2022-09-06T20:16:09,053 Created temporary directory: /tmp/pip-ephem-wheel-cache-vdo6g4ah 2022-09-06T20:16:09,059 Created temporary directory: /tmp/pip-build-tracker-3nenrh92 2022-09-06T20:16:09,060 Initialized build tracking at /tmp/pip-build-tracker-3nenrh92 2022-09-06T20:16:09,060 Created build tracker: /tmp/pip-build-tracker-3nenrh92 2022-09-06T20:16:09,061 Entered build tracker: /tmp/pip-build-tracker-3nenrh92 2022-09-06T20:16:09,062 Created temporary directory: /tmp/pip-wheel-v3jf_tgq 2022-09-06T20:16:09,134 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-09-06T20:16:09,142 2 location(s) to search for versions of anagenex-mdtraj: 2022-09-06T20:16:09,142 * https://pypi.org/simple/anagenex-mdtraj/ 2022-09-06T20:16:09,142 * https://www.piwheels.org/simple/anagenex-mdtraj/ 2022-09-06T20:16:09,143 Fetching project page and analyzing links: https://pypi.org/simple/anagenex-mdtraj/ 2022-09-06T20:16:09,144 Getting page https://pypi.org/simple/anagenex-mdtraj/ 2022-09-06T20:16:09,147 Found index url https://pypi.org/simple 2022-09-06T20:16:09,348 Found link https://files.pythonhosted.org/packages/6d/b0/fd322f30cc3e01045259805ba97313b6de4cb905f7067d5082c5dedb45e7/anagenex-mdtraj-1.9.8.dev0.tar.gz#sha256=47e7d2881ab7ae4dcc63d811222a1c2fc2b21f0e97407b42cfd6d44facc21ba5 (from https://pypi.org/simple/anagenex-mdtraj/), version: 1.9.8.dev0 2022-09-06T20:16:09,349 Skipping link: No binaries permitted for anagenex-mdtraj: https://files.pythonhosted.org/packages/9a/4f/049a6cbd218ae2fffe1d49c08621b441e955eb54ee6ea4262cda8a8f0488/anagenex_mdtraj-1.9.8.dev0-cp310-cp310-macosx_10_9_x86_64.whl#sha256=d80d483c540bf0ca1e82ead7478f6dbdc68057cfba9ca8ec91228f7f3529ae78 (from https://pypi.org/simple/anagenex-mdtraj/) 2022-09-06T20:16:09,349 Skipping link: No binaries permitted for anagenex-mdtraj: https://files.pythonhosted.org/packages/69/29/844b7e93b675d6aac44675c0b220a2cbc744daffe6e25943fc14c036014d/anagenex_mdtraj-1.9.8.dev0-cp310-cp310-macosx_11_0_arm64.whl#sha256=1fbf3d86a38eb67d156c9c609a941feae6e24e2c20adcbc380376cf6da405d44 (from https://pypi.org/simple/anagenex-mdtraj/) 2022-09-06T20:16:09,350 Skipping link: No binaries permitted for anagenex-mdtraj: https://files.pythonhosted.org/packages/06/84/e1f2ab8a2ef56a8f272f8ea2ebff8e0c0d89334bde155510004361e72ccc/anagenex_mdtraj-1.9.8.dev0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=c6947df942ca9e6a5201711749a9098763b1c5b7f1a6545bcb5b4876ccfdb04f (from https://pypi.org/simple/anagenex-mdtraj/) 2022-09-06T20:16:09,350 Fetching project page and analyzing links: https://www.piwheels.org/simple/anagenex-mdtraj/ 2022-09-06T20:16:09,351 Getting page https://www.piwheels.org/simple/anagenex-mdtraj/ 2022-09-06T20:16:09,353 Found index url https://www.piwheels.org/simple 2022-09-06T20:16:09,567 Skipping link: not a file: https://www.piwheels.org/simple/anagenex-mdtraj/ 2022-09-06T20:16:09,568 Skipping link: not a file: https://pypi.org/simple/anagenex-mdtraj/ 2022-09-06T20:16:09,601 Given no hashes to check 1 links for project 'anagenex-mdtraj': discarding no candidates 2022-09-06T20:16:09,633 Collecting anagenex-mdtraj==1.9.8.dev0 2022-09-06T20:16:09,637 Created temporary directory: /tmp/pip-unpack-mb8td28x 2022-09-06T20:16:10,060 Downloading anagenex-mdtraj-1.9.8.dev0.tar.gz (2.2 MB) 2022-09-06T20:16:13,047 Added anagenex-mdtraj==1.9.8.dev0 from https://files.pythonhosted.org/packages/6d/b0/fd322f30cc3e01045259805ba97313b6de4cb905f7067d5082c5dedb45e7/anagenex-mdtraj-1.9.8.dev0.tar.gz#sha256=47e7d2881ab7ae4dcc63d811222a1c2fc2b21f0e97407b42cfd6d44facc21ba5 to build tracker '/tmp/pip-build-tracker-3nenrh92' 2022-09-06T20:16:13,060 Created temporary directory: /tmp/pip-build-env-eo9kdl7w 2022-09-06T20:16:13,075 Created temporary directory: /tmp/pip-standalone-pip-5b3zv1b7 2022-09-06T20:16:15,491 Installing build dependencies: started 2022-09-06T20:16:15,493 Running command pip subprocess to install build dependencies 2022-09-06T20:16:25,138 Using pip 22.1.2 from /tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip (python 3.7) 2022-09-06T20:16:26,930 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-09-06T20:16:31,440 Collecting setuptools 2022-09-06T20:16:31,727 Using cached https://www.piwheels.org/simple/setuptools/setuptools-65.3.0-py3-none-any.whl (1.2 MB) 2022-09-06T20:16:32,388 Collecting wheel 2022-09-06T20:16:32,423 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-09-06T20:16:32,702 Collecting oldest-supported-numpy 2022-09-06T20:16:32,733 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2022.8.16-py3-none-any.whl (3.9 kB) 2022-09-06T20:16:36,250 Collecting Cython>0.28 2022-09-06T20:16:36,734 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.32-cp37-cp37m-linux_armv7l.whl (2.3 MB) 2022-09-06T20:16:40,024 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/7a/7f/5384d4c85a2349bd89ff1c0253bff77c7b617e48af201f2d823fc619189a/numpy-1.22.0rc1.zip#sha256=bc991b3f8ea7c0f6703df2bc23c098cfe6f1a3a5e8a3a901eb6a5619275d53ff (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,036 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/a1/4a/8fd68d9a0a9fe5419cdbb697ffc96259fb716bd952c5c64225991add7551/numpy-1.22.0rc2.zip#sha256=01810dc32c5ac4c895b5c0d285497e1eb52038834919f3d2eaddfb9526b20dc9 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,049 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/17/d4/d3ac79fca81154e8d3e11232967024f480cfdc87dfeef479803716fb20cb/numpy-1.22.0rc3.zip#sha256=0b5642efe2a36f2191102b44bb95ee1479f14c1adb2d7155303e50b2517e43bc (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,062 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/50/e1/9b0c184f04b8cf5f3c941ffa56fbcbe936888bdac9aa7ba6bae405ac752b/numpy-1.22.0.zip#sha256=a955e4128ac36797aaffd49ab44ec74a71c11d6938df83b1285492d277db5397 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,075 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/0a/c8/a62767a6b374a0dfb02d2a0456e5f56a372cdd1689dbc6ffb6bf1ddedbc0/numpy-1.22.1.zip#sha256=e348ccf5bc5235fc405ab19d53bec215bb373300e5523c7b476cc0da8a5e9973 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,086 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/e9/6c/c0a8130fe198f27bab92f1b28631e0cc2572295f6b7a31e87efe7448aa1c/numpy-1.22.2.zip#sha256=076aee5a3763d41da6bef9565fdf3cb987606f567cd8b104aded2b38b7b47abf (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,104 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/64/4a/b008d1f8a7b9f5206ecf70a53f84e654707e7616a771d84c05151a4713e9/numpy-1.22.3.zip#sha256=dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,116 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/f6/d8/ab692a75f584d13c6542c3994f75def5bce52ded9399f52e230fe402819d/numpy-1.22.4.zip#sha256=425b390e4619f58d8526b3dcf656dde069133ae5c240229821f01b5f44ea07af (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,129 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/33/ad/fc5e3fd1077622b2b32fc3fd36176b36475b63da486eb5578d7f8fb2af29/numpy-1.23.0rc1.tar.gz#sha256=3a09d0f564f59b6da54f592909d3fdbd50b492ef9fbe6d699043c992538ba0e0 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,142 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/7b/bc/05e61801a3689f81c8569c057c61fd1d302e989be5c96f6ce7acee46250a/numpy-1.23.0rc2.tar.gz#sha256=8e8a88657c028b8b77f3df6f266a5e6ffb4419cbc3dfb525cbbb80ba710f5da2 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,154 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/a2/bf/1502d20b4a7f5d5f74c5242748834aaf8cd6ff7cb40b7c64ef58ba47a751/numpy-1.23.0rc3.tar.gz#sha256=6a8fc5573cc8cb8108cec555bca5745d2798c54eef107d478b4320c1f6542102 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,167 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/03/c6/14a17e10813b8db20d1e800ff9a3a898e65d25f2b0e9d6a94616f1e3362c/numpy-1.23.0.tar.gz#sha256=bd3fa4fe2e38533d5336e1272fc4e765cabbbde144309ccee8675509d5cd7b05 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,180 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/13/b1/0c22aa7ca1deda4915cdec9562f839546bb252eecf6ad596eaec0592bd35/numpy-1.23.1.tar.gz#sha256=d748ef349bfef2e1194b59da37ed5a29c19ea8d7e6342019921ba2ba4fd8b624 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,195 Link requires a different Python (3.7.3 not in: '>=3.8'): https://files.pythonhosted.org/packages/f4/66/17b8e95770478436bf968353c89683ce6f9e14d92e0d4fb3111c09ba18d2/numpy-1.23.2.tar.gz#sha256=b78d00e48261fbbd04aa0d7427cf78d18401ee0abd89c7559bbf422e5b1c7d01 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8) 2022-09-06T20:16:40,898 Collecting numpy==1.14.5 2022-09-06T20:16:42,254 Using cached https://www.piwheels.org/simple/numpy/numpy-1.14.5-cp37-cp37m-linux_armv7l.whl (7.3 MB) 2022-09-06T20:16:56,557 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2022-09-06T20:16:56,832 Creating /tmp/pip-build-env-eo9kdl7w/overlay/bin 2022-09-06T20:16:56,836 changing mode of /tmp/pip-build-env-eo9kdl7w/overlay/bin/wheel to 755 2022-09-06T20:17:17,784 changing mode of /tmp/pip-build-env-eo9kdl7w/overlay/bin/cygdb to 755 2022-09-06T20:17:17,789 changing mode of /tmp/pip-build-env-eo9kdl7w/overlay/bin/cython to 755 2022-09-06T20:17:17,794 changing mode of /tmp/pip-build-env-eo9kdl7w/overlay/bin/cythonize to 755 2022-09-06T20:17:17,896 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. 2022-09-06T20:17:17,896 espnet-onnx 0.1.9 requires espnet-tts-frontend, which is not installed. 2022-09-06T20:17:17,896 espnet-onnx 0.1.9 requires g2p-en, which is not installed. 2022-09-06T20:17:17,897 espnet-onnx 0.1.9 requires jamo==0.4.1, which is not installed. 2022-09-06T20:17:17,897 espnet-onnx 0.1.9 requires librosa>=0.8.0, which is not installed. 2022-09-06T20:17:17,897 espnet-onnx 0.1.9 requires onnxruntime>=1.4.0, which is not installed. 2022-09-06T20:17:17,898 espnet-onnx 0.1.9 requires sentencepiece!=0.1.92,>=0.1.91, which is not installed. 2022-09-06T20:17:17,898 espnet-onnx 0.1.9 requires typeguard>=2.7.0, which is not installed. 2022-09-06T20:17:17,898 tifffile 2021.11.2 requires numpy>=1.15.1, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,899 scikit-learn 1.0.2 requires numpy>=1.14.6, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,899 scikit-image 0.18.3 requires numpy>=1.16.5, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,899 pywavelets 1.3.0 requires numpy>=1.17.3, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,900 pyerfa 2.0.0.1 requires numpy>=1.17, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,900 photutils 1.3.0 requires numpy>=1.17, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,900 pandas 1.3.5 requires numpy>=1.17.3; platform_machine != "aarch64" and platform_machine != "arm64" and python_version < "3.10", but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,901 matplotlib 3.4.3 requires numpy>=1.16, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,901 astropy 4.3.1 requires numpy>=1.17, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,901 scipy 1.7.3 requires numpy<1.23.0,>=1.16.5, but you have numpy 1.14.5 which is incompatible. 