2022-09-06T20:48:47,616 Created temporary directory: /tmp/pip-ephem-wheel-cache-nt_8uid6 2022-09-06T20:48:47,622 Created temporary directory: /tmp/pip-build-tracker-5vwv1uz_ 2022-09-06T20:48:47,622 Initialized build tracking at /tmp/pip-build-tracker-5vwv1uz_ 2022-09-06T20:48:47,623 Created build tracker: /tmp/pip-build-tracker-5vwv1uz_ 2022-09-06T20:48:47,623 Entered build tracker: /tmp/pip-build-tracker-5vwv1uz_ 2022-09-06T20:48:47,624 Created temporary directory: /tmp/pip-wheel-b_zcvbmh 2022-09-06T20:48:47,698 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-09-06T20:48:47,707 2 location(s) to search for versions of anagenex-mdtraj: 2022-09-06T20:48:47,707 * https://pypi.org/simple/anagenex-mdtraj/ 2022-09-06T20:48:47,707 * https://www.piwheels.org/simple/anagenex-mdtraj/ 2022-09-06T20:48:47,708 Fetching project page and analyzing links: https://pypi.org/simple/anagenex-mdtraj/ 2022-09-06T20:48:47,709 Getting page https://pypi.org/simple/anagenex-mdtraj/ 2022-09-06T20:48:47,712 Found index url https://pypi.org/simple 2022-09-06T20:48:47,843 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 2022-09-06T20:48:47,844 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/) 2022-09-06T20:48:47,844 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/) 2022-09-06T20:48:47,845 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/) 2022-09-06T20:48:47,845 Fetching project page and analyzing links: https://www.piwheels.org/simple/anagenex-mdtraj/ 2022-09-06T20:48:47,846 Getting page https://www.piwheels.org/simple/anagenex-mdtraj/ 2022-09-06T20:48:47,848 Found index url https://www.piwheels.org/simple 2022-09-06T20:48:48,064 Skipping link: No binaries permitted for anagenex-mdtraj: https://www.piwheels.org/simple/anagenex-mdtraj/anagenex_mdtraj-1.9.8.dev0-cp37-cp37m-linux_armv7l.whl#sha256=3294a802a4106ad821f88efe3c291dd1671b0eb6151ee56ac4fabd7b50ab9250 (from https://www.piwheels.org/simple/anagenex-mdtraj/) 2022-09-06T20:48:48,065 Skipping link: No binaries permitted for anagenex-mdtraj: https://www.piwheels.org/simple/anagenex-mdtraj/anagenex_mdtraj-1.9.8.dev0-cp37-cp37m-linux_armv6l.whl#sha256=3294a802a4106ad821f88efe3c291dd1671b0eb6151ee56ac4fabd7b50ab9250 (from https://www.piwheels.org/simple/anagenex-mdtraj/) 2022-09-06T20:48:48,065 Skipping link: not a file: https://www.piwheels.org/simple/anagenex-mdtraj/ 2022-09-06T20:48:48,066 Skipping link: not a file: https://pypi.org/simple/anagenex-mdtraj/ 2022-09-06T20:48:48,110 Given no hashes to check 1 links for project 'anagenex-mdtraj': discarding no candidates 2022-09-06T20:48:48,152 Collecting anagenex-mdtraj==1.9.8.dev0 2022-09-06T20:48:48,157 Created temporary directory: /tmp/pip-unpack-vp5ffzm1 2022-09-06T20:48:48,259 Downloading anagenex-mdtraj-1.9.8.dev0.tar.gz (2.2 MB) 2022-09-06T20:48:51,186 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-5vwv1uz_' 2022-09-06T20:48:51,199 Created temporary directory: /tmp/pip-build-env-e815a6tk 2022-09-06T20:48:51,220 Created temporary directory: /tmp/pip-standalone-pip-8brf597c 2022-09-06T20:48:53,653 Installing build dependencies: started 2022-09-06T20:48:53,656 Running command pip subprocess to install build dependencies 2022-09-06T20:49:04,925 Using pip 22.1.2 from /tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip (python 3.9) 2022-09-06T20:49:06,700 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-09-06T20:49:11,069 Collecting setuptools 2022-09-06T20:49:11,348 Using cached https://www.piwheels.org/simple/setuptools/setuptools-65.3.0-py3-none-any.whl (1.2 MB) 2022-09-06T20:49:12,001 Collecting wheel 2022-09-06T20:49:12,036 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-09-06T20:49:12,319 Collecting oldest-supported-numpy 2022-09-06T20:49:12,350 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2022.8.16-py3-none-any.whl (3.9 kB) 2022-09-06T20:49:15,990 Collecting Cython>0.28 2022-09-06T20:49:17,013 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.32-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-09-06T20:49:21,490 Collecting numpy==1.19.3 2022-09-06T20:49:23,631 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB) 2022-09-06T20:49:32,696 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2022-09-06T20:49:32,990 Creating /tmp/pip-build-env-e815a6tk/overlay/bin 2022-09-06T20:49:32,995 changing mode of /tmp/pip-build-env-e815a6tk/overlay/bin/wheel to 755 2022-09-06T20:49:53,294 changing mode of /tmp/pip-build-env-e815a6tk/overlay/bin/f2py to 755 2022-09-06T20:49:53,298 changing mode of /tmp/pip-build-env-e815a6tk/overlay/bin/f2py3 to 755 2022-09-06T20:49:53,303 changing mode of /tmp/pip-build-env-e815a6tk/overlay/bin/f2py3.9 to 755 2022-09-06T20:49:59,558 changing mode of /tmp/pip-build-env-e815a6tk/overlay/bin/cygdb to 755 2022-09-06T20:49:59,562 changing mode of /tmp/pip-build-env-e815a6tk/overlay/bin/cython to 755 2022-09-06T20:49:59,567 changing mode of /tmp/pip-build-env-e815a6tk/overlay/bin/cythonize to 755 2022-09-06T20:49:59,661 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. 2022-09-06T20:49:59,662 pyldavis 3.3.1 requires numpy>=1.20.0, but you have numpy 1.19.3 which is incompatible. 2022-09-06T20:49:59,663 Successfully installed Cython-0.29.32 numpy-1.19.3 oldest-supported-numpy-2022.8.16 setuptools-65.3.0 wheel-0.37.1 2022-09-06T20:49:59,883 --- Logging error --- 2022-09-06T20:49:59,901 Traceback (most recent call last): 2022-09-06T20:49:59,902 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/utils/logging.py", line 177, in emit 2022-09-06T20:49:59,902 self.console.print(renderable, overflow="ignore", crop=False, style=style) 2022-09-06T20:49:59,902 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_vendor/rich/console.py", line 1752, in print 2022-09-06T20:49:59,903 extend(render(renderable, render_options)) 2022-09-06T20:49:59,903 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_vendor/rich/console.py", line 1390, in render 2022-09-06T20:49:59,903 for render_output in iter_render: 2022-09-06T20:49:59,904 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/utils/logging.py", line 134, in __rich_console__ 2022-09-06T20:49:59,904 for line in lines: 2022-09-06T20:49:59,904 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_vendor/rich/segment.py", line 245, in split_lines 2022-09-06T20:49:59,905 for segment in segments: 2022-09-06T20:49:59,905 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_vendor/rich/console.py", line 1368, in render 2022-09-06T20:49:59,905 renderable = rich_cast(renderable) 2022-09-06T20:49:59,906 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_vendor/rich/protocol.py", line 36, in rich_cast 2022-09-06T20:49:59,906 renderable = cast_method() 2022-09-06T20:49:59,906 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/self_outdated_check.py", line 130, in __rich__ 2022-09-06T20:49:59,907 pip_cmd = get_best_invocation_for_this_pip() 2022-09-06T20:49:59,907 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/utils/entrypoints.py", line 58, in get_best_invocation_for_this_pip 2022-09-06T20:49:59,907 if found_executable and os.path.samefile( 2022-09-06T20:49:59,908 File "/usr/lib/python3.9/genericpath.py", line 101, in samefile 2022-09-06T20:49:59,908 s2 = os.stat(f2) 2022-09-06T20:49:59,908 FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/pip3.9' 2022-09-06T20:49:59,909 Call stack: 2022-09-06T20:49:59,914 File "/usr/lib/python3.9/runpy.py", line 197, in _run_module_as_main 2022-09-06T20:49:59,914 return _run_code(code, main_globals, None, 2022-09-06T20:49:59,914 File "/usr/lib/python3.9/runpy.py", line 87, in _run_code 2022-09-06T20:49:59,915 exec(code, run_globals) 2022-09-06T20:49:59,915 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/__main__.py", line 31, in 2022-09-06T20:49:59,915 sys.exit(_main()) 2022-09-06T20:49:59,916 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/cli/main.py", line 70, in main 2022-09-06T20:49:59,916 return command.main(cmd_args) 2022-09-06T20:49:59,916 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/cli/base_command.py", line 101, in main 2022-09-06T20:49:59,917 return self._main(args) 2022-09-06T20:49:59,917 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/cli/base_command.py", line 223, in _main 2022-09-06T20:49:59,917 self.handle_pip_version_check(options) 2022-09-06T20:49:59,918 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/cli/req_command.py", line 148, in handle_pip_version_check 2022-09-06T20:49:59,918 pip_self_version_check(session, options) 2022-09-06T20:49:59,918 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/self_outdated_check.py", line 237, in pip_self_version_check 2022-09-06T20:49:59,918 logger.info("[present-rich] %s", upgrade_prompt) 2022-09-06T20:49:59,919 File "/usr/lib/python3.9/logging/__init__.py", line 1442, in info 2022-09-06T20:49:59,919 self._log(INFO, msg, args, **kwargs) 2022-09-06T20:49:59,919 File "/usr/lib/python3.9/logging/__init__.py", line 1585, in _log 2022-09-06T20:49:59,920 self.handle(record) 2022-09-06T20:49:59,920 File "/usr/lib/python3.9/logging/__init__.py", line 1595, in handle 2022-09-06T20:49:59,920 self.callHandlers(record) 2022-09-06T20:49:59,920 File "/usr/lib/python3.9/logging/__init__.py", line 1657, in callHandlers 2022-09-06T20:49:59,921 hdlr.handle(record) 2022-09-06T20:49:59,921 File "/usr/lib/python3.9/logging/__init__.py", line 948, in handle 2022-09-06T20:49:59,921 self.emit(record) 2022-09-06T20:49:59,922 File "/tmp/pip-standalone-pip-8brf597c/__env_pip__.zip/pip/_internal/utils/logging.py", line 179, in emit 2022-09-06T20:49:59,922 self.handleError(record) 2022-09-06T20:49:59,922 Message: '[present-rich] %s' 2022-09-06T20:49:59,922 Arguments: (UpgradePrompt(old='22.1.2', new='22.2.2'),) 2022-09-06T20:50:00,617 Installing build dependencies: finished with status 'done' 2022-09-06T20:50:00,663 Getting requirements to build wheel: started 2022-09-06T20:50:00,665 Running command Getting requirements to build wheel 2022-09-06T20:50:03,022 Using built-in specs. 