2025-09-08T03:18:46,522 Created temporary directory: /tmp/pip-build-tracker-kgsj99pc 2025-09-08T03:18:46,522 Initialized build tracking at /tmp/pip-build-tracker-kgsj99pc 2025-09-08T03:18:46,522 Created build tracker: /tmp/pip-build-tracker-kgsj99pc 2025-09-08T03:18:46,522 Entered build tracker: /tmp/pip-build-tracker-kgsj99pc 2025-09-08T03:18:46,523 Created temporary directory: /tmp/pip-wheel-_q72ncib 2025-09-08T03:18:46,526 Created temporary directory: /tmp/pip-ephem-wheel-cache-fykw6rsv 2025-09-08T03:18:46,578 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T03:18:46,581 2 location(s) to search for versions of mdtraj: 2025-09-08T03:18:46,581 * https://pypi.org/simple/mdtraj/ 2025-09-08T03:18:46,581 * https://www.piwheels.org/simple/mdtraj/ 2025-09-08T03:18:46,581 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2025-09-08T03:18:46,581 Getting page https://pypi.org/simple/mdtraj/ 2025-09-08T03:18:46,582 Found index url 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https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp37-cp37m-linux_armv7l.whl#sha256=cb090c5366b7b76d938daa16ca5a431a4fe751344ec320479b3ba8134a6ff4bd (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,900 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv6l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,900 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv7l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,900 Skipping link: No binaries permitted for mdtraj: 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https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,901 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv6l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,901 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,901 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv6l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,901 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv7l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,902 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv6l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,902 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,902 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv6l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,902 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,902 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,902 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv7l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,903 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv6l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,903 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T03:18:46,903 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2025-09-08T03:18:46,903 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2025-09-08T03:18:46,934 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates 2025-09-08T03:18:46,935 Collecting mdtraj==1.5.0 2025-09-08T03:18:46,937 Created temporary directory: /tmp/pip-unpack-o6iij8hr 2025-09-08T03:18:47,081 Downloading mdtraj-1.5.0.zip (17.9 MB) 2025-09-08T03:18:50,234 Added mdtraj==1.5.0 from https://files.pythonhosted.org/packages/b2/2c/1cfc1f7879ea82293afca1edd595f3ca39e25f8411627175e88ea6819f83/mdtraj-1.5.0.zip to build tracker '/tmp/pip-build-tracker-kgsj99pc' 2025-09-08T03:18:50,235 Running setup.py (path:/tmp/pip-wheel-_q72ncib/mdtraj_b659b9e806c94c309ca161d583921af8/setup.py) egg_info for package mdtraj 2025-09-08T03:18:50,236 Created temporary directory: /tmp/pip-pip-egg-info-7p71n6_9 2025-09-08T03:18:50,236 Preparing metadata (setup.py): started 2025-09-08T03:18:50,237 Running command python setup.py egg_info 2025-09-08T03:18:50,949 Using built-in specs. 2025-09-08T03:18:50,950 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T03:18:50,950 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T03:18:50,950 Target: arm-linux-gnueabihf 2025-09-08T03:18:50,950 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --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-libstdcxx-backtrace --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+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T03:18:50,950 Thread model: posix 2025-09-08T03:18:50,950 Supported LTO compression algorithms: zlib zstd 2025-09-08T03:18:50,950 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T03:18:53,621 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T03:18:53,622 !! 2025-09-08T03:18:53,622 ******************************************************************************** 2025-09-08T03:18:53,622 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T03:18:53,622 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T03:18:53,622 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T03:18:53,622 or your builds will no longer be supported. 2025-09-08T03:18:53,622 ******************************************************************************** 2025-09-08T03:18:53,623 !! 2025-09-08T03:18:53,623 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T03:18:54,003 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T03:18:54,003 !! 2025-09-08T03:18:54,004 ******************************************************************************** 2025-09-08T03:18:54,004 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T03:18:54,004 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T03:18:54,004 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T03:18:54,004 ******************************************************************************** 2025-09-08T03:18:54,004 !! 