2022-09-06T20:17:17,902 Successfully installed Cython-0.29.32 numpy-1.14.5 oldest-supported-numpy-2022.8.16 setuptools-65.3.0 wheel-0.37.1 2022-09-06T20:17:18,157 --- Logging error --- 2022-09-06T20:17:18,158 Traceback (most recent call last): 2022-09-06T20:17:18,159 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/utils/logging.py", line 177, in emit 2022-09-06T20:17:18,159 self.console.print(renderable, overflow="ignore", crop=False, style=style) 2022-09-06T20:17:18,159 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_vendor/rich/console.py", line 1752, in print 2022-09-06T20:17:18,160 extend(render(renderable, render_options)) 2022-09-06T20:17:18,160 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_vendor/rich/console.py", line 1390, in render 2022-09-06T20:17:18,160 for render_output in iter_render: 2022-09-06T20:17:18,161 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/utils/logging.py", line 134, in __rich_console__ 2022-09-06T20:17:18,161 for line in lines: 2022-09-06T20:17:18,161 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_vendor/rich/segment.py", line 245, in split_lines 2022-09-06T20:17:18,162 for segment in segments: 2022-09-06T20:17:18,162 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_vendor/rich/console.py", line 1368, in render 2022-09-06T20:17:18,162 renderable = rich_cast(renderable) 2022-09-06T20:17:18,162 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_vendor/rich/protocol.py", line 36, in rich_cast 2022-09-06T20:17:18,163 renderable = cast_method() 2022-09-06T20:17:18,163 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/self_outdated_check.py", line 130, in __rich__ 2022-09-06T20:17:18,163 pip_cmd = get_best_invocation_for_this_pip() 2022-09-06T20:17:18,164 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/utils/entrypoints.py", line 60, in get_best_invocation_for_this_pip 2022-09-06T20:17:18,164 os.path.join(binary_prefix, exe_name), 2022-09-06T20:17:18,164 File "/usr/lib/python3.7/genericpath.py", line 97, in samefile 2022-09-06T20:17:18,165 s2 = os.stat(f2) 2022-09-06T20:17:18,165 FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/pip3.7' 2022-09-06T20:17:18,165 Call stack: 2022-09-06T20:17:18,165 File "/usr/lib/python3.7/runpy.py", line 193, in _run_module_as_main 2022-09-06T20:17:18,166 "__main__", mod_spec) 2022-09-06T20:17:18,166 File "/usr/lib/python3.7/runpy.py", line 85, in _run_code 2022-09-06T20:17:18,166 exec(code, run_globals) 2022-09-06T20:17:18,167 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/__main__.py", line 31, in 2022-09-06T20:17:18,167 sys.exit(_main()) 2022-09-06T20:17:18,167 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/cli/main.py", line 70, in main 2022-09-06T20:17:18,168 return command.main(cmd_args) 2022-09-06T20:17:18,168 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/cli/base_command.py", line 101, in main 2022-09-06T20:17:18,168 return self._main(args) 2022-09-06T20:17:18,169 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/cli/base_command.py", line 223, in _main 2022-09-06T20:17:18,169 self.handle_pip_version_check(options) 2022-09-06T20:17:18,169 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/cli/req_command.py", line 148, in handle_pip_version_check 2022-09-06T20:17:18,169 pip_self_version_check(session, options) 2022-09-06T20:17:18,170 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/self_outdated_check.py", line 237, in pip_self_version_check 2022-09-06T20:17:18,170 logger.info("[present-rich] %s", upgrade_prompt) 2022-09-06T20:17:18,170 File "/usr/lib/python3.7/logging/__init__.py", line 1383, in info 2022-09-06T20:17:18,171 self._log(INFO, msg, args, **kwargs) 2022-09-06T20:17:18,171 File "/usr/lib/python3.7/logging/__init__.py", line 1519, in _log 2022-09-06T20:17:18,171 self.handle(record) 2022-09-06T20:17:18,172 File "/usr/lib/python3.7/logging/__init__.py", line 1529, in handle 2022-09-06T20:17:18,172 self.callHandlers(record) 2022-09-06T20:17:18,172 File "/usr/lib/python3.7/logging/__init__.py", line 1591, in callHandlers 2022-09-06T20:17:18,172 hdlr.handle(record) 2022-09-06T20:17:18,173 File "/usr/lib/python3.7/logging/__init__.py", line 905, in handle 2022-09-06T20:17:18,173 self.emit(record) 2022-09-06T20:17:18,173 File "/tmp/pip-standalone-pip-5b3zv1b7/__env_pip__.zip/pip/_internal/utils/logging.py", line 179, in emit 2022-09-06T20:17:18,174 self.handleError(record) 2022-09-06T20:17:18,174 Message: '[present-rich] %s' 2022-09-06T20:17:18,174 Arguments: (UpgradePrompt(old='22.1.2', new='22.2.2'),) 2022-09-06T20:17:18,802 Installing build dependencies: finished with status 'done' 2022-09-06T20:17:18,847 Getting requirements to build wheel: started 2022-09-06T20:17:18,850 Running command Getting requirements to build wheel 2022-09-06T20:17:21,325 Using built-in specs. 2022-09-06T20:17:21,328 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2022-09-06T20:17:21,329 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/8/lto-wrapper 2022-09-06T20:17:21,330 Target: arm-linux-gnueabihf 2022-09-06T20:17:21,330 Configured with: ../src/configure -v --with-pkgversion='Raspbian 8.3.0-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-8/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-8 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2022-09-06T20:17:21,331 Thread model: posix 2022-09-06T20:17:21,331 gcc version 8.3.0 (Raspbian 8.3.0-6+rpi1) 2022-09-06T20:17:42,123 C compiler: 2022-09-06T20:17:42,124 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-09-06T20:17:42,124 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2022-09-06T20:17:42,125 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2022-09-06T20:17:42,125 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2022-09-06T20:17:42,125 Attempting to autodetect NEON support... Did not detect NEON support 2022-09-06T20:17:42,126 running egg_info 2022-09-06T20:17:42,756 writing anagenex_mdtraj.egg-info/PKG-INFO 2022-09-06T20:17:43,351 writing dependency_links to anagenex_mdtraj.egg-info/dependency_links.txt 2022-09-06T20:17:45,132 writing entry points to anagenex_mdtraj.egg-info/entry_points.txt 2022-09-06T20:17:46,319 writing requirements to anagenex_mdtraj.egg-info/requires.txt 2022-09-06T20:17:46,917 writing top-level names to anagenex_mdtraj.egg-info/top_level.txt 2022-09-06T20:17:47,685 reading manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:17:47,756 reading manifest template 'MANIFEST.in' 2022-09-06T20:17:49,568 no previously-included directories found matching '__pycache__' 2022-09-06T20:17:49,571 no previously-included directories found matching '*.pyc' 2022-09-06T20:17:49,573 adding license file 'LICENSE' 2022-09-06T20:17:49,609 writing manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:17:49,851 Getting requirements to build wheel: finished with status 'done' 2022-09-06T20:17:49,875 Created temporary directory: /tmp/pip-modern-metadata-bmzxtwxa 2022-09-06T20:17:49,881 Preparing metadata (pyproject.toml): started 2022-09-06T20:17:49,883 Running command Preparing metadata (pyproject.toml) 2022-09-06T20:17:52,245 Using built-in specs. 2022-09-06T20:17:52,246 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2022-09-06T20:17:52,247 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/8/lto-wrapper 2022-09-06T20:17:52,247 Target: arm-linux-gnueabihf 2022-09-06T20:17:52,247 Configured with: ../src/configure -v --with-pkgversion='Raspbian 8.3.0-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-8/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-8 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2022-09-06T20:17:52,248 Thread model: posix 2022-09-06T20:17:52,248 gcc version 8.3.0 (Raspbian 8.3.0-6+rpi1) 2022-09-06T20:18:09,731 C compiler: 2022-09-06T20:18:09,732 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-09-06T20:18:09,732 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2022-09-06T20:18:09,732 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2022-09-06T20:18:09,733 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2022-09-06T20:18:09,733 Attempting to autodetect NEON support... Did not detect NEON support 2022-09-06T20:18:14,771 running dist_info 2022-09-06T20:18:15,434 creating /tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info 2022-09-06T20:18:16,061 writing /tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info/PKG-INFO 2022-09-06T20:18:16,653 writing dependency_links to /tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info/dependency_links.txt 2022-09-06T20:18:18,428 writing entry points to /tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info/entry_points.txt 2022-09-06T20:18:19,612 writing requirements to /tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info/requires.txt 2022-09-06T20:18:20,220 writing top-level names to /tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info/top_level.txt 2022-09-06T20:18:20,224 writing manifest file '/tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:18:21,006 reading manifest file '/tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:18:21,011 reading manifest template 'MANIFEST.in' 2022-09-06T20:18:22,835 ./basesetup.py:453: UserWarning: Unrecognized setuptools command ('dist_info --egg-base /tmp/pip-modern-metadata-bmzxtwxa'), proceeding with generating Cython sources and expanding templates 2022-09-06T20:18:22,835 ' '.join(sys.argv[1:]))) 2022-09-06T20:18:22,836 no previously-included directories found matching '__pycache__' 2022-09-06T20:18:22,838 no previously-included directories found matching '*.pyc' 2022-09-06T20:18:22,839 adding license file 'LICENSE' 2022-09-06T20:18:22,867 writing manifest file '/tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:18:22,871 creating '/tmp/pip-modern-metadata-bmzxtwxa/anagenex_mdtraj-1.9.8.dev0.dist-info' 2022-09-06T20:18:23,077 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-09-06T20:18:23,443 Preparing metadata (pyproject.toml): finished with status 'done' 2022-09-06T20:18:23,458 Source in /tmp/pip-wheel-v3jf_tgq/anagenex-mdtraj_cf5223d5495343868f282211bf6fc581 has version 1.9.8.dev0, which satisfies requirement anagenex-mdtraj==1.9.8.dev0 from https://files.pythonhosted.org/packages/6d/b0/fd322f30cc3e01045259805ba97313b6de4cb905f7067d5082c5dedb45e7/anagenex-mdtraj-1.9.8.dev0.tar.gz#sha256=47e7d2881ab7ae4dcc63d811222a1c2fc2b21f0e97407b42cfd6d44facc21ba5 2022-09-06T20:18:23,460 Removed anagenex-mdtraj==1.9.8.dev0 from https://files.pythonhosted.org/packages/6d/b0/fd322f30cc3e01045259805ba97313b6de4cb905f7067d5082c5dedb45e7/anagenex-mdtraj-1.9.8.dev0.tar.gz#sha256=47e7d2881ab7ae4dcc63d811222a1c2fc2b21f0e97407b42cfd6d44facc21ba5 from build tracker '/tmp/pip-build-tracker-3nenrh92' 2022-09-06T20:18:23,470 Created temporary directory: /tmp/pip-unpack-oqbus0zb 2022-09-06T20:18:23,471 Building wheels for collected packages: anagenex-mdtraj 2022-09-06T20:18:23,481 Created temporary directory: /tmp/pip-wheel-bsp05pjl 2022-09-06T20:18:23,482 Destination directory: /tmp/pip-wheel-bsp05pjl 2022-09-06T20:18:23,491 Building wheel for anagenex-mdtraj (pyproject.toml): started 2022-09-06T20:18:23,493 Running command Building wheel for anagenex-mdtraj (pyproject.toml) 2022-09-06T20:18:25,969 Using built-in specs. 