2022-09-06T20:50:03,025 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2022-09-06T20:50:03,026 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2022-09-06T20:50:03,027 Target: arm-linux-gnueabihf 2022-09-06T20:50:03,027 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --enable-libphobos-checking=release --with-target-system-zlib=auto --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 2022-09-06T20:50:03,028 Thread model: posix 2022-09-06T20:50:03,028 Supported LTO compression algorithms: zlib zstd 2022-09-06T20:50:03,029 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2022-09-06T20:50:21,417 C compiler: 2022-09-06T20:50:21,418 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-09-06T20:50:21,418 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2022-09-06T20:50:21,418 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2022-09-06T20:50:21,419 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2022-09-06T20:50:21,419 Attempting to autodetect NEON support... Did not detect NEON support 2022-09-06T20:50:21,419 running egg_info 2022-09-06T20:50:22,009 writing anagenex_mdtraj.egg-info/PKG-INFO 2022-09-06T20:50:22,565 writing dependency_links to anagenex_mdtraj.egg-info/dependency_links.txt 2022-09-06T20:50:24,227 writing entry points to anagenex_mdtraj.egg-info/entry_points.txt 2022-09-06T20:50:25,336 writing requirements to anagenex_mdtraj.egg-info/requires.txt 2022-09-06T20:50:25,891 writing top-level names to anagenex_mdtraj.egg-info/top_level.txt 2022-09-06T20:50:26,610 reading manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:50:26,679 reading manifest template 'MANIFEST.in' 2022-09-06T20:50:28,495 no previously-included directories found matching '__pycache__' 2022-09-06T20:50:28,497 no previously-included directories found matching '*.pyc' 2022-09-06T20:50:28,498 adding license file 'LICENSE' 2022-09-06T20:50:28,533 writing manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:50:28,776 Getting requirements to build wheel: finished with status 'done' 2022-09-06T20:50:28,800 Created temporary directory: /tmp/pip-modern-metadata-koqnjv1j 2022-09-06T20:50:28,805 Preparing metadata (pyproject.toml): started 2022-09-06T20:50:28,807 Running command Preparing metadata (pyproject.toml) 2022-09-06T20:50:31,013 Using built-in specs. 2022-09-06T20:50:31,015 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2022-09-06T20:50:31,016 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2022-09-06T20:50:31,016 Target: arm-linux-gnueabihf 2022-09-06T20:50:31,016 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --enable-libphobos-checking=release --with-target-system-zlib=auto --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 2022-09-06T20:50:31,017 Thread model: posix 2022-09-06T20:50:31,017 Supported LTO compression algorithms: zlib zstd 2022-09-06T20:50:31,017 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2022-09-06T20:50:44,169 ./basesetup.py:451: UserWarning: Unrecognized setuptools command ('dist_info --egg-base /tmp/pip-modern-metadata-koqnjv1j'), proceeding with generating Cython sources and expanding templates 2022-09-06T20:50:44,170 warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 2022-09-06T20:50:46,660 C compiler: 2022-09-06T20:50:46,661 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-09-06T20:50:46,661 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2022-09-06T20:50:46,662 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2022-09-06T20:50:46,662 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2022-09-06T20:50:46,662 Attempting to autodetect NEON support... Did not detect NEON support 2022-09-06T20:50:51,459 running dist_info 2022-09-06T20:50:52,083 creating /tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info 2022-09-06T20:50:52,680 writing /tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info/PKG-INFO 2022-09-06T20:50:53,246 writing dependency_links to /tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info/dependency_links.txt 2022-09-06T20:50:54,931 writing entry points to /tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info/entry_points.txt 2022-09-06T20:50:56,056 writing requirements to /tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info/requires.txt 2022-09-06T20:50:56,619 writing top-level names to /tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info/top_level.txt 2022-09-06T20:50:56,622 writing manifest file '/tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:50:57,355 reading manifest file '/tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:50:57,358 reading manifest template 'MANIFEST.in' 2022-09-06T20:50:59,140 no previously-included directories found matching '__pycache__' 2022-09-06T20:50:59,142 no previously-included directories found matching '*.pyc' 2022-09-06T20:50:59,143 adding license file 'LICENSE' 2022-09-06T20:50:59,172 writing manifest file '/tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T20:50:59,177 creating '/tmp/pip-modern-metadata-koqnjv1j/anagenex_mdtraj-1.9.8.dev0.dist-info' 2022-09-06T20:50:59,377 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-09-06T20:50:59,746 Preparing metadata (pyproject.toml): finished with status 'done' 2022-09-06T20:50:59,761 Source in /tmp/pip-wheel-b_zcvbmh/anagenex-mdtraj_8c35b4df393844818bbf16f69654c6e4 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 2022-09-06T20:50:59,764 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-5vwv1uz_' 2022-09-06T20:50:59,773 Created temporary directory: /tmp/pip-unpack-ig63otcm 2022-09-06T20:50:59,775 Building wheels for collected packages: anagenex-mdtraj 2022-09-06T20:50:59,785 Created temporary directory: /tmp/pip-wheel-6e2rv9z3 2022-09-06T20:50:59,786 Destination directory: /tmp/pip-wheel-6e2rv9z3 2022-09-06T20:50:59,793 Building wheel for anagenex-mdtraj (pyproject.toml): started 2022-09-06T20:50:59,795 Running command Building wheel for anagenex-mdtraj (pyproject.toml) 2022-09-06T20:51:02,055 Using built-in specs. 2022-09-06T20:51:02,058 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2022-09-06T20:51:02,059 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2022-09-06T20:51:02,059 Target: arm-linux-gnueabihf 2022-09-06T20:51:02,060 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --enable-libphobos-checking=release --with-target-system-zlib=auto --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 2022-09-06T20:51:02,060 Thread model: posix 2022-09-06T20:51:02,061 Supported LTO compression algorithms: zlib zstd 2022-09-06T20:51:02,061 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2022-09-06T20:51:17,393 C compiler: 2022-09-06T20:51:17,393 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-09-06T20:51:17,394 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2022-09-06T20:51:17,394 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2022-09-06T20:51:17,395 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2022-09-06T20:51:17,395 Attempting to autodetect NEON support... Did not detect NEON support 2022-09-06T20:51:21,733 running bdist_wheel 2022-09-06T20:51:21,837 running build 2022-09-06T20:51:21,837 running build_py 2022-09-06T20:51:22,442 creating build 2022-09-06T20:51:22,443 creating build/lib.linux-armv7l-cpython-39 2022-09-06T20:51:22,444 creating build/lib.linux-armv7l-cpython-39/mdtraj 2022-09-06T20:51:22,446 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2022-09-06T20:51:22,451 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2022-09-06T20:51:22,454 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2022-09-06T20:51:22,459 creating build/lib.linux-armv7l-cpython-39/mdtraj/core 2022-09-06T20:51:22,460 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2022-09-06T20:51:22,465 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2022-09-06T20:51:22,472 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2022-09-06T20:51:22,483 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2022-09-06T20:51:22,487 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2022-09-06T20:51:22,490 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2022-09-06T20:51:22,496 creating build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2022-09-06T20:51:22,498 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2022-09-06T20:51:22,502 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2022-09-06T20:51:22,506 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2022-09-06T20:51:22,511 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2022-09-06T20:51:22,515 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2022-09-06T20:51:22,520 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2022-09-06T20:51:22,525 creating build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2022-09-06T20:51:22,527 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2022-09-06T20:51:22,533 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2022-09-06T20:51:22,538 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2022-09-06T20:51:22,544 creating build/lib.linux-armv7l-cpython-39/mdtraj/testing 2022-09-06T20:51:22,546 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2022-09-06T20:51:22,552 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2022-09-06T20:51:22,557 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2022-09-06T20:51:22,561 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2022-09-06T20:51:22,567 creating build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2022-09-06T20:51:22,570 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2022-09-06T20:51:22,575 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2022-09-06T20:51:22,580 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2022-09-06T20:51:22,586 creating build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,588 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,594 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,600 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,605 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,609 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,614 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,618 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,623 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,628 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,633 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,637 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,641 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,644 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,647 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,651 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:51:22,658 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,659 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,664 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,667 