2025-09-08T03:18:54,004 self._finalize_license_expression() 2025-09-08T03:18:54,078 C compiler: 2025-09-08T03:18:54,079 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T03:18:54,079 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T03:18:54,079 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T03:18:54,079 running egg_info 2025-09-08T03:18:54,152 creating /tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info 2025-09-08T03:18:54,152 writing /tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info/PKG-INFO 2025-09-08T03:18:54,154 writing dependency_links to /tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info/dependency_links.txt 2025-09-08T03:18:54,154 writing entry points to /tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info/entry_points.txt 2025-09-08T03:18:54,155 writing requirements to /tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info/requires.txt 2025-09-08T03:18:54,155 writing top-level names to /tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info/top_level.txt 2025-09-08T03:18:54,155 writing manifest file '/tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info/SOURCES.txt' 2025-09-08T03:18:54,366 /tmp/pip-wheel-_q72ncib/mdtraj_b659b9e806c94c309ca161d583921af8/basesetup.py:254: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-08T03:18:54,366 import pkg_resources 2025-09-08T03:18:55,038 reading manifest file '/tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info/SOURCES.txt' 2025-09-08T03:18:55,038 reading manifest template 'MANIFEST.in' 2025-09-08T03:18:55,067 writing manifest file '/tmp/pip-pip-egg-info-7p71n6_9/mdtraj.egg-info/SOURCES.txt' 2025-09-08T03:18:55,214 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T03:18:55,218 Source in /tmp/pip-wheel-_q72ncib/mdtraj_b659b9e806c94c309ca161d583921af8 has version 1.5.0, which satisfies requirement mdtraj==1.5.0 from https://files.pythonhosted.org/packages/b2/2c/1cfc1f7879ea82293afca1edd595f3ca39e25f8411627175e88ea6819f83/mdtraj-1.5.0.zip 2025-09-08T03:18:55,219 Removed mdtraj==1.5.0 from https://files.pythonhosted.org/packages/b2/2c/1cfc1f7879ea82293afca1edd595f3ca39e25f8411627175e88ea6819f83/mdtraj-1.5.0.zip from build tracker '/tmp/pip-build-tracker-kgsj99pc' 2025-09-08T03:18:55,223 Created temporary directory: /tmp/pip-unpack-fnfgwu1a 2025-09-08T03:18:55,223 Created temporary directory: /tmp/pip-unpack-zcjcax5_ 2025-09-08T03:18:55,223 Building wheels for collected packages: mdtraj 2025-09-08T03:18:55,225 Created temporary directory: /tmp/pip-wheel-ob5ih7da 2025-09-08T03:18:55,225 DEPRECATION: Building 'mdtraj' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'mdtraj'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T03:18:55,226 Building wheel for mdtraj (setup.py): started 2025-09-08T03:18:55,227 Destination directory: /tmp/pip-wheel-ob5ih7da 2025-09-08T03:18:55,227 Running command python setup.py bdist_wheel 2025-09-08T03:18:55,929 C compiler: 2025-09-08T03:18:55,933 Using built-in specs. 2025-09-08T03:18:55,934 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T03:18:55,934 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T03:18:55,934 Target: arm-linux-gnueabihf 2025-09-08T03:18:55,934 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --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-libstdcxx-backtrace --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+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T03:18:55,934 Thread model: posix 2025-09-08T03:18:55,934 Supported LTO compression algorithms: zlib zstd 2025-09-08T03:18:55,934 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T03:18:57,242 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T03:18:57,857 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T03:18:58,496 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T03:18:58,613 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T03:18:58,613 !! 2025-09-08T03:18:58,613 ******************************************************************************** 2025-09-08T03:18:58,613 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T03:18:58,613 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T03:18:58,614 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T03:18:58,614 or your builds will no longer be supported. 2025-09-08T03:18:58,614 ******************************************************************************** 2025-09-08T03:18:58,614 !! 2025-09-08T03:18:58,614 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T03:18:58,998 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T03:18:58,998 !! 2025-09-08T03:18:58,998 ******************************************************************************** 2025-09-08T03:18:58,998 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T03:18:58,998 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T03:18:58,999 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T03:18:58,999 ******************************************************************************** 2025-09-08T03:18:58,999 !! 2025-09-08T03:18:58,999 self._finalize_license_expression() 2025-09-08T03:18:58,999 running bdist_wheel 2025-09-08T03:18:59,332 /tmp/pip-wheel-_q72ncib/mdtraj_b659b9e806c94c309ca161d583921af8/basesetup.py:254: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-08T03:18:59,332 import pkg_resources 2025-09-08T03:18:59,911 running build 2025-09-08T03:18:59,911 running build_py 2025-09-08T03:18:59,986 creating build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T03:18:59,987 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T03:18:59,987 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T03:18:59,988 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T03:18:59,989 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,989 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,990 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,990 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,991 copying mdtraj/utils/test.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,991 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,992 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,993 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,993 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,994 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:18:59,995 creating build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,995 copying mdtraj/tests/test_zipped.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,996 copying mdtraj/tests/test_xyz.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,996 copying mdtraj/tests/test_xtc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,997 copying mdtraj/tests/test_xml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,997 copying mdtraj/tests/test_trr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,998 copying mdtraj/tests/test_trajectory.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,998 copying mdtraj/tests/test_topology.