2025-09-08T03:18:51,301 Created temporary directory: /tmp/pip-build-tracker-hasdmzac 2025-09-08T03:18:51,302 Initialized build tracking at /tmp/pip-build-tracker-hasdmzac 2025-09-08T03:18:51,302 Created build tracker: /tmp/pip-build-tracker-hasdmzac 2025-09-08T03:18:51,302 Entered build tracker: /tmp/pip-build-tracker-hasdmzac 2025-09-08T03:18:51,302 Created temporary directory: /tmp/pip-wheel-nlbf72sa 2025-09-08T03:18:51,306 Created temporary directory: /tmp/pip-ephem-wheel-cache-od33aehb 2025-09-08T03:18:51,364 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T03:18:51,366 2 location(s) to search for versions of mdtraj: 2025-09-08T03:18:51,366 * https://pypi.org/simple/mdtraj/ 2025-09-08T03:18:51,366 * https://www.piwheels.org/simple/mdtraj/ 2025-09-08T03:18:51,366 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2025-09-08T03:18:51,367 Getting page https://pypi.org/simple/mdtraj/ 2025-09-08T03:18:51,368 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/) 2025-09-08T03:18:51,599 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/) 2025-09-08T03:18:51,599 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/) 2025-09-08T03:18:51,599 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/) 2025-09-08T03:18:51,600 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/) 2025-09-08T03:18:51,600 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/) 2025-09-08T03:18:51,600 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/) 2025-09-08T03:18:51,600 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/) 2025-09-08T03:18:51,600 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/) 2025-09-08T03:18:51,600 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/) 2025-09-08T03:18:51,600 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/) 2025-09-08T03:18:51,601 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/) 2025-09-08T03:18:51,601 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/) 2025-09-08T03:18:51,601 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/) 2025-09-08T03:18:51,601 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/) 2025-09-08T03:18:51,601 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/) 2025-09-08T03:18:51,601 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2025-09-08T03:18:51,602 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2025-09-08T03:18:51,632 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates 2025-09-08T03:18:51,633 Collecting mdtraj==1.5.1 2025-09-08T03:18:51,634 Created temporary directory: /tmp/pip-unpack-zwo_ukiw 2025-09-08T03:18:51,822 Downloading mdtraj-1.5.1.zip (18.7 MB) 2025-09-08T03:18:54,557 Added mdtraj==1.5.1 from https://files.pythonhosted.org/packages/78/ae/82df7eca71fa9e71ad4638f8c222164ccc3583874cb4a6875a04586312bc/mdtraj-1.5.1.zip to build tracker '/tmp/pip-build-tracker-hasdmzac' 2025-09-08T03:18:54,558 Running setup.py (path:/tmp/pip-wheel-nlbf72sa/mdtraj_58cd5c88798d45f8b14b8a38f97e9a6d/setup.py) egg_info for package mdtraj 2025-09-08T03:18:54,558 Created temporary directory: /tmp/pip-pip-egg-info-nft1tf8d 2025-09-08T03:18:54,558 Preparing metadata (setup.py): started 2025-09-08T03:18:54,559 Running command python setup.py egg_info 2025-09-08T03:18:55,513 Using built-in specs. 2025-09-08T03:18:55,514 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T03:18:55,514 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T03:18:55,515 Target: arm-linux-gnueabihf 2025-09-08T03:18:55,515 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 2025-09-08T03:18:55,515 Thread model: posix 2025-09-08T03:18:55,515 Supported LTO compression algorithms: zlib zstd 2025-09-08T03:18:55,515 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T03:19:13,080 performance hint: mdtraj/rmsd/_rmsd.pyx:187:62: Use boundscheck(False) for faster access 2025-09-08T03:19:13,080 performance hint: mdtraj/rmsd/_rmsd.pyx:187:87: Use boundscheck(False) for faster access 2025-09-08T03:19:13,080 performance hint: mdtraj/rmsd/_rmsd.pyx:187:103: Use boundscheck(False) for faster access 2025-09-08T03:19:13,081 performance hint: mdtraj/rmsd/_rmsd.pyx:188:21: Use boundscheck(False) for faster access 2025-09-08T03:19:13,196 C compiler: 2025-09-08T03:19:13,196 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T03:19:13,197 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T03:19:13,197 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T03:19:13,197 Compiling mdtraj/formats/xtc/xtc.pyx because it changed. 2025-09-08T03:19:13,197 Compiling mdtraj/formats/xtc/trr.pyx because it changed. 2025-09-08T03:19:13,197 Compiling mdtraj/formats/dcd/dcd.pyx because it changed. 2025-09-08T03:19:13,197 Compiling mdtraj/formats/binpos/binpos.pyx because it changed. 2025-09-08T03:19:13,197 Compiling mdtraj/formats/dtr/dtr.pyx because it changed. 2025-09-08T03:19:13,197 Compiling mdtraj/rmsd/_rmsd.pyx because it changed. 2025-09-08T03:19:13,197 Compiling mdtraj/rmsd/_lprmsd.pyx because it changed. 2025-09-08T03:19:13,198 Compiling mdtraj/geometry/src/_geometry.pyx because it changed. 2025-09-08T03:19:13,198 Compiling mdtraj/geometry/drid.pyx because it changed. 2025-09-08T03:19:13,198 Compiling mdtraj/geometry/neighbors.pyx because it changed. 2025-09-08T03:19:13,198 [ 1/10] Cythonizing mdtraj/formats/binpos/binpos.pyx 2025-09-08T03:19:13,198 [ 2/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2025-09-08T03:19:13,198 [ 3/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2025-09-08T03:19:13,198 [ 4/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2025-09-08T03:19:13,198 [ 5/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2025-09-08T03:19:13,198 [ 6/10] Cythonizing mdtraj/geometry/drid.pyx 2025-09-08T03:19:13,198 [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx 2025-09-08T03:19:13,198 [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2025-09-08T03:19:13,199 [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2025-09-08T03:19:13,199 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2025-09-08T03:19:13,651 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T03:19:13,651 !! 