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,673 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,677 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,682 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,686 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,692 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,696 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,701 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,705 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,708 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,713 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,718 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,722 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,726 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,731 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,736 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,743 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,745 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,749 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,753 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,759 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,763 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,767 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,770 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,773 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,776 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2022-09-06T20:51:22,781 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2022-09-06T20:51:22,783 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2022-09-06T20:51:22,793 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2022-09-06T20:51:22,797 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2022-09-06T20:51:22,807 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,809 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,814 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,821 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,825 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,830 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,836 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,840 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,845 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,850 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,855 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,862 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,868 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,871 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2022-09-06T20:51:22,880 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2022-09-06T20:51:22,882 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2022-09-06T20:51:22,888 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2022-09-06T20:51:22,914 running build_ext 2022-09-06T20:51:22,922 building 'mdtraj.formats.xtc' extension 2022-09-06T20:51:22,924 creating build/temp.linux-armv7l-cpython-39 2022-09-06T20:51:22,925 creating build/temp.linux-armv7l-cpython-39/mdtraj 2022-09-06T20:51:22,926 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats 2022-09-06T20:51:22,927 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc 2022-09-06T20:51:22,928 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src 2022-09-06T20:51:22,931 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:51:23,227 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:51:23,569 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2022-09-06T20:51:23,570 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:51:23,570 788 | int smallnum, smaller, larger, i, is_smaller, run; 2022-09-06T20:51:23,570 | ^~~~~~ 2022-09-06T20:51:23,571 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:51:23,571 785 | int smallidx, minidx, maxidx; 2022-09-06T20:51:23,572 | ^~~~~~ 2022-09-06T20:51:23,587 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2022-09-06T20:51:23,588 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:51:23,588 1016 | int errval=1; 2022-09-06T20:51:23,589 | ^~~~~~ 2022-09-06T20:51:23,599 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2022-09-06T20:51:23,600 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:51:23,601 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2022-09-06T20:51:23,601 | ^~~~~~ 2022-09-06T20:51:23,602 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:51:23,602 1302 | int smallidx, minidx, maxidx; 2022-09-06T20:51:23,603 | ^~~~~~ 2022-09-06T20:51:23,623 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2022-09-06T20:51:23,625 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:51:23,625 1509 | int errval=1; 2022-09-06T20:51:23,625 | ^~~~~~ 2022-09-06T20:51:28,666 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:51:28,859 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2022-09-06T20:51:28,860 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2022-09-06T20:51:28,860 66 | int i,j,result; 2022-09-06T20:51:28,861 | ^ 2022-09-06T20:51:28,861 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2022-09-06T20:51:28,862 66 | int i,j,result; 2022-09-06T20:51:28,862 | ^ 2022-09-06T20:51:28,864 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2022-09-06T20:51:28,864 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-09-06T20:51:28,865 119 | if (NULL == xd) 2022-09-06T20:51:28,865 | ^~ 2022-09-06T20:51:28,866 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’ 2022-09-06T20:51:28,866 122 | do { 2022-09-06T20:51:28,866 | ^~ 2022-09-06T20:51:29,213 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:51:30,008 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-09-06T20:51:30,008 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:51:30,008 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-09-06T20:51:30,009 from mdtraj/formats/xtc/xtc.c:775: 2022-09-06T20:51:30,009 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-09-06T20:51:30,009 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:51:30,010 | ^~~~~~~ 2022-09-06T20:51:45,747 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2022-09-06T20:51:45,748 mdtraj/formats/xtc/xtc.c:687:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:51:45,748 687 | #define PyInt_FromLong PyLong_FromLong 2022-09-06T20:51:45,748 | ^~~~~~~~~~~~~~~ 2022-09-06T20:51:45,765 mdtraj/formats/xtc/xtc.c:9554:7: note: ‘__pyx_v_status’ was declared here 2022-09-06T20:51:45,765 9554 | int __pyx_v_status; 2022-09-06T20:51:45,765 | ^~~~~~~~~~~~~~ 2022-09-06T20:52:07,425 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2022-09-06T20:52:07,438 mdtraj/formats/xtc/xtc.c:8073:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,439 8073 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2022-09-06T20:52:07,439 | ^ 2022-09-06T20:52:07,452 mdtraj/formats/xtc/xtc.c:8069:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,452 8069 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2022-09-06T20:52:07,453 | ^ 2022-09-06T20:52:07,465 mdtraj/formats/xtc/xtc.c:8065:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,466 8065 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:52:07,466 | ^ 2022-09-06T20:52:07,479 mdtraj/formats/xtc/xtc.c:8025:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,479 8025 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:52:07,479 | ^ 2022-09-06T20:52:07,492 mdtraj/formats/xtc/xtc.c:8007:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,492 8007 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:52:07,492 | ^ 2022-09-06T20:52:07,503 mdtraj/formats/xtc/xtc.c:8083:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,503 8083 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:52:07,504 | ^ 2022-09-06T20:52:07,516 mdtraj/formats/xtc/xtc.c:8045:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,517 8045 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2022-09-06T20:52:07,517 | ^ 2022-09-06T20:52:07,528 mdtraj/formats/xtc/xtc.c:8041:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,529 8041 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2022-09-06T20:52:07,529 | ^ 2022-09-06T20:52:07,540 mdtraj/formats/xtc/xtc.c:8037:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,541 8037 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:52:07,541 | ^ 2022-09-06T20:52:07,552 mdtraj/formats/xtc/xtc.c:7660:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,552 7660 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2022-09-06T20:52:07,552 | ^ 2022-09-06T20:52:07,563 mdtraj/formats/xtc/xtc.c:7656:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:07,563 7656 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2022-09-06T20:52:07,564 | ^ 2022-09-06T20:52:18,058 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/xtc.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so 2022-09-06T20:52:18,498 building 'mdtraj.formats.trr' extension 2022-09-06T20:52:18,500 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:52:18,790 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:52:19,119 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2022-09-06T20:52:19,120 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:52:19,121 788 | int smallnum, smaller, larger, i, is_smaller, run; 2022-09-06T20:52:19,121 | ^~~~~~ 2022-09-06T20:52:19,122 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:52:19,123 785 | int smallidx, minidx, maxidx; 2022-09-06T20:52:19,123 | ^~~~~~ 2022-09-06T20:52:19,140 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2022-09-06T20:52:19,142 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:52:19,142 1016 | int errval=1; 2022-09-06T20:52:19,143 | ^~~~~~ 2022-09-06T20:52:19,154 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2022-09-06T20:52:19,156 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:52:19,156 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2022-09-06T20:52:19,156 | ^~~~~~ 2022-09-06T20:52:19,157 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:52:19,158 1302 | int smallidx, minidx, maxidx; 2022-09-06T20:52:19,158 | ^~~~~~ 2022-09-06T20:52:19,178 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2022-09-06T20:52:19,180 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2022-09-06T20:52:19,180 1509 | int errval=1; 2022-09-06T20:52:19,181 | ^~~~~~ 2022-09-06T20:52:24,238 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:52:25,842 