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,999 copying mdtraj/tests/test_selection.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:18:59,999 copying mdtraj/tests/test_rmsd_memmap.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,000 copying mdtraj/tests/test_rmsd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,001 copying mdtraj/tests/test_restart.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,001 copying mdtraj/tests/test_reporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,002 copying mdtraj/tests/test_quaternion.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,002 copying mdtraj/tests/test_psf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,003 copying mdtraj/tests/test_prmtop.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,003 copying mdtraj/tests/test_nmr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,004 copying mdtraj/tests/test_netcdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,004 copying mdtraj/tests/test_mol2.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,005 copying mdtraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,005 copying mdtraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,006 copying mdtraj/tests/test_lprmsd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,006 copying mdtraj/tests/test_lh5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,007 copying mdtraj/tests/test_lammpstrj.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,007 copying mdtraj/tests/test_io.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,008 copying mdtraj/tests/test_hoomdxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,008 copying mdtraj/tests/test_hdf5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,009 copying mdtraj/tests/test_gro.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,009 copying mdtraj/tests/test_element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,010 copying mdtraj/tests/test_dtr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,010 copying mdtraj/tests/test_docstrings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,011 copying mdtraj/tests/test_dcd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,011 copying mdtraj/tests/test_crd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,012 copying mdtraj/tests/test_capi.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,012 copying mdtraj/tests/test_binpos.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,013 copying mdtraj/tests/test_arc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,013 copying mdtraj/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:00,014 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:00,014 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:00,015 copying mdtraj/testing/nosetester.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:00,016 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:00,016 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:00,017 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:00,017 creating build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T03:19:00,018 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T03:19:00,018 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T03:19:00,019 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T03:19:00,020 creating build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:00,020 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:00,021 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:00,021 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:00,022 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:00,022 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:00,023 creating build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T03:19:00,023 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T03:19:00,024 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T03:19:00,024 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T03:19:00,025 creating build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:00,025 copying mdtraj/html/trajectory_widget.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:00,026 copying mdtraj/html/linked_heatmap.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:00,026 copying mdtraj/html/install.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:00,027 copying mdtraj/html/imagebutton_widget.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:00,027 copying mdtraj/html/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:00,028 creating build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,029 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,029 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,030 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,030 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,031 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,031 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,032 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,032 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,033 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,034 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,034 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,035 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,035 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,036 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:00,037 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,037 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,038 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,038 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,039 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,039 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,040 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,040 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,041 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,041 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,042 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,043 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,043 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,044 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,044 