2025-09-08T03:19:13,651 ******************************************************************************** 2025-09-08T03:19:13,651 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T03:19:13,651 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T03:19:13,651 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T03:19:13,651 ******************************************************************************** 2025-09-08T03:19:13,652 !! 2025-09-08T03:19:13,652 self._finalize_license_expression() 2025-09-08T03:19:13,725 running egg_info 2025-09-08T03:19:13,804 creating /tmp/pip-pip-egg-info-nft1tf8d/mdtraj.egg-info 2025-09-08T03:19:13,804 writing /tmp/pip-pip-egg-info-nft1tf8d/mdtraj.egg-info/PKG-INFO 2025-09-08T03:19:13,805 writing dependency_links to /tmp/pip-pip-egg-info-nft1tf8d/mdtraj.egg-info/dependency_links.txt 2025-09-08T03:19:13,806 writing entry points to /tmp/pip-pip-egg-info-nft1tf8d/mdtraj.egg-info/entry_points.txt 2025-09-08T03:19:13,806 writing top-level names to /tmp/pip-pip-egg-info-nft1tf8d/mdtraj.egg-info/top_level.txt 2025-09-08T03:19:13,807 writing manifest file '/tmp/pip-pip-egg-info-nft1tf8d/mdtraj.egg-info/SOURCES.txt' 2025-09-08T03:19:14,031 /tmp/pip-wheel-nlbf72sa/mdtraj_58cd5c88798d45f8b14b8a38f97e9a6d/basesetup.py:262: 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. 2025-09-08T03:19:14,031 import pkg_resources 2025-09-08T03:19:14,457 reading manifest file '/tmp/pip-pip-egg-info-nft1tf8d/mdtraj.egg-info/SOURCES.txt' 2025-09-08T03:19:14,458 reading manifest template 'MANIFEST.in' 2025-09-08T03:19:14,487 writing manifest file '/tmp/pip-pip-egg-info-nft1tf8d/mdtraj.egg-info/SOURCES.txt' 2025-09-08T03:19:15,771 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T03:19:15,775 Source in /tmp/pip-wheel-nlbf72sa/mdtraj_58cd5c88798d45f8b14b8a38f97e9a6d has version 1.5.1, which satisfies requirement mdtraj==1.5.1 from https://files.pythonhosted.org/packages/78/ae/82df7eca71fa9e71ad4638f8c222164ccc3583874cb4a6875a04586312bc/mdtraj-1.5.1.zip 2025-09-08T03:19:15,776 Removed mdtraj==1.5.1 from https://files.pythonhosted.org/packages/78/ae/82df7eca71fa9e71ad4638f8c222164ccc3583874cb4a6875a04586312bc/mdtraj-1.5.1.zip from build tracker '/tmp/pip-build-tracker-hasdmzac' 2025-09-08T03:19:15,779 Created temporary directory: /tmp/pip-unpack-xlxi334x 2025-09-08T03:19:15,779 Created temporary directory: /tmp/pip-unpack-nww2n2yw 2025-09-08T03:19:15,779 Building wheels for collected packages: mdtraj 2025-09-08T03:19:15,781 Created temporary directory: /tmp/pip-wheel-4z6u689g 2025-09-08T03:19:15,781 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 2025-09-08T03:19:15,782 Building wheel for mdtraj (setup.py): started 2025-09-08T03:19:15,783 Destination directory: /tmp/pip-wheel-4z6u689g 2025-09-08T03:19:15,783 Running command python setup.py bdist_wheel 2025-09-08T03:19:16,715 C compiler: 2025-09-08T03:19:16,720 Using built-in specs. 2025-09-08T03:19:16,720 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T03:19:16,720 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T03:19:16,720 Target: arm-linux-gnueabihf 2025-09-08T03:19:16,720 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 2025-09-08T03:19:16,721 Thread model: posix 2025-09-08T03:19:16,721 Supported LTO compression algorithms: zlib zstd 2025-09-08T03:19:16,721 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T03:19:18,237 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T03:19:18,860 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T03:19:19,488 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T03:19:20,589 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T03:19:20,589 !! 2025-09-08T03:19:20,589 ******************************************************************************** 2025-09-08T03:19:20,589 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T03:19:20,590 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T03:19:20,590 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T03:19:20,590 ******************************************************************************** 2025-09-08T03:19:20,590 !! 2025-09-08T03:19:20,590 self._finalize_license_expression() 2025-09-08T03:19:20,590 running bdist_wheel 2025-09-08T03:19:20,904 /tmp/pip-wheel-nlbf72sa/mdtraj_58cd5c88798d45f8b14b8a38f97e9a6d/basesetup.py:262: 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. 2025-09-08T03:19:20,904 import pkg_resources 2025-09-08T03:19:21,224 running build 2025-09-08T03:19:21,225 running build_py 2025-09-08T03:19:21,304 creating build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T03:19:21,305 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T03:19:21,305 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T03:19:21,306 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T03:19:21,307 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,307 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,308 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,308 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,309 copying mdtraj/utils/test.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,309 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,310 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,311 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,311 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,312 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T03:19:21,313 creating build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,313 copying mdtraj/tests/test_zipped.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,314 copying mdtraj/tests/test_xyz.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,314 copying mdtraj/tests/test_xtc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,315 copying mdtraj/tests/test_xml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,315 copying mdtraj/tests/test_trr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,316 copying mdtraj/tests/test_trajectory.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,316 copying mdtraj/tests/test_topology.