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:52:26,627 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-09-06T20:52:26,628 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:52:26,628 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-09-06T20:52:26,629 from mdtraj/formats/xtc/trr.c:775: 2022-09-06T20:52:26,629 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-09-06T20:52:26,630 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:52:26,630 | ^~~~~~~ 2022-09-06T20:52:43,055 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2022-09-06T20:52:43,056 mdtraj/formats/xtc/trr.c:687:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:52:43,056 687 | #define PyInt_FromLong PyLong_FromLong 2022-09-06T20:52:43,056 | ^~~~~~~~~~~~~~~ 2022-09-06T20:52:43,072 mdtraj/formats/xtc/trr.c:11080:7: note: ‘__pyx_v_status’ was declared here 2022-09-06T20:52:43,072 11080 | int __pyx_v_status; 2022-09-06T20:52:43,073 | ^~~~~~~~~~~~~~ 2022-09-06T20:53:05,356 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2022-09-06T20:53:05,368 mdtraj/formats/xtc/trr.c:8433:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,369 8433 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2022-09-06T20:53:05,369 | ^ 2022-09-06T20:53:05,381 mdtraj/formats/xtc/trr.c:8429:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,382 8429 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:53:05,382 | ^ 2022-09-06T20:53:05,383 mdtraj/formats/xtc/trr.c:1920:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,383 1920 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2022-09-06T20:53:05,384 | ^ 2022-09-06T20:53:05,393 mdtraj/formats/xtc/trr.c:6970:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2022-09-06T20:53:05,393 6970 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2022-09-06T20:53:05,393 | ^~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:53:05,404 mdtraj/formats/xtc/trr.c:8423:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,404 8423 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2022-09-06T20:53:05,405 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2022-09-06T20:53:05,416 mdtraj/formats/xtc/trr.c:8376:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,417 8376 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2022-09-06T20:53:05,417 | ^ 2022-09-06T20:53:05,429 mdtraj/formats/xtc/trr.c:8372:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,430 8372 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:53:05,430 | ^ 2022-09-06T20:53:05,431 mdtraj/formats/xtc/trr.c:1920:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,431 1920 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2022-09-06T20:53:05,432 | ^ 2022-09-06T20:53:05,441 mdtraj/formats/xtc/trr.c:6986:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2022-09-06T20:53:05,441 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2022-09-06T20:53:05,441 | ^~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:53:05,452 mdtraj/formats/xtc/trr.c:8366:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,452 8366 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2022-09-06T20:53:05,452 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2022-09-06T20:53:05,463 mdtraj/formats/xtc/trr.c:8766:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,463 8766 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:53:05,463 | ^ 2022-09-06T20:53:05,476 mdtraj/formats/xtc/trr.c:8762:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,476 8762 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2022-09-06T20:53:05,477 | ^ 2022-09-06T20:53:05,489 mdtraj/formats/xtc/trr.c:8607:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,489 8607 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:53:05,489 | ^ 2022-09-06T20:53:05,502 mdtraj/formats/xtc/trr.c:8603:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,502 8603 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2022-09-06T20:53:05,502 | ^ 2022-09-06T20:53:05,512 mdtraj/formats/xtc/trr.c:8659:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,513 8659 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2022-09-06T20:53:05,513 | ^ 2022-09-06T20:53:05,525 mdtraj/formats/xtc/trr.c:8655:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:05,526 8655 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2022-09-06T20:53:05,526 | ^ 2022-09-06T20:53:20,228 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/trr.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so 2022-09-06T20:53:20,670 building 'mdtraj.formats.tng' extension 2022-09-06T20:53:20,673 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng 2022-09-06T20:53:20,675 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src 2022-09-06T20:53:20,676 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression 2022-09-06T20:53:20,680 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib 2022-09-06T20:53:20,682 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwlzh.o 2022-09-06T20:53:22,399 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwt.o 2022-09-06T20:53:23,324 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/coder.o 2022-09-06T20:53:25,014 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/dict.o 2022-09-06T20:53:25,329 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/fixpoint.o 2022-09-06T20:53:25,762 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffman.o 2022-09-06T20:53:27,394 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffmem.o 2022-09-06T20:53:28,474 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/lz77.o 2022-09-06T20:53:29,204 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/merge_sort.o 2022-09-06T20:53:29,634 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/mtf.o 2022-09-06T20:53:29,837 mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: 2022-09-06T20:53:29,838 mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-09-06T20:53:29,838 196 | while (dict[ptr]!=v) 2022-09-06T20:53:29,838 | ^~ 2022-09-06T20:53:30,563 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/rle.o 2022-09-06T20:53:30,680 mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: 2022-09-06T20:53:30,681 mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-09-06T20:53:30,682 56 | if (v==vals[i]) 2022-09-06T20:53:30,682 | ^~ 2022-09-06T20:53:30,993 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/tng_compress.o 2022-09-06T20:53:36,444 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/vals16.o 2022-09-06T20:53:36,764 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/warnmalloc.o 2022-09-06T20:53:37,114 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/widemuldiv.o 2022-09-06T20:53:37,694 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc2.o 2022-09-06T20:53:41,537 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc3.o 2022-09-06T20:53:46,943 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/md5.o 2022-09-06T20:53:47,938 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/tng_io.o 2022-09-06T20:53:48,356 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: 2022-09-06T20:53:48,365 mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:53:48,366 1064 | tng_data->input_endianness_swap_func_32 = 2022-09-06T20:53:48,366 | ^ 2022-09-06T20:53:48,367 mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:53:48,368 1073 | tng_data->input_endianness_swap_func_64 = 2022-09-06T20:53:48,368 | ^ 2022-09-06T20:53:48,369 mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:53:48,369 1089 | tng_data->input_endianness_swap_func_32 = 2022-09-06T20:53:48,370 | ^ 2022-09-06T20:53:48,371 mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:53:48,371 1098 | tng_data->input_endianness_swap_func_64 = 2022-09-06T20:53:48,371 | ^ 2022-09-06T20:53:48,578 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: 2022-09-06T20:53:48,590 mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 2022-09-06T20:53:48,590 9565 | if(tng_data->output_endianness_swap_func_32 == 2022-09-06T20:53:48,590 | ^~ 2022-09-06T20:53:48,601 mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 2022-09-06T20:53:48,602 9570 | else if(tng_data->output_endianness_swap_func_32 == 2022-09-06T20:53:48,602 | ^~ 2022-09-06T20:53:48,613 mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 2022-09-06T20:53:48,613 9588 | if(tng_data->output_endianness_swap_func_64 == 2022-09-06T20:53:48,614 | ^~ 2022-09-06T20:53:48,624 mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 2022-09-06T20:53:48,625 9593 | else if(tng_data->output_endianness_swap_func_64 == 2022-09-06T20:53:48,625 | ^~ 2022-09-06T20:53:48,631 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: 2022-09-06T20:53:48,642 mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:53:48,642 9651 | tng_data->output_endianness_swap_func_32 = 2022-09-06T20:53:48,643 | ^ 2022-09-06T20:53:48,654 mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:53:48,655 9660 | tng_data->output_endianness_swap_func_64 = 2022-09-06T20:53:48,655 | ^ 2022-09-06T20:53:48,666 mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:53:48,667 9673 | tng_data->output_endianness_swap_func_32 = 2022-09-06T20:53:48,667 | ^ 2022-09-06T20:53:48,678 mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2022-09-06T20:53:48,679 9682 | tng_data->output_endianness_swap_func_64 = 2022-09-06T20:53:48,679 | ^ 2022-09-06T20:53:53,117 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: 2022-09-06T20:53:53,134 mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2022-09-06T20:53:53,135 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2022-09-06T20:53:53,135 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:53:53,152 mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 2022-09-06T20:53:53,153 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2022-09-06T20:53:53,153 | ^~~~~~~~~~~~~~~~~~ 2022-09-06T20:53:55,662 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: 2022-09-06T20:53:55,670 mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:55,670 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; 2022-09-06T20:53:55,671 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2022-09-06T20:53:55,675 mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:53:55,676 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, 2022-09-06T20:53:55,676 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:53:55,676 4309 | (int)n_frames, 2022-09-06T20:53:55,677 | ~~~~~~~~~~~~~~ 2022-09-06T20:53:55,677 4310 | f_precision, 2022-09-06T20:53:55,677 | ~~~~~~~~~~~~ 2022-09-06T20:53:55,677 4311 | 0, alt_algo, 2022-09-06T20:53:55,678 | ~~~~~~~~~~~~ 2022-09-06T20:53:55,678 4312 | &compressed_len); 2022-09-06T20:53:55,678 | ~~~~~~~~~~~~~~~~ 2022-09-06T20:53:55,685 mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 2022-09-06T20:53:55,685 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; 2022-09-06T20:53:55,685 | ^~~~~~~~~~~ 2022-09-06T20:54:21,546 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/tng.