2022-09-06T20:18:25,971 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2022-09-06T20:18:25,972 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/8/lto-wrapper 2022-09-06T20:18:25,972 Target: arm-linux-gnueabihf 2022-09-06T20:18:25,973 Configured with: ../src/configure -v --with-pkgversion='Raspbian 8.3.0-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-8/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-8 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2022-09-06T20:18:25,973 Thread model: posix 2022-09-06T20:18:25,973 gcc version 8.3.0 (Raspbian 8.3.0-6+rpi1) 2022-09-06T20:18:42,732 C compiler: 2022-09-06T20:18:42,732 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-09-06T20:18:42,732 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2022-09-06T20:18:42,733 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2022-09-06T20:18:42,733 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2022-09-06T20:18:42,733 Attempting to autodetect NEON support... Did not detect NEON support 2022-09-06T20:18:47,273 running bdist_wheel 2022-09-06T20:18:47,390 running build 2022-09-06T20:18:47,391 running build_py 2022-09-06T20:18:48,028 creating build 2022-09-06T20:18:48,029 creating build/lib.linux-armv7l-cpython-37 2022-09-06T20:18:48,031 creating build/lib.linux-armv7l-cpython-37/mdtraj 2022-09-06T20:18:48,034 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj 2022-09-06T20:18:48,039 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-37/mdtraj 2022-09-06T20:18:48,044 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-37/mdtraj 2022-09-06T20:18:48,050 creating build/lib.linux-armv7l-cpython-37/mdtraj/scripts 2022-09-06T20:18:48,052 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/scripts 2022-09-06T20:18:48,056 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-37/mdtraj/scripts 2022-09-06T20:18:48,062 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-37/mdtraj/scripts 2022-09-06T20:18:48,068 creating build/lib.linux-armv7l-cpython-37/mdtraj/reporters 2022-09-06T20:18:48,070 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-37/mdtraj/reporters 2022-09-06T20:18:48,074 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-37/mdtraj/reporters 2022-09-06T20:18:48,078 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/reporters 2022-09-06T20:18:48,081 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-37/mdtraj/reporters 2022-09-06T20:18:48,085 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-37/mdtraj/reporters 2022-09-06T20:18:48,088 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-37/mdtraj/reporters 2022-09-06T20:18:48,094 creating build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,095 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,099 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,103 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,106 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,110 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,114 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,118 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,122 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,126 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils 2022-09-06T20:18:48,131 creating build/lib.linux-armv7l-cpython-37/mdtraj/core 2022-09-06T20:18:48,133 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-37/mdtraj/core 2022-09-06T20:18:48,137 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/core 2022-09-06T20:18:48,140 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-37/mdtraj/core 2022-09-06T20:18:48,144 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-37/mdtraj/core 2022-09-06T20:18:48,149 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-37/mdtraj/core 2022-09-06T20:18:48,156 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-37/mdtraj/core 2022-09-06T20:18:48,168 creating build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,169 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,173 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,179 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,182 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,186 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,190 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,196 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,201 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,206 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,211 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,215 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,219 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,224 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,227 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,232 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,236 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,240 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,245 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,250 creating build/lib.linux-armv7l-cpython-37/mdtraj/nmr 2022-09-06T20:18:48,252 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/nmr 2022-09-06T20:18:48,255 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-37/mdtraj/nmr 2022-09-06T20:18:48,260 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-37/mdtraj/nmr 2022-09-06T20:18:48,265 creating build/lib.linux-armv7l-cpython-37/mdtraj/testing 2022-09-06T20:18:48,267 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-37/mdtraj/testing 2022-09-06T20:18:48,271 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/testing 2022-09-06T20:18:48,274 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-37/mdtraj/testing 2022-09-06T20:18:48,278 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-37/mdtraj/testing 2022-09-06T20:18:48,285 creating build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,287 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,292 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,295 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,298 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,303 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,307 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,311 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,316 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,321 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,326 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,330 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,334 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,338 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,342 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,348 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:18:48,355 creating build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,357 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,361 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,365 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,370 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,374 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,378 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,384 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,389 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,393 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,397 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,402 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,406 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,411 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit 2022-09-06T20:18:48,418 creating build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb 2022-09-06T20:18:48,420 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb 2022-09-06T20:18:48,424 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb 2022-09-06T20:18:48,430 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb 2022-09-06T20:18:48,439 creating build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb/data 2022-09-06T20:18:48,441 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb/data 2022-09-06T20:18:48,447 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb/data 2022-09-06T20:18:48,472 running build_ext 2022-09-06T20:18:48,482 building 'mdtraj.formats.xtc' extension 2022-09-06T20:18:48,484 creating build/temp.linux-armv7l-cpython-37 2022-09-06T20:18:48,485 creating build/temp.linux-armv7l-cpython-37/mdtraj 2022-09-06T20:18:48,486 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats 2022-09-06T20:18:48,488 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc 2022-09-06T20:18:48,490 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src 2022-09-06T20:18:48,492 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:18:48,828 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:18:49,189 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2022-09-06T20:18:49,190 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:18:49,190 int smallnum, smaller, larger, i, is_smaller, run; 2022-09-06T20:18:49,190 ^~~~~~ 2022-09-06T20:18:49,191 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:18:49,192 int smallidx, minidx, maxidx; 2022-09-06T20:18:49,192 ^~~~~~ 2022-09-06T20:18:49,212 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2022-09-06T20:18:49,213 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:18:49,213 int errval=1; 2022-09-06T20:18:49,214 ^~~~~~ 2022-09-06T20:18:49,224 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2022-09-06T20:18:49,225 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:18:49,226 int smallnum, smaller, larger, i, is_smaller, run; 2022-09-06T20:18:49,226 ^~~~~~ 2022-09-06T20:18:49,227 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:18:49,227 int smallidx, minidx, maxidx; 2022-09-06T20:18:49,228 ^~~~~~ 2022-09-06T20:18:49,248 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2022-09-06T20:18:49,248 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:18:49,249 int errval=1; 2022-09-06T20:18:49,249 ^~~~~~ 2022-09-06T20:18:54,155 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:18:54,340 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2022-09-06T20:18:54,340 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2022-09-06T20:18:54,341 int i,j,result; 2022-09-06T20:18:54,341 ^ 2022-09-06T20:18:54,341 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2022-09-06T20:18:54,342 int i,j,result; 2022-09-06T20:18:54,342 ^ 2022-09-06T20:18:54,343 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2022-09-06T20:18:54,343 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-09-06T20:18:54,344 if (NULL == xd) 2022-09-06T20:18:54,344 ^~ 2022-09-06T20:18:54,345 mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2022-09-06T20:18:54,345 do { 2022-09-06T20:18:54,345 ^~ 2022-09-06T20:18:54,666 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:18:55,437 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-09-06T20:18:55,438 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:18:55,439 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-09-06T20:18:55,439 from mdtraj/formats/xtc/xtc.c:775: 2022-09-06T20:18:55,439 /usr/local/lib/python3.7/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] 2022-09-06T20:18:55,440 #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:18:55,440 ^~~~~~~ 2022-09-06T20:19:13,567 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write.isra.55’: 2022-09-06T20:19:13,567 mdtraj/formats/xtc/xtc.c:687:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:13,568 #define PyInt_FromLong PyLong_FromLong 2022-09-06T20:19:13,568 ^~~~~~~~~~~~~~~ 2022-09-06T20:19:13,571 mdtraj/formats/xtc/xtc.c:9554:7: note: ‘__pyx_v_status’ was declared here 2022-09-06T20:19:13,572 int __pyx_v_status; 2022-09-06T20:19:13,572 ^~~~~~~~~~~~~~ 2022-09-06T20:19:21,426 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2022-09-06T20:19:21,430 mdtraj/formats/xtc/xtc.c:8073:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,430 } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2022-09-06T20:19:21,431 ^ 2022-09-06T20:19:21,434 mdtraj/formats/xtc/xtc.c:8069:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,434 } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2022-09-06T20:19:21,434 ^ 2022-09-06T20:19:21,438 mdtraj/formats/xtc/xtc.c:8065:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,438 } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:19:21,438 ^ 2022-09-06T20:19:21,441 mdtraj/formats/xtc/xtc.c:8025:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,442 } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:19:21,442 ^ 2022-09-06T20:19:21,445 mdtraj/formats/xtc/xtc.c:8007:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,446 } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:19:21,446 ^ 2022-09-06T20:19:21,447 mdtraj/formats/xtc/xtc.c:8083:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,448 } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:19:21,448 ^ 2022-09-06T20:19:21,451 mdtraj/formats/xtc/xtc.c:8045:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,452 } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2022-09-06T20:19:21,452 ^ 2022-09-06T20:19:21,455 mdtraj/formats/xtc/xtc.c:8041:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,455 } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2022-09-06T20:19:21,456 ^ 2022-09-06T20:19:21,459 mdtraj/formats/xtc/xtc.c:8037:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,459 } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:19:21,460 ^ 2022-09-06T20:19:21,462 mdtraj/formats/xtc/xtc.c:7660:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,463 } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2022-09-06T20:19:21,463 ^ 2022-09-06T20:19:21,466 mdtraj/formats/xtc/xtc.c:7656:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:19:21,467 } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:19:21,467 ^ 2022-09-06T20:19:48,859 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/xtc.o -L/usr/lib -o build/lib.linux-armv7l-cpython-37/mdtraj/formats/xtc.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:20:34,528 building 'mdtraj.formats.trr' extension 2022-09-06T20:20:34,530 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:20:34,836 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:20:35,153 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2022-09-06T20:20:35,154 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:20:35,154 int smallnum, smaller, larger, i, is_smaller, run; 2022-09-06T20:20:35,154 ^~~~~~ 2022-09-06T20:20:35,155 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:20:35,155 int smallidx, minidx, maxidx; 2022-09-06T20:20:35,155 ^~~~~~ 2022-09-06T20:20:35,169 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2022-09-06T20:20:35,170 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:20:35,170 int errval=1; 2022-09-06T20:20:35,170 ^~~~~~ 2022-09-06T20:20:35,179 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2022-09-06T20:20:35,180 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:20:35,180 int smallnum, smaller, larger, i, is_smaller, run; 2022-09-06T20:20:35,181 ^~~~~~ 2022-09-06T20:20:35,181 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:20:35,181 int smallidx, minidx, maxidx; 2022-09-06T20:20:35,182 ^~~~~~ 2022-09-06T20:20:35,199 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2022-09-06T20:20:35,200 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:20:35,200 int errval=1; 2022-09-06T20:20:35,201 ^~~~~~ 2022-09-06T20:20:40,085 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:20:41,577 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:20:42,248 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-09-06T20:20:42,249 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:20:42,249 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-09-06T20:20:42,250 from mdtraj/formats/xtc/trr.c:775: 2022-09-06T20:20:42,250 /usr/local/lib/python3.7/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] 2022-09-06T20:20:42,250 #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:20:42,251 ^~~~~~~ 2022-09-06T20:20:59,471 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write.isra.54’: 2022-09-06T20:20:59,472 mdtraj/formats/xtc/trr.c:687:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:20:59,472 #define PyInt_FromLong PyLong_FromLong 2022-09-06T20:20:59,473 ^~~~~~~~~~~~~~~ 2022-09-06T20:20:59,478 mdtraj/formats/xtc/trr.c:11080:7: note: ‘__pyx_v_status’ was declared here 2022-09-06T20:20:59,479 int __pyx_v_status; 2022-09-06T20:20:59,479 ^~~~~~~~~~~~~~ 2022-09-06T20:21:15,337 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2022-09-06T20:21:15,341 mdtraj/formats/xtc/trr.c:8433:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,342 } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2022-09-06T20:21:15,342 ^ 2022-09-06T20:21:15,347 mdtraj/formats/xtc/trr.c:8429:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,347 } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:21:15,348 ^ 2022-09-06T20:21:15,349 mdtraj/formats/xtc/trr.c:1920:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,349 #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2022-09-06T20:21:15,350 ^ 2022-09-06T20:21:15,352 mdtraj/formats/xtc/trr.c:6970:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2022-09-06T20:21:15,352 __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2022-09-06T20:21:15,352 ^~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:21:15,353 mdtraj/formats/xtc/trr.c:6970:21: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,355 mdtraj/formats/xtc/trr.c:8376:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,355 } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2022-09-06T20:21:15,355 ^ 2022-09-06T20:21:15,359 mdtraj/formats/xtc/trr.c:8372:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,359 } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:21:15,360 ^ 2022-09-06T20:21:15,360 mdtraj/formats/xtc/trr.c:1920:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,360 #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2022-09-06T20:21:15,361 ^ 2022-09-06T20:21:15,362 mdtraj/formats/xtc/trr.c:6986:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2022-09-06T20:21:15,363 __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2022-09-06T20:21:15,363 ^~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:21:15,364 mdtraj/formats/xtc/trr.c:6986:21: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,366 mdtraj/formats/xtc/trr.c:8766:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,366 } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:21:15,366 ^ 2022-09-06T20:21:15,370 mdtraj/formats/xtc/trr.c:8762:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,370 } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2022-09-06T20:21:15,371 ^ 2022-09-06T20:21:15,374 mdtraj/formats/xtc/trr.c:8607:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,374 } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:21:15,375 ^ 2022-09-06T20:21:15,378 mdtraj/formats/xtc/trr.c:8603:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,378 } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2022-09-06T20:21:15,379 ^ 2022-09-06T20:21:15,380 mdtraj/formats/xtc/trr.c:8659:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,381 } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:21:15,381 ^ 2022-09-06T20:21:15,384 mdtraj/formats/xtc/trr.c:8655:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:21:15,385 } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2022-09-06T20:21:15,385 ^ 2022-09-06T20:21:42,399 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/xtc/trr.o -L/usr/lib -o build/lib.linux-armv7l-cpython-37/mdtraj/formats/trr.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:22:35,631 mdtraj/formats/xtc/include/trr_header.h:28:5: warning: type of ‘do_trnheader’ does not match original declaration [-Wlto-type-mismatch] 2022-09-06T20:22:35,632 int do_trnheader(XDRFILE *xd, char bRead, t_trnheader *sh); 2022-09-06T20:22:35,632 ^ 2022-09-06T20:22:35,632 mdtraj/formats/xtc/src/xdrfile_trr.c:90:12: note: type mismatch in parameter 2 2022-09-06T20:22:35,633 extern int do_trnheader(XDRFILE *xd,mybool bRead,t_trnheader *sh) 2022-09-06T20:22:35,633 ^ 2022-09-06T20:22:35,633 mdtraj/formats/xtc/src/xdrfile_trr.c:90:12: note: type ‘mybool’ should match type ‘char’ 2022-09-06T20:22:35,634 mdtraj/formats/xtc/src/xdrfile_trr.c:90:12: note: ‘do_trnheader’ was previously declared here 2022-09-06T20:22:35,642 building 'mdtraj.formats.tng' extension 2022-09-06T20:22:35,644 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng 2022-09-06T20:22:35,645 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src 2022-09-06T20:22:35,646 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression 2022-09-06T20:22:35,650 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/lib 2022-09-06T20:22:35,651 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/bwlzh.o 2022-09-06T20:22:37,358 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/bwt.o 2022-09-06T20:22:38,248 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/coder.o 2022-09-06T20:22:39,910 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/dict.o 2022-09-06T20:22:40,207 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/fixpoint.o 2022-09-06T20:22:40,653 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/huffman.o 2022-09-06T20:22:42,024 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/huffmem.o 2022-09-06T20:22:43,072 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/lz77.o 2022-09-06T20:22:44,028 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/merge_sort.o 2022-09-06T20:22:44,439 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/mtf.o 2022-09-06T20:22:44,633 mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: 2022-09-06T20:22:44,633 mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-09-06T20:22:44,634 while (dict[ptr]!