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,317 copying mdtraj/tests/test_selection.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,317 copying mdtraj/tests/test_rmsd_memmap.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,318 copying mdtraj/tests/test_rmsd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,318 copying mdtraj/tests/test_restart.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,319 copying mdtraj/tests/test_reporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,319 copying mdtraj/tests/test_quaternion.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,320 copying mdtraj/tests/test_psf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,321 copying mdtraj/tests/test_prmtop.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,321 copying mdtraj/tests/test_nmr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,322 copying mdtraj/tests/test_netcdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,322 copying mdtraj/tests/test_mol2.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,323 copying mdtraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,323 copying mdtraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,324 copying mdtraj/tests/test_lprmsd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,324 copying mdtraj/tests/test_lh5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,325 copying mdtraj/tests/test_lammpstrj.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,325 copying mdtraj/tests/test_io.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,326 copying mdtraj/tests/test_hoomdxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,326 copying mdtraj/tests/test_hdf5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,327 copying mdtraj/tests/test_gro.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,327 copying mdtraj/tests/test_element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,328 copying mdtraj/tests/test_dtr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,328 copying mdtraj/tests/test_docstrings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,329 copying mdtraj/tests/test_dcd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,329 copying mdtraj/tests/test_crd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,330 copying mdtraj/tests/test_capi.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,330 copying mdtraj/tests/test_binpos.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,331 copying mdtraj/tests/test_arc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,331 copying mdtraj/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T03:19:21,332 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:21,332 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:21,333 copying mdtraj/testing/nosetester.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:21,333 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:21,334 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:21,334 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T03:19:21,335 creating build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T03:19:21,335 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T03:19:21,336 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T03:19:21,337 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T03:19:21,337 creating build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:21,338 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:21,338 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:21,339 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:21,339 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:21,340 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T03:19:21,341 creating build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T03:19:21,341 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T03:19:21,341 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T03:19:21,342 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T03:19:21,343 creating build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:21,343 copying mdtraj/html/trajectory_widget.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:21,343 copying mdtraj/html/linked_heatmap.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:21,344 copying mdtraj/html/install.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:21,344 copying mdtraj/html/imagebutton_widget.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:21,345 copying mdtraj/html/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T03:19:21,346 creating build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,346 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,347 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,347 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,348 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,348 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,349 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,349 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,350 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,351 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,351 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,352 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,352 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,353 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,353 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T03:19:21,354 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,355 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,355 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,356 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,356 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,357 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,357 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,358 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,358 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,359 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,360 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,360 