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/tng.o 2022-09-06T20:54:22,353 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-09-06T20:54:22,354 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:54:22,354 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-09-06T20:54:22,354 from mdtraj/formats/tng/tng.c:801: 2022-09-06T20:54:22,355 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-09-06T20:54:22,355 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:54:22,356 | ^~~~~~~ 2022-09-06T20:54:22,557 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’: 2022-09-06T20:54:22,563 mdtraj/formats/tng/tng.c:3713:104: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,563 3713 | __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); 2022-09-06T20:54:22,564 | ^~ 2022-09-06T20:54:22,570 mdtraj/formats/tng/tng.c:3768:88: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,570 3768 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:54:22,570 | ^~ 2022-09-06T20:54:22,576 mdtraj/formats/tng/tng.c:3800:90: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,576 3800 | __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); 2022-09-06T20:54:22,577 | ^~ 2022-09-06T20:54:22,582 mdtraj/formats/tng/tng.c:3832:95: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,583 3832 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:54:22,583 | ^~ 2022-09-06T20:54:22,590 mdtraj/formats/tng/tng.c:3902:113: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,590 3902 | __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); 2022-09-06T20:54:22,591 | ^~ 2022-09-06T20:54:22,599 mdtraj/formats/tng/tng.c:3946:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,600 3946 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:54:22,600 | ^~ 2022-09-06T20:54:22,641 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’: 2022-09-06T20:54:22,648 mdtraj/formats/tng/tng.c:4742:106: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,649 4742 | __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); 2022-09-06T20:54:22,649 | ^~ 2022-09-06T20:54:22,657 mdtraj/formats/tng/tng.c:4787:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,658 4787 | __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); 2022-09-06T20:54:22,658 | ^~ 2022-09-06T20:54:22,673 mdtraj/formats/tng/tng.c:4894:115: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,673 4894 | __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); 2022-09-06T20:54:22,673 | ^~ 2022-09-06T20:54:22,680 mdtraj/formats/tng/tng.c:4924:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,681 4924 | __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); 2022-09-06T20:54:22,681 | ^~ 2022-09-06T20:54:22,697 mdtraj/formats/tng/tng.c:5052:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,697 5052 | __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); 2022-09-06T20:54:22,698 | ^~ 2022-09-06T20:54:22,748 mdtraj/formats/tng/tng.c:5653:126: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,749 5653 | __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); 2022-09-06T20:54:22,749 | ^~ 2022-09-06T20:54:22,769 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’: 2022-09-06T20:54:22,779 mdtraj/formats/tng/tng.c:6063:152: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,779 6063 | __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); 2022-09-06T20:54:22,780 | ^~ 2022-09-06T20:54:22,825 mdtraj/formats/tng/tng.c:6331:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,825 6331 | __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); 2022-09-06T20:54:22,826 | ^~ 2022-09-06T20:54:22,844 mdtraj/formats/tng/tng.c:6433:304: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:22,844 6433 | __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); 2022-09-06T20:54:22,845 | ^~ 2022-09-06T20:54:23,031 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’: 2022-09-06T20:54:23,045 mdtraj/formats/tng/tng.c:8925:94: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:23,046 8925 | __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); 2022-09-06T20:54:23,046 | ^~ 2022-09-06T20:54:23,061 mdtraj/formats/tng/tng.c:8957:75: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:23,062 8957 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:54:23,062 | ^~ 2022-09-06T20:54:23,077 mdtraj/formats/tng/tng.c:8989:81: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:23,078 8989 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:54:23,078 | ^~ 2022-09-06T20:54:23,118 mdtraj/formats/tng/tng.c:9312:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:23,119 9312 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2022-09-06T20:54:23,119 | ^~ 2022-09-06T20:54:23,191 mdtraj/formats/tng/tng.c:9503:372: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:23,191 9503 | __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); 2022-09-06T20:54:23,191 | ^~ 2022-09-06T20:54:23,248 mdtraj/formats/tng/tng.c:9555:378: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:23,249 9555 | __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); 2022-09-06T20:54:23,249 | ^~ 2022-09-06T20:54:23,269 mdtraj/formats/tng/tng.c:9617:89: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2022-09-06T20:54:23,269 9617 | __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); 2022-09-06T20:54:23,270 | ^~ 2022-09-06T20:55:01,005 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so 2022-09-06T20:55:01,776 building 'mdtraj.formats.dcd' extension 2022-09-06T20:55:01,778 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd 2022-09-06T20:55:01,780 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src 2022-09-06T20:55:01,783 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:55:02,569 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-09-06T20:55:02,570 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:55:02,570 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-09-06T20:55:02,570 from mdtraj/formats/dcd/dcd.c:773: 2022-09-06T20:55:02,571 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-09-06T20:55:02,571 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:55:02,571 | ^~~~~~~ 2022-09-06T20:55:19,960 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2022-09-06T20:55:19,961 mdtraj/formats/dcd/dcd.c:685:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:55:19,961 685 | #define PyInt_FromLong PyLong_FromLong 2022-09-06T20:55:19,961 | ^~~~~~~~~~~~~~~ 2022-09-06T20:55:19,968 mdtraj/formats/dcd/dcd.c:5452:7: note: ‘__pyx_v_i’ was declared here 2022-09-06T20:55:19,968 5452 | int __pyx_v_i; 2022-09-06T20:55:19,969 | ^~~~~~~~~ 2022-09-06T20:55:27,161 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:55:30,404 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so 2022-09-06T20:55:30,750 building 'mdtraj.formats.binpos' extension 2022-09-06T20:55:30,752 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos 2022-09-06T20:55:30,754 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src 2022-09-06T20:55:30,757 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:55:31,553 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-09-06T20:55:31,554 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:55:31,554 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-09-06T20:55:31,555 from mdtraj/formats/binpos/binpos.c:773: 2022-09-06T20:55:31,555 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-09-06T20:55:31,555 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:55:31,556 | ^~~~~~~ 2022-09-06T20:55:50,520 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2022-09-06T20:55:50,528 mdtraj/formats/binpos/binpos.c:5527:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:55:50,528 5527 | if (__pyx_t_2) { 2022-09-06T20:55:50,528 | ^ 2022-09-06T20:55:50,535 mdtraj/formats/binpos/binpos.c:5007:7: note: ‘__pyx_v_status’ was declared here 2022-09-06T20:55:50,535 5007 | int __pyx_v_status; 2022-09-06T20:55:50,536 | ^~~~~~~~~~~~~~ 2022-09-06T20:55:50,536 mdtraj/formats/binpos/binpos.c:685:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:55:50,536 685 | #define PyInt_FromLong PyLong_FromLong 2022-09-06T20:55:50,537 | ^~~~~~~~~~~~~~~ 2022-09-06T20:55:50,543 mdtraj/formats/binpos/binpos.c:5004:7: note: ‘__pyx_v_i’ was declared here 2022-09-06T20:55:50,543 5004 | int __pyx_v_i; 2022-09-06T20:55:50,544 | ^~~~~~~~~ 2022-09-06T20:55:53,894 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:55:54,676 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/binpos.