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,045 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,046 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:00,046 creating build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:00,047 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:00,047 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:00,048 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:00,049 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:00,049 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:00,050 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:00,051 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,051 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,052 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,052 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,053 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,053 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,054 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,054 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,055 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,055 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,056 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,057 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,057 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,058 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:00,058 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T03:19:00,059 copying mdtraj/utils/external/pyparsing.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T03:19:00,060 copying mdtraj/utils/external/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T03:19:00,061 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:00,061 copying mdtraj/utils/external/astor/treewalk.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:00,062 copying mdtraj/utils/external/astor/misc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:00,062 copying mdtraj/utils/external/astor/codegen.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:00,063 copying mdtraj/utils/external/astor/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:00,064 creating build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,064 copying mdtraj/geometry/tests/test_thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,064 copying mdtraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,065 copying mdtraj/geometry/tests/test_rdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,065 copying mdtraj/geometry/tests/test_order.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,066 copying mdtraj/geometry/tests/test_neighbors.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,066 copying mdtraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,067 copying mdtraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,067 copying mdtraj/geometry/tests/test_dssp.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,068 copying mdtraj/geometry/tests/test_drid.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,068 copying mdtraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,069 copying mdtraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,070 copying mdtraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,070 copying mdtraj/geometry/tests/test_angles.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,071 copying mdtraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,071 copying mdtraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:00,072 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T03:19:00,072 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T03:19:00,073 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T03:19:00,073 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T03:19:00,074 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T03:19:00,074 copying mdtraj/formats/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T03:19:00,075 copying mdtraj/formats/pdb/tests/test_element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T03:19:00,075 copying mdtraj/formats/pdb/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T03:19:00,089 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,089 copying mdtraj/testing/reference/well-mixed.hoomdxml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,092 copying mdtraj/testing/reference/water_hex.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,098 copying mdtraj/testing/reference/v_error.gro -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,099 copying mdtraj/testing/reference/tz2.truncoct.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,103 copying mdtraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,104 copying mdtraj/testing/reference/tip3p_300K_1ATM_all-all_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,104 copying mdtraj/testing/reference/tip3p_300K_1ATM_O-O_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,105 copying mdtraj/testing/reference/tip3p_300K_1ATM_O-H_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,106 copying mdtraj/testing/reference/tip3p_300K_1ATM.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,110 copying mdtraj/testing/reference/tip3p_300K_1ATM.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,111 copying mdtraj/testing/reference/test_hoomdxml.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,117 copying mdtraj/testing/reference/test_good.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,125 copying mdtraj/testing/reference/test_bad.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,133 copying mdtraj/testing/reference/test.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,143 copying mdtraj/testing/reference/status-bits.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,143 copying mdtraj/testing/reference/smooth.txt -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,144 copying mdtraj/testing/reference/overflow.crd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,150 copying mdtraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,150 copying mdtraj/testing/reference/no_ions.hoomdxml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,151 copying mdtraj/testing/reference/no_chains.hoomdxml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,152 copying mdtraj/testing/reference/nitrogen.