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,361 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,361 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,362 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,363 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,363 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T03:19:21,364 creating build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:21,364 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:21,365 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:21,366 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:21,366 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:21,367 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:21,367 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T03:19:21,368 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,369 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,369 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,370 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,371 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,371 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,372 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,372 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,373 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,373 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,374 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,374 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,375 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,376 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T03:19:21,376 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T03:19:21,377 copying mdtraj/utils/external/pyparsing.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T03:19:21,378 copying mdtraj/utils/external/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T03:19:21,378 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:21,379 copying mdtraj/utils/external/astor/treewalk.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:21,379 copying mdtraj/utils/external/astor/misc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:21,380 copying mdtraj/utils/external/astor/codegen.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:21,380 copying mdtraj/utils/external/astor/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T03:19:21,381 creating build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,382 copying mdtraj/geometry/tests/test_thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,382 copying mdtraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,383 copying mdtraj/geometry/tests/test_rdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,383 copying mdtraj/geometry/tests/test_order.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,384 copying mdtraj/geometry/tests/test_neighbors.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,384 copying mdtraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,385 copying mdtraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,385 copying mdtraj/geometry/tests/test_dssp.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,386 copying mdtraj/geometry/tests/test_drid.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,386 copying mdtraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,387 copying mdtraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,387 copying mdtraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,388 copying mdtraj/geometry/tests/test_angles.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,388 copying mdtraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,389 copying mdtraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T03:19:21,390 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T03:19:21,390 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T03:19:21,391 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T03:19:21,391 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T03:19:21,392 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T03:19:21,392 copying mdtraj/formats/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T03:19:21,393 copying mdtraj/formats/pdb/tests/test_element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T03:19:21,393 copying mdtraj/formats/pdb/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T03:19:21,407 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,407 copying mdtraj/testing/reference/well-mixed.hoomdxml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,410 copying mdtraj/testing/reference/water_hex.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,416 copying mdtraj/testing/reference/v_error.gro -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,417 copying mdtraj/testing/reference/tz2.truncoct.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,421 copying mdtraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,422 copying mdtraj/testing/reference/tip3p_300K_1ATM_all-all_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,422 copying mdtraj/testing/reference/tip3p_300K_1ATM_O-O_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,423 copying mdtraj/testing/reference/tip3p_300K_1ATM_O-H_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,423 copying mdtraj/testing/reference/tip3p_300K_1ATM.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,428 copying mdtraj/testing/reference/tip3p_300K_1ATM.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,429 copying mdtraj/testing/reference/test_hoomdxml.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,436 copying mdtraj/testing/reference/test_good.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,443 copying mdtraj/testing/reference/test_bad.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,451 copying mdtraj/testing/reference/test.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,461 copying mdtraj/testing/reference/status-bits.