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so 2022-09-06T20:55:54,999 building 'mdtraj.formats.dtr' extension 2022-09-06T20:55:55,002 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr 2022-09-06T20:55:55,003 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src 2022-09-06T20:55:55,006 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:55:55,632 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-09-06T20:55:55,633 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:55:55,633 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-09-06T20:55:55,633 from mdtraj/formats/dtr/dtr.cpp:794: 2022-09-06T20:55:55,634 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-09-06T20:55:55,634 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:55:55,634 | ^~~~~~~ 2022-09-06T20:56:24,464 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:56:28,515 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2022-09-06T20:56:28,515 mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2022-09-06T20:56:28,516 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2022-09-06T20:56:28,516 | ~~^ ~ 2022-09-06T20:56:28,516 | | | 2022-09-06T20:56:28,517 | | size_t {aka unsigned int} 2022-09-06T20:56:28,517 | long int 2022-09-06T20:56:28,517 | %d 2022-09-06T20:56:28,518 mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:56:28,518 487 | printf("size %d framesize %d\n\n", 2022-09-06T20:56:28,519 | ~^ 2022-09-06T20:56:28,519 | | 2022-09-06T20:56:28,519 | int 2022-09-06T20:56:28,520 | %lld 2022-09-06T20:56:28,520 488 | keys[i].size(), m_framesize); 2022-09-06T20:56:28,520 | ~~~~~~~~~~~~~~ 2022-09-06T20:56:28,521 | | 2022-09-06T20:56:28,521 | uint64_t {aka long long unsigned int} 2022-09-06T20:56:28,521 mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:56:28,522 487 | printf("size %d framesize %d\n\n", 2022-09-06T20:56:28,522 | ~^ 2022-09-06T20:56:28,522 | | 2022-09-06T20:56:28,523 | int 2022-09-06T20:56:28,523 | %lld 2022-09-06T20:56:28,523 488 | keys[i].size(), m_framesize); 2022-09-06T20:56:28,524 | ~~~~~~~~~~~ 2022-09-06T20:56:28,524 | | 2022-09-06T20:56:28,525 | uint64_t {aka long long unsigned int} 2022-09-06T20:56:28,525 mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2022-09-06T20:56:28,525 494 | "non-constant time interval at frame %ld\n", i); 2022-09-06T20:56:28,526 | ~~^ ~ 2022-09-06T20:56:28,526 | | | 2022-09-06T20:56:28,526 | | size_t {aka unsigned int} 2022-09-06T20:56:28,527 | long int 2022-09-06T20:56:28,527 | %d 2022-09-06T20:56:28,527 mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2022-09-06T20:56:28,528 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2022-09-06T20:56:28,528 | ~~^ ~ 2022-09-06T20:56:28,529 | | | 2022-09-06T20:56:28,529 | | size_t {aka unsigned int} 2022-09-06T20:56:28,529 | long int 2022-09-06T20:56:28,529 | %d 2022-09-06T20:56:28,816 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2022-09-06T20:56:28,816 mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:56:28,817 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2022-09-06T20:56:28,817 | ~~^ 2022-09-06T20:56:28,817 | | 2022-09-06T20:56:28,818 | long int 2022-09-06T20:56:28,818 | %lld 2022-09-06T20:56:28,818 1302 | 3*natoms, pos.count); 2022-09-06T20:56:28,819 | ~~~~~~~~~ 2022-09-06T20:56:28,819 | | 2022-09-06T20:56:28,819 | uint64_t {aka long long unsigned int} 2022-09-06T20:56:28,820 mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:56:28,820 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2022-09-06T20:56:28,821 | ~~^ 2022-09-06T20:56:28,821 | | 2022-09-06T20:56:28,821 | long int 2022-09-06T20:56:28,822 | %lld 2022-09-06T20:56:28,822 1311 | 3*natoms, vel.count); 2022-09-06T20:56:28,822 | ~~~~~~~~~ 2022-09-06T20:56:28,822 | | 2022-09-06T20:56:28,823 | uint64_t {aka long long unsigned int} 2022-09-06T20:56:28,877 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2022-09-06T20:56:28,878 mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2022-09-06T20:56:28,878 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2022-09-06T20:56:28,879 | ~~^ 2022-09-06T20:56:28,879 | | 2022-09-06T20:56:28,879 | long int 2022-09-06T20:56:28,880 | %lld 2022-09-06T20:56:28,880 1573 | velblob.count, 3*natoms); 2022-09-06T20:56:28,880 | ~~~~~~~~~~~~~ 2022-09-06T20:56:28,881 | | 2022-09-06T20:56:28,881 | uint64_t {aka long long unsigned int} 2022-09-06T20:56:31,257 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: 2022-09-06T20:56:31,257 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 2022-09-06T20:56:31,258 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2022-09-06T20:56:31,258 | ~~~~~~~~^~~~~ 2022-09-06T20:56:36,480 In file included from /usr/include/c++/10/map:60, 2022-09-06T20:56:36,480 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2022-09-06T20:56:36,481 /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2022-09-06T20:56:36,481 /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2022-09-06T20:56:36,481 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2022-09-06T20:56:36,482 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:36,629 /usr/include/c++/10/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2022-09-06T20:56:36,629 /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2022-09-06T20:56:36,630 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2022-09-06T20:56:36,630 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:36,631 /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2022-09-06T20:56:36,762 In file included from /usr/include/c++/10/map:61, 2022-09-06T20:56:36,762 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2022-09-06T20:56:36,762 /usr/include/c++/10/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2022-09-06T20:56:36,763 /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2022-09-06T20:56:36,763 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-09-06T20:56:36,763 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:36,764 521 | std::forward_as_tuple(std::move(__k)), 2022-09-06T20:56:36,764 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:36,764 522 | std::tuple<>()); 2022-09-06T20:56:36,765 | ~~~~~~~~~~~~~~~ 2022-09-06T20:56:38,611 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: 2022-09-06T20:56:38,612 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2022-09-06T20:56:38,612 706 | sprintf(sub, "%03x/", i); 2022-09-06T20:56:38,613 | ^~~~ 2022-09-06T20:56:38,613 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 2022-09-06T20:56:38,613 706 | sprintf(sub, "%03x/", i); 2022-09-06T20:56:38,614 | ^~~~~~~ 2022-09-06T20:56:38,614 mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2022-09-06T20:56:38,615 706 | sprintf(sub, "%03x/", i); 2022-09-06T20:56:38,615 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2022-09-06T20:56:38,615 mdtraj/formats/dtr/src/dtrplugin.cxx:714:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2022-09-06T20:56:38,616 714 | sprintf(subsub, "%03x", j); 2022-09-06T20:56:38,616 | ^~~~ 2022-09-06T20:56:38,616 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 2022-09-06T20:56:38,617 714 | sprintf(subsub, "%03x", j); 2022-09-06T20:56:38,617 | ^~~~~~ 2022-09-06T20:56:38,617 mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2022-09-06T20:56:38,618 714 | sprintf(subsub, "%03x", j); 2022-09-06T20:56:38,618 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:39,567 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: 2022-09-06T20:56:39,568 mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2022-09-06T20:56:39,568 667 | sprintf(answer, "%03x/", d1); 2022-09-06T20:56:39,569 | ^ 2022-09-06T20:56:39,569 mdtraj/formats/dtr/src/dtrplugin.cxx:667:13: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2022-09-06T20:56:39,569 667 | sprintf(answer, "%03x/", d1); 2022-09-06T20:56:39,570 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:39,570 mdtraj/formats/dtr/src/dtrplugin.cxx:665:28: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 2022-09-06T20:56:39,570 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2022-09-06T20:56:39,571 | ^~~~ 2022-09-06T20:56:39,571 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2022-09-06T20:56:39,571 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2022-09-06T20:56:39,572 | ^~~~~~~~~~~~ 2022-09-06T20:56:39,572 mdtraj/formats/dtr/src/dtrplugin.cxx:665:13: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2022-09-06T20:56:39,572 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2022-09-06T20:56:39,573 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:45,921 In file included from /usr/include/c++/10/map:61, 2022-09-06T20:56:45,922 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2022-09-06T20:56:45,922 /usr/include/c++/10/bits/stl_map.h: In member function ‘int desres::molfile::DtrReader::frame_from_bytes(const void*, uint64_t, molfile_timestep_t*) const’: 2022-09-06T20:56:45,922 /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2022-09-06T20:56:45,923 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-09-06T20:56:45,923 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:45,923 521 | std::forward_as_tuple(std::move(__k)), 2022-09-06T20:56:45,924 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:56:45,924 522 | std::tuple<>()); 2022-09-06T20:56:45,925 | ~~~~~~~~~~~~~~~ 2022-09-06T20:56:57,911 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so 2022-09-06T20:56:58,806 building 'mdtraj._rmsd' extension 2022-09-06T20:56:58,808 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd 2022-09-06T20:56:58,810 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src 2022-09-06T20:56:58,813 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:58:18,780 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:58:19,294 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:58:19,907 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:58:21,539 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so 2022-09-06T20:58:22,388 building 'mdtraj._lprmsd' extension 2022-09-06T20:58:22,391 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:58:23,048 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-09-06T20:58:23,049 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:58:23,049 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-09-06T20:58:23,049 from mdtraj/rmsd/_lprmsd.cpp:805: 2022-09-06T20:58:23,050 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-09-06T20:58:23,050 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:58:23,050 | ^~~~~~~ 2022-09-06T20:58:48,024 mdtraj/rmsd/_lprmsd.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: 2022-09-06T20:58:48,025 mdtraj/rmsd/_lprmsd.cpp:4113:14: warning: ‘__pyx_pybuffernd_ref_xyz_frame_dis.__Pyx_LocalBuf_ND::diminfo[0].