/tmp/pip-build-tracker-z1ocde1i'