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,462 copying mdtraj/testing/reference/smooth.txt -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,462 copying mdtraj/testing/reference/overflow.crd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,468 copying mdtraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,468 copying mdtraj/testing/reference/no_ions.hoomdxml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,469 copying mdtraj/testing/reference/no_chains.hoomdxml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,470 copying mdtraj/testing/reference/nitrogen.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,474 copying mdtraj/testing/reference/nitrogen.arc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,477 copying mdtraj/testing/reference/ncinpcrd.rst7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,478 copying mdtraj/testing/reference/native2.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,478 copying mdtraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,479 copying mdtraj/testing/reference/native.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,479 copying mdtraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,480 copying mdtraj/testing/reference/monolayer.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,486 copying mdtraj/testing/reference/monolayer.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,487 copying mdtraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,489 copying mdtraj/testing/reference/md.mdp -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,489 copying mdtraj/testing/reference/lysozyme-ligand-tripos.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,490 copying mdtraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,491 copying mdtraj/testing/reference/inpcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,492 copying mdtraj/testing/reference/imatinib.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,493 copying mdtraj/testing/reference/imatinib.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,493 copying mdtraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,495 copying mdtraj/testing/reference/freesolve_v0.3.tar.bz2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,497 copying mdtraj/testing/reference/frame0.xyz.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,497 copying mdtraj/testing/reference/frame0.xyz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,500 copying mdtraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,501 copying mdtraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,502 copying mdtraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,504 copying mdtraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,508 copying mdtraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,509 copying mdtraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,512 copying mdtraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,514 copying mdtraj/testing/reference/frame0.lammpstrj -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,516 copying mdtraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,517 copying mdtraj/testing/reference/frame0.gro -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,519 copying mdtraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,520 copying mdtraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,521 copying mdtraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,523 copying mdtraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,524 copying mdtraj/testing/reference/custom.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,524 copying mdtraj/testing/reference/custom.lammpstrj -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,525 copying mdtraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,525 copying mdtraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,526 copying mdtraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,526 copying mdtraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,527 copying mdtraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,528 copying mdtraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,528 copying mdtraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,529 copying mdtraj/testing/reference/alanine.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,529 copying mdtraj/testing/reference/alanine-dipeptide-implicit.prmtop -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,530 copying mdtraj/testing/reference/alanine-dipeptide-explicit.prmtop -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,532 copying mdtraj/testing/reference/alanine-dipeptide-explicit.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,533 copying mdtraj/testing/reference/alanine-dipeptide-explicit.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,534 copying mdtraj/testing/reference/ala_dipeptide.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,535 copying mdtraj/testing/reference/ala_dipeptide.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,536 copying mdtraj/testing/reference/ala_ala_ala.xpsf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,536 copying mdtraj/testing/reference/ala_ala_ala.psf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,537 copying mdtraj/testing/reference/ala_ala_ala.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,537 copying mdtraj/testing/reference/ala_ala_ala.mdcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,538 copying mdtraj/testing/reference/ala3_chamber.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,538 copying mdtraj/testing/reference/adp.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,539 copying mdtraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,540 copying mdtraj/testing/reference/README.md -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,540 copying mdtraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,542 copying mdtraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,542 copying mdtraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,543 copying mdtraj/testing/reference/4OH9.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,544 copying mdtraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,545 copying mdtraj/testing/reference/3pqr_memb.psf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,644 copying mdtraj/testing/reference/3nch.