__Pyx_Buf_DimInfo::shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:58:48,025 4113 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; 2022-09-06T20:58:48,025 | ^~ 2022-09-06T20:59:11,619 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:59:17,370 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:59:17,864 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:59:20,367 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:59:21,094 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:59:21,710 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:59:23,356 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so 2022-09-06T20:59:24,133 building 'mdtraj.core.lib.libtheobald' extension 2022-09-06T20:59:24,134 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2022-09-06T20:59:25,752 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2022-09-06T20:59:26,246 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o 2022-09-06T20:59:26,323 building 'mdtraj.geometry._geometry' extension 2022-09-06T20:59:26,324 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry 2022-09-06T20:59:26,325 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src 2022-09-06T20:59:26,328 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T20:59:26,998 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-09-06T20:59:26,998 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-09-06T20:59:26,998 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-09-06T20:59:26,999 from mdtraj/geometry/src/_geometry.cpp:807: 2022-09-06T20:59:26,999 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-09-06T20:59:26,999 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-09-06T20:59:27,000 | ^~~~~~~ 2022-09-06T20:59:39,449 mdtraj/geometry/src/_geometry.cpp: In function ‘void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’: 2022-09-06T20:59:39,450 mdtraj/geometry/src/_geometry.cpp:6104:224: warning: ‘__pyx_v_delta[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:59:39,450 6104 | (__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)) )))))); 2022-09-06T20:59:39,451 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:59:39,451 mdtraj/geometry/src/_geometry.cpp:6118:277: warning: ‘__pyx_v_delta[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T20:59:39,452 6118 | (__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)) ))))))); 2022-09-06T20:59:39,452 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2022-09-06T20:59:39,453 mdtraj/geometry/src/_geometry.cpp:6118:277: warning: ‘__pyx_v_offset[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T21:00:34,656 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:01:12,419 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:01:20,804 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:01:23,212 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/sasa.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so 2022-09-06T21:01:24,245 building 'mdtraj.geometry.drid' extension 2022-09-06T21:01:24,247 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:02:21,664 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:02:23,104 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:02:23,386 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/moments.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so 2022-09-06T21:02:24,179 building 'mdtraj.geometry.neighbors' extension 2022-09-06T21:02:24,182 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:03:17,804 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:03:20,582 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighbors.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so 2022-09-06T21:03:21,333 building 'mdtraj.geometry.neighborlist' extension 2022-09-06T21:03:21,336 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:04:09,176 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2022-09-06T21:04:19,322 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2022-09-06T21:04:19,323 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors[0][0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T21:04:19,323 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2022-09-06T21:04:19,324 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2022-09-06T21:04:19,324 mdtraj/geometry/src/neighborlist.cpp:51:53: warning: ‘periodicBoxVectors[1][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T21:04:19,325 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; 2022-09-06T21:04:19,325 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2022-09-06T21:04:19,326 mdtraj/geometry/src/neighborlist.cpp:52:53: warning: ‘periodicBoxVectors[2][2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T21:04:19,326 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; 2022-09-06T21:04:19,326 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2022-09-06T21:04:19,327 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors[0][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-09-06T21:04:19,327 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2022-09-06T21:04:19,327 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2022-09-06T21:04:21,695 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighborlist.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so 2022-09-06T21:04:23,774 installing to build/bdist.linux-armv7l/wheel 2022-09-06T21:04:23,775 running install 2022-09-06T21:04:23,837 running install_lib 2022-09-06T21:04:24,445 creating build/bdist.linux-armv7l 2022-09-06T21:04:24,446 creating build/bdist.linux-armv7l/wheel 2022-09-06T21:04:24,450 creating build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T21:04:24,454 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T21:04:24,457 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T21:04:24,462 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T21:04:24,470 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T21:04:24,479 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T21:04:24,486 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2022-09-06T21:04:24,488 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2022-09-06T21:04:24,493 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2022-09-06T21:04:24,501 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2022-09-06T21:04:24,506 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T21:04:24,509 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2022-09-06T21:04:24,516 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T21:04:24,518 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T21:04:24,523 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T21:04:24,528 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T21:04:24,533 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T21:04:24,537 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T21:04:24,542 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2022-09-06T21:04:24,545 copying build/lib.linux-armv7l-cpython-39/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T21:04:24,550 copying build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T21:04:24,649 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2022-09-06T21:04:24,652 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2022-09-06T21:04:24,657 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2022-09-06T21:04:24,662 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2022-09-06T21:04:24,666 copying build/lib.linux-armv7l-cpython-39/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T21:04:24,671 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T21:04:24,673 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T21:04:24,679 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T21:04:24,684 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T21:04:24,689 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2022-09-06T21:04:24,694 copying build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T21:04:24,760 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2022-09-06T21:04:24,762 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2022-09-06T21:04:24,768 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2022-09-06T21:04:24,773 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2022-09-06T21:04:24,778 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,780 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,786 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,792 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,798 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,803 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,807 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,812 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,817 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,978 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,983 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,988 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,992 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,996 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:24,999 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:25,073 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:25,149 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:25,152 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:25,238 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:25,243 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2022-09-06T21:04:25,248 copying build/lib.linux-armv7l-cpython-39/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2022-09-06T21:04:25,254 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,256 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,261 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,266 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,272 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,278 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,284 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,288 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,295 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,336 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,409 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,562 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,568 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,645 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2022-09-06T21:04:25,646 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2022-09-06T21:04:25,653 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2022-09-06T21:04:25,654 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2022-09-06T21:04:25,660 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2022-09-06T21:04:25,664 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2022-09-06T21:04:25,668 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2022-09-06T21:04:25,674 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,679 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,683 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,798 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,802 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,808 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,812 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,816 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,819 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,825 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,861 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,865 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2022-09-06T21:04:25,870 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,872 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,876 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,881 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,882 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,886 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,892 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,896 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,900 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,905 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,908 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,912 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,917 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,921 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,926 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,930 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,933 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2022-09-06T21:04:25,938 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/six.