=v) 2022-09-06T20:22:44,634 ^~ 2022-09-06T20:22:45,328 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/rle.o 2022-09-06T20:22:45,431 mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: 2022-09-06T20:22:45,431 mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-09-06T20:22:45,432 if (v==vals[i]) 2022-09-06T20:22:45,432 ^~ 2022-09-06T20:22:45,742 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/tng_compress.o 2022-09-06T20:22:50,708 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/vals16.o 2022-09-06T20:22:51,010 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/warnmalloc.o 2022-09-06T20:22:51,364 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/widemuldiv.o 2022-09-06T20:22:51,938 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/xtc2.o 2022-09-06T20:22:54,917 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/xtc3.o 2022-09-06T20:22:59,758 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/lib/md5.o 2022-09-06T20:23:00,708 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/lib/tng_io.o 2022-09-06T20:23:01,320 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: 2022-09-06T20:23:01,327 mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:23:01,328 tng_data->input_endianness_swap_func_32 = 2022-09-06T20:23:01,329 ^ 2022-09-06T20:23:01,329 mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:23:01,329 tng_data->input_endianness_swap_func_64 = 2022-09-06T20:23:01,330 ^ 2022-09-06T20:23:01,330 mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:23:01,330 tng_data->input_endianness_swap_func_32 = 2022-09-06T20:23:01,331 ^ 2022-09-06T20:23:01,331 mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:23:01,332 tng_data->input_endianness_swap_func_64 = 2022-09-06T20:23:01,332 ^ 2022-09-06T20:23:01,521 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: 2022-09-06T20:23:01,523 mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 2022-09-06T20:23:01,524 if(tng_data->output_endianness_swap_func_32 == 2022-09-06T20:23:01,524 ^~ 2022-09-06T20:23:01,525 mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 2022-09-06T20:23:01,526 else if(tng_data->output_endianness_swap_func_32 == 2022-09-06T20:23:01,526 ^~ 2022-09-06T20:23:01,527 mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 2022-09-06T20:23:01,528 if(tng_data->output_endianness_swap_func_64 == 2022-09-06T20:23:01,528 ^~ 2022-09-06T20:23:01,529 mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 2022-09-06T20:23:01,530 else if(tng_data->output_endianness_swap_func_64 == 2022-09-06T20:23:01,530 ^~ 2022-09-06T20:23:01,534 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: 2022-09-06T20:23:01,536 mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:23:01,536 tng_data->output_endianness_swap_func_32 = 2022-09-06T20:23:01,537 ^ 2022-09-06T20:23:01,538 mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:23:01,539 tng_data->output_endianness_swap_func_64 = 2022-09-06T20:23:01,539 ^ 2022-09-06T20:23:01,541 mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:23:01,541 tng_data->output_endianness_swap_func_32 = 2022-09-06T20:23:01,541 ^ 2022-09-06T20:23:01,543 mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘enum (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:23:01,543 tng_data->output_endianness_swap_func_64 = 2022-09-06T20:23:01,543 ^ 2022-09-06T20:23:06,477 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: 2022-09-06T20:23:06,568 mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2022-09-06T20:23:06,568 strncpy(data->block_name, block_name, strlen(block_name) + 1); 2022-09-06T20:23:06,569 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:23:06,569 mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 2022-09-06T20:23:06,569 strncpy(data->block_name, block_name, strlen(block_name) + 1); 2022-09-06T20:23:06,569 ^~~~~~~~~~~~~~~~~~ 2022-09-06T20:23:08,911 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write’: 2022-09-06T20:23:08,913 mdtraj/formats/tng/src/lib/tng_io.c:5684:26: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:23:08,914 int64_t n_particles, num_first_particle, n_frames, stride_length; 2022-09-06T20:23:08,914 ^~~~~~~~~~~~~~~~~~ 2022-09-06T20:23:08,916 mdtraj/formats/tng/src/lib/tng_io.c:5684:13: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:23:08,916 int64_t n_particles, num_first_particle, n_frames, stride_length; 2022-09-06T20:23:08,916 ^~~~~~~~~~~ 2022-09-06T20:23:32,354 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/tng/tng.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/tng.o 2022-09-06T20:23:33,025 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-09-06T20:23:33,026 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:23:33,026 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-09-06T20:23:33,026 from mdtraj/formats/tng/tng.c:801: 2022-09-06T20:23:33,026 /usr/local/lib/python3.7/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] 2022-09-06T20:23:33,027 #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:23:33,027 ^~~~~~~ 2022-09-06T20:23:33,238 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’: 2022-09-06T20:23:33,240 mdtraj/formats/tng/tng.c:3713:104: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,240 __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,240 ^~ 2022-09-06T20:23:33,242 mdtraj/formats/tng/tng.c:3768:88: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,242 __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,243 ^~ 2022-09-06T20:23:33,244 mdtraj/formats/tng/tng.c:3800:90: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,244 __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,245 ^~ 2022-09-06T20:23:33,246 mdtraj/formats/tng/tng.c:3832:95: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,247 __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,247 ^~ 2022-09-06T20:23:33,249 mdtraj/formats/tng/tng.c:3902:113: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,250 __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,250 ^~ 2022-09-06T20:23:33,255 mdtraj/formats/tng/tng.c:3946:77: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,255 __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,255 ^~ 2022-09-06T20:23:33,303 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’: 2022-09-06T20:23:33,304 mdtraj/formats/tng/tng.c:4742:106: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,304 __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,304 ^~ 2022-09-06T20:23:33,307 mdtraj/formats/tng/tng.c:4787:108: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,307 __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,308 ^~ 2022-09-06T20:23:33,316 mdtraj/formats/tng/tng.c:4894:115: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,317 __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,317 ^~ 2022-09-06T20:23:33,318 mdtraj/formats/tng/tng.c:4924:105: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,319 __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,319 ^~ 2022-09-06T20:23:33,330 mdtraj/formats/tng/tng.c:5052:105: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,331 __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,331 ^~ 2022-09-06T20:23:33,387 mdtraj/formats/tng/tng.c:5653:126: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,388 __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,388 ^~ 2022-09-06T20:23:33,418 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’: 2022-09-06T20:23:33,419 mdtraj/formats/tng/tng.c:6063:152: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,419 __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,420 ^~ 2022-09-06T20:23:33,451 mdtraj/formats/tng/tng.c:6331:108: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,452 __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,452 ^~ 2022-09-06T20:23:33,460 mdtraj/formats/tng/tng.c:6433:304: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,460 __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,461 ^~ 2022-09-06T20:23:33,689 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’: 2022-09-06T20:23:33,691 mdtraj/formats/tng/tng.c:8925:94: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,691 __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,691 ^~ 2022-09-06T20:23:33,694 mdtraj/formats/tng/tng.c:8957:75: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,695 __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,695 ^~ 2022-09-06T20:23:33,698 mdtraj/formats/tng/tng.c:8989:81: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,698 __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,698 ^~ 2022-09-06T20:23:33,728 mdtraj/formats/tng/tng.c:9312:77: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,729 __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,729 ^~ 2022-09-06T20:23:33,769 mdtraj/formats/tng/tng.c:9503:372: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,770 __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,770 ^~ 2022-09-06T20:23:33,800 mdtraj/formats/tng/tng.c:9555:378: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,800 __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,801 ^~ 2022-09-06T20:23:33,807 mdtraj/formats/tng/tng.c:9617:89: warning: comparison between ‘tng_function_status’ {aka ‘enum ’} and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:23:33,807 __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:23:33,807 ^~ 2022-09-06T20:24:14,014 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-37/mdtraj/formats/tng.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:25:30,282 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: 2022-09-06T20:25:30,282 mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2022-09-06T20:25:30,283 strncpy(data->block_name, block_name, strlen(block_name) + 1); 2022-09-06T20:25:30,283 ^ 2022-09-06T20:25:30,283 mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 2022-09-06T20:25:30,284 strncpy(data->block_name, block_name, strlen(block_name) + 1); 2022-09-06T20:25:30,284 ^ 2022-09-06T20:25:30,293 building 'mdtraj.formats.dcd' extension 2022-09-06T20:25:30,295 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/dcd 2022-09-06T20:25:30,297 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/dcd/src 2022-09-06T20:25:30,308 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:25:31,003 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-09-06T20:25:31,003 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:25:31,004 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-09-06T20:25:31,004 from mdtraj/formats/dcd/dcd.c:773: 2022-09-06T20:25:31,004 /usr/local/lib/python3.7/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] 2022-09-06T20:25:31,005 #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:25:31,005 ^~~~~~~ 2022-09-06T20:25:49,250 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2022-09-06T20:25:49,251 mdtraj/formats/dcd/dcd.c:685:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:25:49,252 #define PyInt_FromLong PyLong_FromLong 2022-09-06T20:25:49,252 ^~~~~~~~~~~~~~~ 2022-09-06T20:25:49,253 mdtraj/formats/dcd/dcd.c:5452:7: note: ‘__pyx_v_i’ was declared here 2022-09-06T20:25:49,253 int __pyx_v_i; 2022-09-06T20:25:49,253 ^~~~~~~~~ 2022-09-06T20:25:56,470 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:25:59,490 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-37/mdtraj/formats/dcd.