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,646 copying mdtraj/testing/reference/3lines.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,647 copying mdtraj/testing/reference/2lines.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,647 copying mdtraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,650 copying mdtraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,657 copying mdtraj/testing/reference/1vii.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,658 copying mdtraj/testing/reference/1vii.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,658 copying mdtraj/testing/reference/1ncw.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,660 copying mdtraj/testing/reference/1line.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,660 copying mdtraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,661 copying mdtraj/testing/reference/1am7_uncorrected.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,663 copying mdtraj/testing/reference/1am7_protein.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,665 copying mdtraj/testing/reference/1am7_corrected.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T03:19:21,667 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:21,667 copying mdtraj/testing/reference/ala_dipeptide_trj/timekeys -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:21,668 copying mdtraj/testing/reference/ala_dipeptide_trj/metadata -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:21,668 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000002 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:21,669 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000001 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:21,670 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000000 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:21,671 copying mdtraj/testing/reference/ala_dipeptide_trj/clickme.dtr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T03:19:21,671 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:21,671 copying mdtraj/testing/reference/frame0.dtr/timekeys -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:21,672 copying mdtraj/testing/reference/frame0.dtr/metadata -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:21,672 copying mdtraj/testing/reference/frame0.dtr/frame000000001 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:21,676 copying mdtraj/testing/reference/frame0.dtr/frame000000000 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:21,681 copying mdtraj/testing/reference/frame0.dtr/clickme.dtr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T03:19:21,681 creating build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:21,682 copying mdtraj/html/static/widget_trajectory.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:21,682 copying mdtraj/html/static/widget_imagebutton.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:21,683 copying mdtraj/html/static/surface.min.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:21,683 copying mdtraj/html/static/objexporter.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:21,684 copying mdtraj/html/static/iview.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:21,685 copying mdtraj/html/static/filesaver.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:21,685 copying mdtraj/html/static/context.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T03:19:21,686 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T03:19:21,686 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T03:19:21,687 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T03:19:21,693 running build_ext 2025-09-08T03:19:21,696 building 'mdtraj.formats.xtc' extension 2025-09-08T03:19:21,697 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src 2025-09-08T03:19:21,698 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/formats/xtc -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 2025-09-08T03:19:21,839 mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2025-09-08T03:19:21,839 mdtraj/formats/xtc/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:21,839 495 | while (size >= num && num_of_bits < 32) 2025-09-08T03:19:21,839 | ^~ 2025-09-08T03:19:21,840 mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2025-09-08T03:19:21,840 mdtraj/formats/xtc/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:21,840 541 | while (bytes[num_of_bytes] >= num) 2025-09-08T03:19:21,840 | ^~ 2025-09-08T03:19:21,841 mdtraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2025-09-08T03:19:21,841 mdtraj/formats/xtc/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:21,842 650 | if (num_of_bits >= num_of_bytes * 8) 2025-09-08T03:19:21,842 | ^~ 2025-09-08T03:19:21,842 mdtraj/formats/xtc/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:21,842 652 | for (i = 0; i < num_of_bytes; i++) 2025-09-08T03:19:21,842 | ^ 2025-09-08T03:19:21,842 mdtraj/formats/xtc/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:21,842 660 | for (i = 0; i < num_of_bytes-1; i++) 2025-09-08T03:19:21,843 | ^ 2025-09-08T03:19:21,843 mdtraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2025-09-08T03:19:21,844 mdtraj/formats/xtc/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:21,844 700 | if (lastbits < num_of_bits) 2025-09-08T03:19:21,844 | ^ 2025-09-08T03:19:21,845 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2025-09-08T03:19:21,846 mdtraj/formats/xtc/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:21,846 815 | if(size3>xfp->buf1size) 2025-09-08T03:19:21,846 | ^ 2025-09-08T03:19:21,848 mdtraj/formats/xtc/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:21,848 869 | maxidx = (LASTIDX size3) 2025-09-08T03:19:21,850 | ^ 2025-09-08T03:19:21,852 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-09-08T03:19:21,852 788 | int smallnum, smaller, larger, i, is_smaller, run; 2025-09-08T03:19:21,852 | ^~~~~~ 2025-09-08T03:19:21,852 