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,943 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,947 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,951 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,955 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,958 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,961 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2022-09-06T21:04:25,964 running install_egg_info 2022-09-06T21:04:27,216 running egg_info 2022-09-06T21:04:27,819 writing anagenex_mdtraj.egg-info/PKG-INFO 2022-09-06T21:04:28,385 writing dependency_links to anagenex_mdtraj.egg-info/dependency_links.txt 2022-09-06T21:04:30,081 writing entry points to anagenex_mdtraj.egg-info/entry_points.txt 2022-09-06T21:04:31,217 writing requirements to anagenex_mdtraj.egg-info/requires.txt 2022-09-06T21:04:31,792 writing top-level names to anagenex_mdtraj.egg-info/top_level.txt 2022-09-06T21:04:31,903 reading manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T21:04:31,957 reading manifest template 'MANIFEST.in' 2022-09-06T21:04:33,858 no previously-included directories found matching '__pycache__' 2022-09-06T21:04:33,861 no previously-included directories found matching '*.pyc' 2022-09-06T21:04:33,862 adding license file 'LICENSE' 2022-09-06T21:04:33,899 writing manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2022-09-06T21:04:33,904 Copying anagenex_mdtraj.egg-info to build/bdist.linux-armv7l/wheel/anagenex_mdtraj-1.9.8.dev0-py3.9.egg-info 2022-09-06T21:04:33,933 running install_scripts 2022-09-06T21:04:34,070 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-09-06T21:04:34,131 creating build/bdist.linux-armv7l/wheel/anagenex_mdtraj-1.9.8.dev0.dist-info/WHEEL 2022-09-06T21:04:34,137 creating '/tmp/pip-wheel-6e2rv9z3/tmptox_9gol/anagenex_mdtraj-1.9.8.dev0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-09-06T21:04:34,145 adding 'mdtraj/__init__.py' 2022-09-06T21:04:34,744 adding 'mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:35,669 adding 'mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:35,712 adding 'mdtraj/io.py' 2022-09-06T21:04:35,715 adding 'mdtraj/version.py' 2022-09-06T21:04:35,719 adding 'mdtraj/core/__init__.py' 2022-09-06T21:04:35,725 adding 'mdtraj/core/element.py' 2022-09-06T21:04:35,733 adding 'mdtraj/core/residue_names.py' 2022-09-06T21:04:35,738 adding 'mdtraj/core/selection.py' 2022-09-06T21:04:35,757 adding 'mdtraj/core/topology.py' 2022-09-06T21:04:35,780 adding 'mdtraj/core/trajectory.py' 2022-09-06T21:04:35,786 adding 'mdtraj/core/lib/center.h' 2022-09-06T21:04:35,809 adding 'mdtraj/core/lib/libtheobald.a' 2022-09-06T21:04:35,813 adding 'mdtraj/core/lib/theobald_rmsd.h' 2022-09-06T21:04:35,819 adding 'mdtraj/formats/__init__.py' 2022-09-06T21:04:35,827 adding 'mdtraj/formats/amberrst.py' 2022-09-06T21:04:35,833 adding 'mdtraj/formats/arc.py' 2022-09-06T21:04:36,174 adding 'mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:36,575 adding 'mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:37,623 adding 'mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:37,677 adding 'mdtraj/formats/gro.py' 2022-09-06T21:04:37,682 adding 'mdtraj/formats/gsd.py' 2022-09-06T21:04:37,693 adding 'mdtraj/formats/hdf5.py' 2022-09-06T21:04:37,698 adding 'mdtraj/formats/hoomdxml.py' 2022-09-06T21:04:37,705 adding 'mdtraj/formats/lammpstrj.py' 2022-09-06T21:04:37,712 adding 'mdtraj/formats/lh5.py' 2022-09-06T21:04:37,718 adding 'mdtraj/formats/mdcrd.py' 2022-09-06T21:04:37,723 adding 'mdtraj/formats/mol2.py' 2022-09-06T21:04:37,731 adding 'mdtraj/formats/netcdf.py' 2022-09-06T21:04:37,735 adding 'mdtraj/formats/openmmxml.py' 2022-09-06T21:04:37,740 adding 'mdtraj/formats/pdbx.py' 2022-09-06T21:04:37,745 adding 'mdtraj/formats/prmtop.py' 2022-09-06T21:04:37,749 adding 'mdtraj/formats/psf.py' 2022-09-06T21:04:37,753 adding 'mdtraj/formats/registry.py' 2022-09-06T21:04:38,769 adding 'mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:39,476 adding 'mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:40,143 adding 'mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:40,174 adding 'mdtraj/formats/xyzfile.py' 2022-09-06T21:04:40,178 adding 'mdtraj/formats/pdb/__init__.py' 2022-09-06T21:04:40,187 adding 'mdtraj/formats/pdb/pdbfile.py' 2022-09-06T21:04:40,198 adding 'mdtraj/formats/pdb/pdbstructure.py' 2022-09-06T21:04:40,203 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2022-09-06T21:04:40,208 adding 'mdtraj/formats/pdb/data/residues.xml' 2022-09-06T21:04:40,212 adding 'mdtraj/geometry/__init__.py' 2022-09-06T21:04:41,509 adding 'mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:41,583 adding 'mdtraj/geometry/alignment.py' 2022-09-06T21:04:41,587 adding 'mdtraj/geometry/angle.py' 2022-09-06T21:04:41,591 adding 'mdtraj/geometry/contact.py' 2022-09-06T21:04:41,596 adding 'mdtraj/geometry/dihedral.py' 2022-09-06T21:04:41,602 adding 'mdtraj/geometry/distance.py' 2022-09-06T21:04:42,301 adding 'mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:42,331 adding 'mdtraj/geometry/dssp.py' 2022-09-06T21:04:42,337 adding 'mdtraj/geometry/hbond.py' 2022-09-06T21:04:42,343 adding 'mdtraj/geometry/internal.py' 2022-09-06T21:04:43,083 adding 'mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:43,792 adding 'mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so' 2022-09-06T21:04:43,823 adding 'mdtraj/geometry/order.py' 2022-09-06T21:04:43,827 adding 'mdtraj/geometry/rdf.py' 2022-09-06T21:04:43,830 adding 'mdtraj/geometry/rg.py' 2022-09-06T21:04:43,834 adding 'mdtraj/geometry/sasa.py' 2022-09-06T21:04:43,837 adding 'mdtraj/geometry/shape.py' 2022-09-06T21:04:43,841 adding 'mdtraj/geometry/thermodynamic_properties.py' 2022-09-06T21:04:43,844 adding 'mdtraj/nmr/__init__.py' 2022-09-06T21:04:43,847 adding 'mdtraj/nmr/scalar_couplings.py' 2022-09-06T21:04:43,852 adding 'mdtraj/nmr/shift_wrappers.py' 2022-09-06T21:04:43,855 adding 'mdtraj/reporters/__init__.py' 2022-09-06T21:04:43,859 adding 'mdtraj/reporters/basereporter.py' 2022-09-06T21:04:43,862 adding 'mdtraj/reporters/dcdreporter.py' 2022-09-06T21:04:43,866 adding 'mdtraj/reporters/hdf5reporter.py' 2022-09-06T21:04:43,868 adding 'mdtraj/reporters/netcdfreporter.py' 2022-09-06T21:04:43,872 adding 'mdtraj/reporters/xtcreporter.py' 2022-09-06T21:04:43,875 adding 'mdtraj/scripts/__init__.py' 2022-09-06T21:04:43,881 adding 'mdtraj/scripts/mdconvert.py' 2022-09-06T21:04:43,885 adding 'mdtraj/scripts/mdinspect.py' 2022-09-06T21:04:43,889 adding 'mdtraj/testing/__init__.py' 2022-09-06T21:04:43,895 adding 'mdtraj/testing/docscrape.py' 2022-09-06T21:04:43,899 adding 'mdtraj/testing/docstrings.py' 2022-09-06T21:04:43,902 adding 'mdtraj/testing/testing.py' 2022-09-06T21:04:43,907 adding 'mdtraj/utils/__init__.py' 2022-09-06T21:04:43,909 adding 'mdtraj/utils/contextmanagers.py' 2022-09-06T21:04:43,913 adding 'mdtraj/utils/delay_import.py' 2022-09-06T21:04:43,916 adding 'mdtraj/utils/rotation.py' 2022-09-06T21:04:43,919 adding 'mdtraj/utils/singleton.py' 2022-09-06T21:04:43,924 adding 'mdtraj/utils/six.py' 2022-09-06T21:04:43,928 adding 'mdtraj/utils/unitcell.py' 2022-09-06T21:04:43,932 adding 'mdtraj/utils/validation.py' 2022-09-06T21:04:43,934 adding 'mdtraj/utils/zipped.py' 2022-09-06T21:04:43,939 adding 'mdtraj/utils/unit/__init__.py' 2022-09-06T21:04:43,942 adding 'mdtraj/utils/unit/basedimension.py' 2022-09-06T21:04:43,946 adding 'mdtraj/utils/unit/baseunit.py' 2022-09-06T21:04:43,948 adding 'mdtraj/utils/unit/constants.py' 2022-09-06T21:04:43,955 adding 'mdtraj/utils/unit/doctests.py' 2022-09-06T21:04:43,960 adding 'mdtraj/utils/unit/mymatrix.py' 2022-09-06T21:04:43,963 adding 'mdtraj/utils/unit/prefix.py' 2022-09-06T21:04:43,972 adding 'mdtraj/utils/unit/quantity.py' 2022-09-06T21:04:43,975 adding 'mdtraj/utils/unit/standard_dimensions.py' 2022-09-06T21:04:43,983 adding 'mdtraj/utils/unit/unit.py' 2022-09-06T21:04:43,988 adding 'mdtraj/utils/unit/unit_definitions.py' 2022-09-06T21:04:43,991 adding 'mdtraj/utils/unit/unit_math.py' 2022-09-06T21:04:43,994 adding 'mdtraj/utils/unit/unit_operators.py' 2022-09-06T21:04:44,004 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/LICENSE' 2022-09-06T21:04:44,007 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/METADATA' 2022-09-06T21:04:44,009 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/WHEEL' 2022-09-06T21:04:44,010 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/entry_points.txt' 2022-09-06T21:04:44,012 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/top_level.txt' 2022-09-06T21:04:44,016 adding 'anagenex_mdtraj-1.9.8.dev0.dist-info/RECORD' 2022-09-06T21:04:44,236 removing build/bdist.linux-armv7l/wheel 2022-09-06T21:04:44,721 Building wheel for anagenex-mdtraj (pyproject.toml): finished with status 'done' 2022-09-06T21:04:45,092 Created wheel for anagenex-mdtraj: filename=anagenex_mdtraj-1.9.8.dev0-cp39-cp39-linux_armv7l.whl size=7088155 sha256=00c759fc5a471a013bb75798993f0b783fa4e860d20b3297f588e8252daaf42d 2022-09-06T21:04:45,095 Stored in directory: /tmp/pip-ephem-wheel-cache-nt_8uid6/wheels/e1/e0/7c/57b0793d525ac97b864fbff60532430870353705132209c375 2022-09-06T21:04:45,136 Successfully built anagenex-mdtraj 2022-09-06T21:04:45,560 Removed build tracker: '/tmp/pip-build-tracker-5vwv1uz_'