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:26:20,658 building 'mdtraj.formats.binpos' extension 2022-09-06T20:26:20,660 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/binpos 2022-09-06T20:26:20,661 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/binpos/src 2022-09-06T20:26:20,663 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:26:21,330 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-09-06T20:26:21,331 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:26:21,331 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-09-06T20:26:21,331 from mdtraj/formats/binpos/binpos.c:773: 2022-09-06T20:26:21,332 /usr/local/lib/python3.7/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] 2022-09-06T20:26:21,332 #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:26:21,332 ^~~~~~~ 2022-09-06T20:26:33,954 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2022-09-06T20:26:33,957 mdtraj/formats/binpos/binpos.c:5527:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:26:33,957 if (__pyx_t_2) { 2022-09-06T20:26:33,958 ^ 2022-09-06T20:26:33,960 mdtraj/formats/binpos/binpos.c:5007:7: note: ‘__pyx_v_status’ was declared here 2022-09-06T20:26:33,961 int __pyx_v_status; 2022-09-06T20:26:33,961 ^~~~~~~~~~~~~~ 2022-09-06T20:26:33,961 mdtraj/formats/binpos/binpos.c:685:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:26:33,962 #define PyInt_FromLong PyLong_FromLong 2022-09-06T20:26:33,962 ^~~~~~~~~~~~~~~ 2022-09-06T20:26:33,964 mdtraj/formats/binpos/binpos.c:5004:7: note: ‘__pyx_v_i’ was declared here 2022-09-06T20:26:33,964 int __pyx_v_i; 2022-09-06T20:26:33,964 ^~~~~~~~~ 2022-09-06T20:26:43,781 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:26:44,549 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/formats/binpos/binpos.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-37/mdtraj/formats/binpos.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:27:01,533 building 'mdtraj.formats.dtr' extension 2022-09-06T20:27:01,535 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/dtr 2022-09-06T20:27:01,537 creating build/temp.linux-armv7l-cpython-37/mdtraj/formats/dtr/src 2022-09-06T20:27:01,539 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:27:02,146 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-09-06T20:27:02,147 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:27:02,147 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-09-06T20:27:02,148 from mdtraj/formats/dtr/dtr.cpp:794: 2022-09-06T20:27:02,149 /usr/local/lib/python3.7/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] 2022-09-06T20:27:02,149 #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:27:02,149 ^~~~~~~ 2022-09-06T20:27:31,805 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-37/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:27:35,342 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2022-09-06T20:27:35,343 mdtraj/formats/dtr/src/dtrplugin.cxx:486:29: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2022-09-06T20:27:35,343 fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2022-09-06T20:27:35,344 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ 2022-09-06T20:27:35,345 mdtraj/formats/dtr/src/dtrplugin.cxx:487:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:27:35,345 printf("size %d framesize %d\n\n", 2022-09-06T20:27:35,346 ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:27:35,346 keys[i].size(), m_framesize); 2022-09-06T20:27:35,346 ~~~~~~~~~~~~~~ 2022-09-06T20:27:35,347 mdtraj/formats/dtr/src/dtrplugin.cxx:487:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:27:35,349 mdtraj/formats/dtr/src/dtrplugin.cxx:494:21: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2022-09-06T20:27:35,349 "non-constant time interval at frame %ld\n", i); 2022-09-06T20:27:35,349 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ 2022-09-06T20:27:35,351 mdtraj/formats/dtr/src/dtrplugin.cxx:499:29: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2022-09-06T20:27:35,351 fprintf(stderr, "unexpected offset for frame %ld\n", i); 2022-09-06T20:27:35,351 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ 2022-09-06T20:27:35,598 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2022-09-06T20:27:35,599 mdtraj/formats/dtr/src/dtrplugin.cxx:1301:21: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:27:35,599 fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2022-09-06T20:27:35,599 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:27:35,600 3*natoms, pos.count); 2022-09-06T20:27:35,600 ~~~~~~~~~ 2022-09-06T20:27:35,603 mdtraj/formats/dtr/src/dtrplugin.cxx:1310:23: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:27:35,604 fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2022-09-06T20:27:35,604 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:27:35,604 3*natoms, vel.count); 2022-09-06T20:27:35,605 ~~~~~~~~~ 2022-09-06T20:27:35,646 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2022-09-06T20:27:35,647 mdtraj/formats/dtr/src/dtrplugin.cxx:1572:23: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:27:35,647 fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2022-09-06T20:27:35,647 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:27:35,648 velblob.count, 3*natoms); 2022-09-06T20:27:35,648 ~~~~~~~~~~~~~ 2022-09-06T20:27:38,041 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘(anonymous namespace)::DDException::DDException(std::__cxx11::basic_string, std::allocator > const&, int)’: 2022-09-06T20:27:38,041 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘this_7(D)->eno’ is used uninitialized in this function [-Wuninitialized] 2022-09-06T20:27:38,042 : std::runtime_error(text + strerror(eno)), eno(_eno){} 2022-09-06T20:27:38,042 ~~~~~~~~^~~~~ 2022-09-06T20:27:46,999 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘framefile(std::__cxx11::basic_string, std::allocator > const&, unsigned int, unsigned int, int, int)’: 2022-09-06T20:27:47,000 mdtraj/formats/dtr/src/dtrplugin.cxx:667:22: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2022-09-06T20:27:47,000 sprintf(answer, "%03x/", d1); 2022-09-06T20:27:47,001 ^~~~~~~ 2022-09-06T20:27:47,001 mdtraj/formats/dtr/src/dtrplugin.cxx:667:13: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2022-09-06T20:27:47,002 sprintf(answer, "%03x/", d1); 2022-09-06T20:27:47,002 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:27:47,002 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 2022-09-06T20:27:47,003 sprintf(answer, "%03x/%03x/", d1, d2); 2022-09-06T20:27:47,003 ^~~~~~~~~~~~ 2022-09-06T20:27:47,003 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2022-09-06T20:27:47,003 mdtraj/formats/dtr/src/dtrplugin.cxx:665:13: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2022-09-06T20:27:47,004 sprintf(answer, "%03x/%03x/", d1, d2); 2022-09-06T20:27:47,004 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:27:51,163 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘DDmkdir(std::__cxx11::basic_string, std::allocator > const&, unsigned int, int, int)’: 2022-09-06T20:27:51,164 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2022-09-06T20:27:51,164 sprintf(sub, "%03x/", i); 2022-09-06T20:27:51,165 ^~~~~~~ 2022-09-06T20:27:51,165 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483647] 2022-09-06T20:27:51,165 mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2022-09-06T20:27:51,166 sprintf(sub, "%03x/", i); 2022-09-06T20:27:51,166 ~~~~~~~^~~~~~~~~~~~~~~~~ 2022-09-06T20:27:51,167 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2022-09-06T20:27:51,167 sprintf(subsub, "%03x", j); 2022-09-06T20:27:51,167 ^~~~~~ 2022-09-06T20:27:51,167 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483647] 2022-09-06T20:27:51,168 mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2022-09-06T20:27:51,168 sprintf(subsub, "%03x", j); 2022-09-06T20:27:51,169 ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2022-09-06T20:28:04,024 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-37/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-37/mdtraj/formats/dtr.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:28:39,688 building 'mdtraj._rmsd' extension 2022-09-06T20:28:39,689 creating build/temp.linux-armv7l-cpython-37/mdtraj/rmsd 2022-09-06T20:28:39,691 creating build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src 2022-09-06T20:28:39,693 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:29:46,979 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:29:47,602 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:29:48,177 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:29:49,784 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-37/mdtraj/_rmsd.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:30:41,506 building 'mdtraj._lprmsd' extension 2022-09-06T20:30:41,509 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:30:42,064 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-09-06T20:30:42,064 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:30:42,065 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-09-06T20:30:42,065 from mdtraj/rmsd/_lprmsd.cpp:805: 2022-09-06T20:30:42,065 /usr/local/lib/python3.7/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] 2022-09-06T20:30:42,066 #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:30:42,066 ^~~~~~~ 2022-09-06T20:31:04,475 mdtraj/rmsd/_lprmsd.cpp: In function ‘__pyx_pf_6mdtraj_7_lprmsd_lprmsd(_object*, _object*, _object*, int, _object*, _object*, _longobject*, _longobject*) [clone .isra.82]’: 2022-09-06T20:31:04,476 mdtraj/rmsd/_lprmsd.cpp:4113:14: warning: ‘__pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:31:04,477 } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; 2022-09-06T20:31:04,477 ^~ 2022-09-06T20:31:23,040 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:31:28,545 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:31:29,001 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:31:31,381 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:31:32,149 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:31:32,728 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:31:34,320 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-37/mdtraj/_lprmsd.