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,155 copying mdtraj/testing/reference/nitrogen.arc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,158 copying mdtraj/testing/reference/ncinpcrd.rst7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,159 copying mdtraj/testing/reference/native2.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,160 copying mdtraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,160 copying mdtraj/testing/reference/native.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,161 copying mdtraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,162 copying mdtraj/testing/reference/monolayer.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,167 copying mdtraj/testing/reference/monolayer.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,168 copying mdtraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,170 copying mdtraj/testing/reference/md.mdp -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,171 copying mdtraj/testing/reference/lysozyme-ligand-tripos.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,171 copying mdtraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,172 copying mdtraj/testing/reference/inpcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,173 copying mdtraj/testing/reference/imatinib.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,174 copying mdtraj/testing/reference/imatinib.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,174 copying mdtraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,176 copying mdtraj/testing/reference/freesolve_v0.3.tar.bz2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,178 copying mdtraj/testing/reference/frame0.xyz.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,179 copying mdtraj/testing/reference/frame0.xyz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,181 copying mdtraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,182 copying mdtraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,183 copying mdtraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,185 copying mdtraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,189 copying mdtraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,190 copying mdtraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,193 copying mdtraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,195 copying mdtraj/testing/reference/frame0.lammpstrj -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,197 copying mdtraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,198 copying mdtraj/testing/reference/frame0.gro -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,200 copying mdtraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,201 copying mdtraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,202 copying mdtraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,204 copying mdtraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,205 copying mdtraj/testing/reference/custom.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,205 copying mdtraj/testing/reference/custom.lammpstrj -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,206 copying mdtraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,206 copying mdtraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,207 copying mdtraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,207 copying mdtraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,208 copying mdtraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,209 copying mdtraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,209 copying mdtraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,210 copying mdtraj/testing/reference/alanine.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,210 copying mdtraj/testing/reference/alanine-dipeptide-implicit.prmtop -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,211 copying mdtraj/testing/reference/alanine-dipeptide-explicit.prmtop -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,213 copying mdtraj/testing/reference/alanine-dipeptide-explicit.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,214 copying mdtraj/testing/reference/alanine-dipeptide-explicit.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,215 copying mdtraj/testing/reference/ala_dipeptide.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,216 copying mdtraj/testing/reference/ala_dipeptide.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,217 copying mdtraj/testing/reference/ala_ala_ala.xpsf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,217 copying mdtraj/testing/reference/ala_ala_ala.psf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,218 copying mdtraj/testing/reference/ala_ala_ala.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,218 copying mdtraj/testing/reference/ala_ala_ala.mdcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,219 copying mdtraj/testing/reference/ala3_chamber.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,220 copying mdtraj/testing/reference/adp.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,220 copying mdtraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,221 copying mdtraj/testing/reference/README.md -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,221 copying mdtraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,223 copying mdtraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,223 copying mdtraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,224 copying mdtraj/testing/reference/4OH9.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,225 copying mdtraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,226 copying mdtraj/testing/reference/3pqr_memb.psf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,327 copying mdtraj/testing/reference/3nch.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,330 copying mdtraj/testing/reference/3lines.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,330 copying mdtraj/testing/reference/2lines.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,331 copying mdtraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,334 copying mdtraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,341 copying mdtraj/testing/reference/1vii.