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-09-08T03:19:21,852 785 | int smallidx, minidx, maxidx; 2025-09-08T03:19:21,852 | ^~~~~~ 2025-09-08T03:19:21,853 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2025-09-08T03:19:21,853 mdtraj/formats/xtc/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:21,854 1027 | if(size3>xfp->buf1size) 2025-09-08T03:19:21,854 | ^ 2025-09-08T03:19:21,858 mdtraj/formats/xtc/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:21,858 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2025-09-08T03:19:21,859 | ^ 2025-09-08T03:19:21,859 mdtraj/formats/xtc/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:21,859 1156 | maxidx = (LASTIDXxfp->buf1size) 2025-09-08T03:19:21,867 | ^ 2025-09-08T03:19:21,869 mdtraj/formats/xtc/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:21,869 1383 | maxidx = (LASTIDXxfp->buf1size) { 2025-09-08T03:19:21,877 | ^ 2025-09-08T03:19:21,883 mdtraj/formats/xtc/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T03:19:21,884 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2025-09-08T03:19:21,884 | ^ 2025-09-08T03:19:21,885 mdtraj/formats/xtc/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T03:19:21,885 1639 | maxidx = (LASTIDX -- a caller that pip uses to run setup.py 2025-09-08T03:19:25,384 # 2025-09-08T03:19:25,384 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T03:19:25,384 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T03:19:25,384 # - It provides a clear error message when setuptools is not installed. 2025-09-08T03:19:25,384 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T03:19:25,384 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T03:19:25,384 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T03:19:25,384 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T03:19:25,384 import os, sys, tokenize, traceback 2025-09-08T03:19:25,384 2025-09-08T03:19:25,384 try: 2025-09-08T03:19:25,384 import setuptools 2025-09-08T03:19:25,384 except ImportError: 2025-09-08T03:19:25,384 print( 2025-09-08T03:19:25,384 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T03:19:25,384 "the build environment with exception:", 2025-09-08T03:19:25,384 file=sys.stderr, 2025-09-08T03:19:25,384 ) 2025-09-08T03:19:25,384 traceback.print_exc() 2025-09-08T03:19:25,384 sys.exit(1) 2025-09-08T03:19:25,384 2025-09-08T03:19:25,384 __file__ = %r 2025-09-08T03:19:25,384 sys.argv[0] = __file__ 2025-09-08T03:19:25,384 2025-09-08T03:19:25,384 if os.path.exists(__file__): 2025-09-08T03:19:25,384 filename = __file__ 2025-09-08T03:19:25,384 with tokenize.open(__file__) as f: 2025-09-08T03:19:25,384 setup_py_code = f.read() 2025-09-08T03:19:25,384 else: 2025-09-08T03:19:25,384 filename = "" 2025-09-08T03:19:25,384 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T03:19:25,384 2025-09-08T03:19:25,384 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T03:19:25,384 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-nlbf72sa/mdtraj_58cd5c88798d45f8b14b8a38f97e9a6d/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-4z6u689g[/] 2025-09-08T03:19:25,384 [bold magenta]cwd[/]: /tmp/pip-wheel-nlbf72sa/mdtraj_58cd5c88798d45f8b14b8a38f97e9a6d/ 2025-09-08T03:19:25,385 Building wheel for mdtraj (setup.py): finished with status 'error' 2025-09-08T03:19:25,385 ERROR: Failed building wheel for mdtraj 2025-09-08T03:19:25,386 Running setup.py clean for mdtraj 2025-09-08T03:19:25,387 Running command python setup.py clean 2025-09-08T03:19:26,304 C compiler: 2025-09-08T03:19:26,308 Using built-in specs. 2025-09-08T03:19:26,309 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T03:19:26,309 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T03:19:26,309 Target: arm-linux-gnueabihf 2025-09-08T03:19:26,309 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 2025-09-08T03:19:26,309 Thread model: posix 2025-09-08T03:19:26,309 Supported LTO compression algorithms: zlib zstd 2025-09-08T03:19:26,310 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T03:19:27,600 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T03:19:28,218 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T03:19:28,823 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T03:19:29,922 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T03:19:29,922 !! 2025-09-08T03:19:29,922 ******************************************************************************** 2025-09-08T03:19:29,922 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T03:19:29,922 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T03:19:29,923 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T03:19:29,923 ******************************************************************************** 2025-09-08T03:19:29,923 !! 2025-09-08T03:19:29,923 self._finalize_license_expression() 2025-09-08T03:19:29,997 running clean 2025-09-08T03:19:30,140 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T03:19:30,141 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T03:19:30,169 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T03:19:30,169 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T03:19:30,169 removing 'build' 2025-09-08T03:19:30,342 Failed to build mdtraj 2025-09-08T03:19:30,342 ERROR: Failed to build one or more wheels 2025-09-08T03:19:30,343 Exception information: 2025-09-08T03:19:30,343 Traceback (most recent call last): 2025-09-08T03:19:30,343 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T03:19:30,343 status = _inner_run() 2025-09-08T03:19:30,343 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T03:19:30,343 return self.run(options, args) 2025-09-08T03:19:30,343 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T03:19:30,343 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T03:19:30,343 return func(self, options, args) 2025-09-08T03:19:30,343 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T03:19:30,343 raise CommandError("Failed to build one or more wheels") 2025-09-08T03:19:30,343 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T03:19:30,347 Removed build tracker: '/tmp/pip-build-tracker-hasdmzac'