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:32:11,283 building 'mdtraj.core.lib.libtheobald' extension 2022-09-06T20:32:11,284 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2022-09-06T20:32:12,866 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2022-09-06T20:32:13,316 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-37/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-37/mdtraj/rmsd/src/center.o 2022-09-06T20:32:13,406 building 'mdtraj.geometry._geometry' extension 2022-09-06T20:32:13,407 creating build/temp.linux-armv7l-cpython-37/mdtraj/geometry 2022-09-06T20:32:13,408 creating build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src 2022-09-06T20:32:13,410 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:32:13,990 In file included from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2022-09-06T20:32:13,990 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:32:13,990 from /usr/local/lib/python3.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-09-06T20:32:13,991 from mdtraj/geometry/src/_geometry.cpp:807: 2022-09-06T20:32:13,991 /usr/local/lib/python3.7/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] 2022-09-06T20:32:13,991 #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:32:13,992 ^~~~~~~ 2022-09-06T20:32:28,110 mdtraj/geometry/src/_geometry.cpp: In function ‘__pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice) [clone .isra.26]’: 2022-09-06T20:32:28,111 mdtraj/geometry/src/_geometry.cpp:6104:224: warning: ‘__pyx_v_delta[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:32:28,112 (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); 2022-09-06T20:32:28,112 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:32:28,113 mdtraj/geometry/src/_geometry.cpp:6118:277: warning: ‘__pyx_v_delta[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:32:28,113 (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); 2022-09-06T20:32:28,113 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:32:28,114 mdtraj/geometry/src/_geometry.cpp:6118:277: warning: ‘__pyx_v_offset[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:33:13,127 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:33:57,163 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:34:05,520 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:34:07,761 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/sasa.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-37/mdtraj/geometry/_geometry.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:35:18,413 building 'mdtraj.geometry.drid' extension 2022-09-06T20:35:18,417 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:36:06,938 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:36:08,303 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:36:08,590 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/moments.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-37/mdtraj/geometry/drid.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:36:45,958 building 'mdtraj.geometry.neighbors' extension 2022-09-06T20:36:45,961 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:37:30,477 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:37:33,183 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/neighbors.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-37/mdtraj/geometry/neighbors.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:38:05,868 building 'mdtraj.geometry.neighborlist' extension 2022-09-06T20:38:05,871 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:38:45,771 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:38:57,568 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-armv7l-cpython-37/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-37/mdtraj/geometry/src/neighborlist.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-37/mdtraj/geometry/neighborlist.cpython-37m-arm-linux-gnueabihf.so 2022-09-06T20:39:34,748 installing to build/bdist.linux-armv7l/wheel 2022-09-06T20:39:34,749 running install 2022-09-06T20:39:34,818 running install_lib 2022-09-06T20:39:35,461 creating build/bdist.linux-armv7l 2022-09-06T20:39:35,461 creating build/bdist.linux-armv7l/wheel 2022-09-06T20:39:35,465 creating build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T20:39:35,466 copying build/lib.linux-armv7l-cpython-37/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T20:39:35,470 copying build/lib.linux-armv7l-cpython-37/mdtraj/_rmsd.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T20:39:35,507 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2022-09-06T20:39:35,509 copying build/lib.linux-armv7l-cpython-37/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2022-09-06T20:39:35,512 copying build/lib.linux-armv7l-cpython-37/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2022-09-06T20:39:35,517 copying build/lib.linux-armv7l-cpython-37/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2022-09-06T20:39:35,521 copying build/lib.linux-armv7l-cpython-37/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T20:39:35,527 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T20:39:35,529 copying build/lib.linux-armv7l-cpython-37/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T20:39:35,533 copying build/lib.linux-armv7l-cpython-37/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T20:39:35,538 copying build/lib.linux-armv7l-cpython-37/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T20:39:35,542 copying build/lib.linux-armv7l-cpython-37/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T20:39:35,547 copying build/lib.linux-armv7l-cpython-37/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T20:39:35,551 copying build/lib.linux-armv7l-cpython-37/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T20:39:35,557 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,559 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,563 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,568 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,572 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,576 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/six.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,582 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,587 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,591 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,595 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T20:39:35,601 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,603 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,608 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,613 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,619 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,623 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,628 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,635 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,639 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,643 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,647 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,652 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,656 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,662 copying build/lib.linux-armv7l-cpython-37/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T20:39:35,667 copying build/lib.linux-armv7l-cpython-37/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T20:39:35,672 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T20:39:35,674 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T20:39:35,679 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T20:39:35,682 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T20:39:35,687 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T20:39:35,693 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2022-09-06T20:39:35,695 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2022-09-06T20:39:35,699 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2022-09-06T20:39:35,703 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2022-09-06T20:39:35,713 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T20:39:35,720 copying build/lib.linux-armv7l-cpython-37/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T20:39:35,728 copying build/lib.linux-armv7l-cpython-37/mdtraj/_lprmsd.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T20:39:35,759 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,760 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,764 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,769 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/dtr.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,817 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,821 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2022-09-06T20:39:35,824 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2022-09-06T20:39:35,825 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2022-09-06T20:39:35,830 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2022-09-06T20:39:35,834 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2022-09-06T20:39:35,837 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2022-09-06T20:39:35,842 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2022-09-06T20:39:35,848 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/tng.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,890 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,894 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,899 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,904 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,909 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,914 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,918 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/xtc.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,947 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,952 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,957 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/binpos.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,974 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,978 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,981 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,986 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,991 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:35,995 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/dcd.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:36,015 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/trr.