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,341 copying mdtraj/testing/reference/1vii.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,342 copying mdtraj/testing/reference/1ncw.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,344 copying mdtraj/testing/reference/1line.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,344 copying mdtraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,345 copying mdtraj/testing/reference/1am7_uncorrected.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,347 copying mdtraj/testing/reference/1am7_protein.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,348 copying mdtraj/testing/reference/1am7_corrected.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:00,351 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:00,351 copying mdtraj/testing/reference/ala_dipeptide_trj/timekeys -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:00,352 copying mdtraj/testing/reference/ala_dipeptide_trj/metadata -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:00,352 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000002 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:00,353 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000001 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:00,354 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000000 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:00,354 copying mdtraj/testing/reference/ala_dipeptide_trj/clickme.dtr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:00,355 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:00,355 copying mdtraj/testing/reference/frame0.dtr/timekeys -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:00,355 copying mdtraj/testing/reference/frame0.dtr/metadata -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:00,356 copying mdtraj/testing/reference/frame0.dtr/frame000000001 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:00,360 copying mdtraj/testing/reference/frame0.dtr/frame000000000 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:00,365 copying mdtraj/testing/reference/frame0.dtr/clickme.dtr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:00,365 creating build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:00,365 copying mdtraj/html/static/widget_trajectory.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:00,366 copying mdtraj/html/static/widget_imagebutton.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:00,366 copying mdtraj/html/static/surface.min.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:00,367 copying mdtraj/html/static/objexporter.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:00,368 copying mdtraj/html/static/iview.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:00,368 copying mdtraj/html/static/filesaver.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:00,369 copying mdtraj/html/static/context.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:00,369 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T03:19:00,370 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T03:19:00,370 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T03:19:00,376 running build_ext 2025-09-08T03:19:00,840 Compiling mdtraj/formats/xtc/xtc.pyx because it changed. 2025-09-08T03:19:00,841 [1/1] Cythonizing mdtraj/formats/xtc/xtc.pyx 2025-09-08T03:19:02,969 building 'mdtraj.formats.xtc' extension 2025-09-08T03:19:02,971 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src 2025-09-08T03:19:02,972 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.13/dist-packages/numpy/core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src/xdrfile.o 2025-09-08T03:19:03,107 mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2025-09-08T03:19:03,107 mdtraj/formats/xtc/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:03,107 495 | while (size >= num && num_of_bits < 32) 2025-09-08T03:19:03,107 | ^~ 2025-09-08T03:19:03,107 mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2025-09-08T03:19:03,108 mdtraj/formats/xtc/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:03,108 541 | while (bytes[num_of_bytes] >= num) 2025-09-08T03:19:03,108 | ^~ 2025-09-08T03:19:03,109 mdtraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2025-09-08T03:19:03,109 mdtraj/formats/xtc/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:03,110 650 | if (num_of_bits >= num_of_bytes * 8) 2025-09-08T03:19:03,110 | ^~ 2025-09-08T03:19:03,110 mdtraj/formats/xtc/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:03,110 652 | for (i = 0; i < num_of_bytes; i++) 2025-09-08T03:19:03,110 | ^ 2025-09-08T03:19:03,110 mdtraj/formats/xtc/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:03,110 660 | for (i = 0; i < num_of_bytes-1; i++) 2025-09-08T03:19:03,111 | ^ 2025-09-08T03:19:03,111 mdtraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2025-09-08T03:19:03,112 mdtraj/formats/xtc/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:03,112 700 | if (lastbits < num_of_bits) 2025-09-08T03:19:03,112 | ^ 2025-09-08T03:19:03,114 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2025-09-08T03:19:03,114 mdtraj/formats/xtc/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:03,114 815 | if(size3>xfp->buf1size) 2025-09-08T03:19:03,114 | ^ 2025-09-08T03:19:03,116 mdtraj/formats/xtc/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:03,116 869 | maxidx = (LASTIDX size3) 2025-09-08T03:19:03,119 | ^ 2025-09-08T03:19:03,120 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-09-08T03:19:03,120 788 | int smallnum, smaller, larger, i, is_smaller, run; 2025-09-08T03:19:03,120 | ^~~~~~ 2025-09-08T03:19:03,121 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-09-08T03:19:03,121 785 | int smallidx, minidx, maxidx; 2025-09-08T03:19:03,121 | ^~~~~~ 2025-09-08T03:19:03,122 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2025-09-08T03:19:03,122 mdtraj/formats/xtc/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:03,122 1027 | if(size3>xfp->buf1size) 2025-09-08T03:19:03,122 | ^ 2025-09-08T03:19:03,127 mdtraj/formats/xtc/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:03,128 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2025-09-08T03:19:03,128 | ^ 2025-09-08T03:19:03,128 mdtraj/formats/xtc/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:03,128 1156 | maxidx = (LASTIDXxfp->buf1size) 2025-09-08T03:19:03,136 | ^ 2025-09-08T03:19:03,138 mdtraj/formats/xtc/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:03,138 1383 | maxidx = (LASTIDXxfp->buf1size) { 2025-09-08T03:19:03,146 | ^ 2025-09-08T03:19:03,153 mdtraj/formats/xtc/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:03,153 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2025-09-08T03:19:03,153 | ^ 2025-09-08T03:19:03,154 mdtraj/formats/xtc/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:03,154 1639 | maxidx = (LASTIDX -- a caller that pip uses to run setup.py 2025-09-08T03:19:06,863 # 2025-09-08T03:19:06,863 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T03:19:06,863 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T03:19:06,863 # - It provides a clear error message when setuptools is not installed. 