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:36,045 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:36,050 copying build/lib.linux-armv7l-cpython-37/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T20:39:36,056 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2022-09-06T20:39:36,058 copying build/lib.linux-armv7l-cpython-37/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2022-09-06T20:39:36,061 copying build/lib.linux-armv7l-cpython-37/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2022-09-06T20:39:36,066 copying build/lib.linux-armv7l-cpython-37/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2022-09-06T20:39:36,071 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T20:39:36,072 copying build/lib.linux-armv7l-cpython-37/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T20:39:36,076 copying build/lib.linux-armv7l-cpython-37/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T20:39:36,079 copying build/lib.linux-armv7l-cpython-37/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T20:39:36,083 copying build/lib.linux-armv7l-cpython-37/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T20:39:36,090 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,091 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,095 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,099 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,102 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,107 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,110 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,114 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,118 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,123 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/drid.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,146 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,151 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,156 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,160 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,165 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/neighborlist.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,201 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,205 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/neighbors.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,237 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,242 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,248 copying build/lib.linux-armv7l-cpython-37/mdtraj/geometry/_geometry.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T20:39:36,323 running install_egg_info 2022-09-06T20:39:37,622 running egg_info 2022-09-06T20:39:38,250 writing anagenex_mdtraj.egg-info/PKG-INFO 2022-09-06T20:39:38,843 writing dependency_links to anagenex_mdtraj.egg-info/dependency_links.txt 2022-09-06T20:39:40,624 writing entry points to anagenex_mdtraj.egg-info/entry_points.txt 2022-09-06T20:39:41,813 writing requirements to anagenex_mdtraj.egg-info/requires.txt 2022-09-06T20:39:42,411 writing top-level names to anagenex_mdtraj.egg-info/top_level.txt 2022-09-06T20:39:42,522 reading manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:39:42,575 reading manifest template 'MANIFEST.in' 2022-09-06T20:39:44,368 no previously-included directories found matching '__pycache__' 2022-09-06T20:39:44,371 no previously-included directories found matching '*.pyc' 2022-09-06T20:39:44,372 adding license file 'LICENSE' 2022-09-06T20:39:44,412 writing manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:39:44,416 Copying anagenex_mdtraj.egg-info to build/bdist.linux-armv7l/wheel/anagenex_mdtraj-1.9.8.dev0-py3.7.egg-info 2022-09-06T20:39:44,445 running install_scripts 2022-09-06T20:39:44,569 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-09-06T20:39:44,617 creating build/bdist.linux-armv7l/wheel/anagenex_mdtraj-1.9.8.dev0.dist-info/WHEEL 2022-09-06T20:39:44,622 creating '/tmp/pip-wheel-bsp05pjl/tmpxdwcjwcn/anagenex_mdtraj-1.9.8.dev0-cp37-cp37m-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-09-06T20:39:44,630 adding 'mdtraj/__init__.py' 2022-09-06T20:39:44,871 adding 'mdtraj/_lprmsd.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:45,158 adding 'mdtraj/_rmsd.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:45,175 adding 'mdtraj/io.py' 2022-09-06T20:39:45,178 adding 'mdtraj/version.py' 2022-09-06T20:39:45,181 adding 'mdtraj/core/__init__.py' 2022-09-06T20:39:45,186 adding 'mdtraj/core/element.py' 2022-09-06T20:39:45,193 adding 'mdtraj/core/residue_names.py' 2022-09-06T20:39:45,198 adding 'mdtraj/core/selection.py' 2022-09-06T20:39:45,216 adding 'mdtraj/core/topology.py' 2022-09-06T20:39:45,239 adding 'mdtraj/core/trajectory.py' 2022-09-06T20:39:45,244 adding 'mdtraj/core/lib/center.h' 2022-09-06T20:39:45,287 adding 'mdtraj/core/lib/libtheobald.a' 2022-09-06T20:39:45,292 adding 'mdtraj/core/lib/theobald_rmsd.h' 2022-09-06T20:39:45,297 adding 'mdtraj/formats/__init__.py' 2022-09-06T20:39:45,304 adding 'mdtraj/formats/amberrst.py' 2022-09-06T20:39:45,309 adding 'mdtraj/formats/arc.py' 2022-09-06T20:39:45,425 adding 'mdtraj/formats/binpos.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:45,564 adding 'mdtraj/formats/dcd.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:45,918 adding 'mdtraj/formats/dtr.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:45,942 adding 'mdtraj/formats/gro.py' 2022-09-06T20:39:45,947 adding 'mdtraj/formats/gsd.py' 2022-09-06T20:39:45,957 adding 'mdtraj/formats/hdf5.py' 2022-09-06T20:39:45,961 adding 'mdtraj/formats/hoomdxml.py' 2022-09-06T20:39:45,968 adding 'mdtraj/formats/lammpstrj.py' 2022-09-06T20:39:45,974 adding 'mdtraj/formats/lh5.py' 2022-09-06T20:39:45,979 adding 'mdtraj/formats/mdcrd.py' 2022-09-06T20:39:45,984 adding 'mdtraj/formats/mol2.py' 2022-09-06T20:39:45,990 adding 'mdtraj/formats/netcdf.py' 2022-09-06T20:39:45,994 adding 'mdtraj/formats/openmmxml.py' 2022-09-06T20:39:45,998 adding 'mdtraj/formats/pdbx.py' 2022-09-06T20:39:46,002 adding 'mdtraj/formats/prmtop.py' 2022-09-06T20:39:46,006 adding 'mdtraj/formats/psf.py' 2022-09-06T20:39:46,009 adding 'mdtraj/formats/registry.py' 2022-09-06T20:39:46,397 adding 'mdtraj/formats/tng.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:46,653 adding 'mdtraj/formats/trr.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:46,895 adding 'mdtraj/formats/xtc.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:46,911 adding 'mdtraj/formats/xyzfile.py' 2022-09-06T20:39:46,915 adding 'mdtraj/formats/pdb/__init__.py' 2022-09-06T20:39:46,924 adding 'mdtraj/formats/pdb/pdbfile.py' 2022-09-06T20:39:46,935 adding 'mdtraj/formats/pdb/pdbstructure.py' 2022-09-06T20:39:46,940 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2022-09-06T20:39:46,945 adding 'mdtraj/formats/pdb/data/residues.xml' 2022-09-06T20:39:46,949 adding 'mdtraj/geometry/__init__.py' 2022-09-06T20:39:47,370 adding 'mdtraj/geometry/_geometry.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:47,392 adding 'mdtraj/geometry/alignment.py' 2022-09-06T20:39:47,395 adding 'mdtraj/geometry/angle.py' 2022-09-06T20:39:47,400 adding 'mdtraj/geometry/contact.py' 2022-09-06T20:39:47,405 adding 'mdtraj/geometry/dihedral.py' 2022-09-06T20:39:47,411 adding 'mdtraj/geometry/distance.py' 2022-09-06T20:39:47,638 adding 'mdtraj/geometry/drid.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:47,650 adding 'mdtraj/geometry/dssp.py' 2022-09-06T20:39:47,656 adding 'mdtraj/geometry/hbond.py' 2022-09-06T20:39:47,662 adding 'mdtraj/geometry/internal.py' 2022-09-06T20:39:47,939 adding 'mdtraj/geometry/neighborlist.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:48,183 adding 'mdtraj/geometry/neighbors.cpython-37m-arm-linux-gnueabihf.so' 2022-09-06T20:39:48,196 adding 'mdtraj/geometry/order.py' 2022-09-06T20:39:48,200 adding 'mdtraj/geometry/rdf.py' 2022-09-06T20:39:48,203 adding 'mdtraj/geometry/rg.py' 2022-09-06T20:39:48,207 adding 'mdtraj/geometry/sasa.py' 2022-09-06T20:39:48,210 adding 'mdtraj/geometry/shape.py' 2022-09-06T20:39:48,214 adding 'mdtraj/geometry/thermodynamic_properties.py' 2022-09-06T20:39:48,217 adding 'mdtraj/nmr/__init__.py' 2022-09-06T20:39:48,220 adding 'mdtraj/nmr/scalar_couplings.py' 2022-09-06T20:39:48,224 adding 'mdtraj/nmr/shift_wrappers.py' 2022-09-06T20:39:48,228 adding 'mdtraj/reporters/__init__.py' 2022-09-06T20:39:48,232 adding 'mdtraj/reporters/basereporter.py' 2022-09-06T20:39:48,235 adding 'mdtraj/reporters/dcdreporter.py' 2022-09-06T20:39:48,238 adding 'mdtraj/reporters/hdf5reporter.py' 2022-09-06T20:39:48,240 adding 'mdtraj/reporters/netcdfreporter.py' 2022-09-06T20:39:48,244 adding 'mdtraj/reporters/xtcreporter.py' 2022-09-06T20:39:48,247 adding 'mdtraj/scripts/__init__.py' 2022-09-06T20:39:48,252 adding 'mdtraj/scripts/mdconvert.py' 2022-09-06T20:39:48,256 adding 'mdtraj/scripts/mdinspect.py' 2022-09-06T20:39:48,260 adding 'mdtraj/testing/__init__.py' 2022-09-06T20:39:48,266 adding 'mdtraj/testing/docscrape.py' 2022-09-06T20:39:48,269 adding 'mdtraj/testing/docstrings.py' 2022-09-06T20:39:48,273 adding 'mdtraj/testing/testing.py' 2022-09-06T20:39:48,277 adding 'mdtraj/utils/__init__.py' 2022-09-06T20:39:48,279 adding 'mdtraj/utils/contextmanagers.py' 2022-09-06T20:39:48,283 adding 'mdtraj/utils/delay_import.py' 2022-09-06T20:39:48,286 adding 'mdtraj/utils/rotation.py' 2022-09-06T20:39:48,288 adding 'mdtraj/utils/singleton.py' 2022-09-06T20:39:48,293 adding 'mdtraj/utils/six.py' 2022-09-06T20:39:48,297 adding 'mdtraj/utils/unitcell.py' 2022-09-06T20:39:48,300 adding 'mdtraj/utils/validation.py' 2022-09-06T20:39:48,303 adding 'mdtraj/utils/zipped.py' 2022-09-06T20:39:48,308 adding 'mdtraj/utils/unit/__init__.py' 2022-09-06T20:39:48,311 adding 'mdtraj/utils/unit/basedimension.py' 2022-09-06T20:39:48,314 adding 'mdtraj/utils/unit/baseunit.py' 2022-09-06T20:39:48,317 adding 'mdtraj/utils/unit/constants.py' 2022-09-06T20:39:48,323 adding 'mdtraj/utils/unit/doctests.py' 2022-09-06T20:39:48,328 adding 'mdtraj/utils/unit/mymatrix.py' 2022-09-06T20:39:48,331 adding 'mdtraj/utils/unit/prefix.py' 2022-09-06T20:39:48,341 adding 'mdtraj/utils/unit/quantity.py' 2022-09-06T20:39:48,344 adding 'mdtraj/utils/unit/standard_dimensions.py' 2022-09-06T20:39:48,352 adding 'mdtraj/utils/unit/unit.py' 2022-09-06T20:39:48,357 adding 'mdtraj/utils/unit/unit_definitions.py' 2022-09-06T20:39:48,360 adding 'mdtraj/utils/unit/unit_math.py' 2022-09-06T20:39:48,363 adding 'mdtraj/utils/unit/unit_operators.py' 2022-09-06T20:39:48,373 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/LICENSE' 2022-09-06T20:39:48,375 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/METADATA' 2022-09-06T20:39:48,377 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/WHEEL' 2022-09-06T20:39:48,379 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/entry_points.txt' 2022-09-06T20:39:48,380 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/top_level.txt' 2022-09-06T20:39:48,385 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/RECORD' 2022-09-06T20:39:48,504 removing build/bdist.linux-armv7l/wheel 2022-09-06T20:39:48,962 Building wheel for anagenex-mdtraj (pyproject.toml): finished with status 'done' 2022-09-06T20:39:49,162 Created wheel for anagenex-mdtraj: filename=anagenex_mdtraj-1.9.8.dev0-cp37-cp37m-linux_armv7l.whl size=2939683 sha256=3294a802a4106ad821f88efe3c291dd1671b0eb6151ee56ac4fabd7b50ab9250 2022-09-06T20:39:49,164 Stored in directory: /tmp/pip-ephem-wheel-cache-vdo6g4ah/wheels/43/17/f5/12b610226bbef839e88f85e91a883481f0c50cc51df1507679 2022-09-06T20:39:49,199 Successfully built anagenex-mdtraj 2022-09-06T20:39:49,413 Removed build tracker: '/tmp/pip-build-tracker-3nenrh92'