2025-09-08T03:19:06,863 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T03:19:06,863 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T03:19:06,863 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T03:19:06,863 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T03:19:06,863 import os, sys, tokenize, traceback 2025-09-08T03:19:06,863 2025-09-08T03:19:06,863 try: 2025-09-08T03:19:06,863 import setuptools 2025-09-08T03:19:06,863 except ImportError: 2025-09-08T03:19:06,863 print( 2025-09-08T03:19:06,863 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T03:19:06,863 "the build environment with exception:", 2025-09-08T03:19:06,863 file=sys.stderr, 2025-09-08T03:19:06,863 ) 2025-09-08T03:19:06,863 traceback.print_exc() 2025-09-08T03:19:06,863 sys.exit(1) 2025-09-08T03:19:06,863 2025-09-08T03:19:06,863 __file__ = %r 2025-09-08T03:19:06,863 sys.argv[0] = __file__ 2025-09-08T03:19:06,863 2025-09-08T03:19:06,863 if os.path.exists(__file__): 2025-09-08T03:19:06,863 filename = __file__ 2025-09-08T03:19:06,863 with tokenize.open(__file__) as f: 2025-09-08T03:19:06,863 setup_py_code = f.read() 2025-09-08T03:19:06,863 else: 2025-09-08T03:19:06,863 filename = "" 2025-09-08T03:19:06,863 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T03:19:06,863 2025-09-08T03:19:06,863 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T03:19:06,863 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-_q72ncib/mdtraj_b659b9e806c94c309ca161d583921af8/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ob5ih7da[/] 2025-09-08T03:19:06,863 [bold magenta]cwd[/]: /tmp/pip-wheel-_q72ncib/mdtraj_b659b9e806c94c309ca161d583921af8/ 2025-09-08T03:19:06,863 Building wheel for mdtraj (setup.py): finished with status 'error' 2025-09-08T03:19:06,864 ERROR: Failed building wheel for mdtraj 2025-09-08T03:19:06,865 Running setup.py clean for mdtraj 2025-09-08T03:19:06,866 Running command python setup.py clean 2025-09-08T03:19:07,569 C compiler: 2025-09-08T03:19:07,573 Using built-in specs. 2025-09-08T03:19:07,573 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T03:19:07,573 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T03:19:07,573 Target: arm-linux-gnueabihf 2025-09-08T03:19:07,573 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --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-libstdcxx-backtrace --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+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T03:19:07,574 Thread model: posix 2025-09-08T03:19:07,574 Supported LTO compression algorithms: zlib zstd 2025-09-08T03:19:07,574 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T03:19:08,867 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T03:19:09,487 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T03:19:10,104 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T03:19:10,226 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T03:19:10,226 !! 2025-09-08T03:19:10,226 ******************************************************************************** 2025-09-08T03:19:10,226 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T03:19:10,226 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T03:19:10,227 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T03:19:10,227 or your builds will no longer be supported. 2025-09-08T03:19:10,227 ******************************************************************************** 2025-09-08T03:19:10,227 !! 2025-09-08T03:19:10,227 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T03:19:10,618 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T03:19:10,618 !! 2025-09-08T03:19:10,618 ******************************************************************************** 2025-09-08T03:19:10,619 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T03:19:10,619 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T03:19:10,619 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T03:19:10,619 ******************************************************************************** 2025-09-08T03:19:10,619 !! 2025-09-08T03:19:10,619 self._finalize_license_expression() 2025-09-08T03:19:10,695 running clean 2025-09-08T03:19:10,842 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T03:19:10,842 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T03:19:10,870 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T03:19:10,870 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T03:19:10,870 removing 'build' 2025-09-08T03:19:10,984 Failed to build mdtraj 2025-09-08T03:19:10,985 ERROR: Failed to build one or more wheels 2025-09-08T03:19:10,986 Exception information: 2025-09-08T03:19:10,986 Traceback (most recent call last): 2025-09-08T03:19:10,986 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T03:19:10,986 status = _inner_run() 2025-09-08T03:19:10,986 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T03:19:10,986 return self.run(options, args) 2025-09-08T03:19:10,986 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T03:19:10,986 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T03:19:10,986 return func(self, options, args) 2025-09-08T03:19:10,986 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T03:19:10,986 raise CommandError("Failed to build one or more wheels") 2025-09-08T03:19:10,986 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T03:19:10,990 Removed build tracker: '/tmp/pip-build-tracker-kgsj99pc'