2026-02-06T14:28:51,101 Created temporary directory: /tmp/pip-ephem-wheel-cache-fd7efg_7 2026-02-06T14:28:51,104 Created temporary directory: /tmp/pip-build-tracker-96u9uwjt 2026-02-06T14:28:51,105 Initialized build tracking at /tmp/pip-build-tracker-96u9uwjt 2026-02-06T14:28:51,105 Created build tracker: /tmp/pip-build-tracker-96u9uwjt 2026-02-06T14:28:51,106 Entered build tracker: /tmp/pip-build-tracker-96u9uwjt 2026-02-06T14:28:51,107 Created temporary directory: /tmp/pip-wheel-up4ec8aj 2026-02-06T14:28:51,110 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-06T14:28:51,113 Created temporary directory: /tmp/pip-ephem-wheel-cache-l2gxfpp5 2026-02-06T14:28:51,146 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-06T14:28:51,150 2 location(s) to search for versions of mdtraj: 2026-02-06T14:28:51,150 * https://pypi.org/simple/mdtraj/ 2026-02-06T14:28:51,150 * https://www.piwheels.org/simple/mdtraj/ 2026-02-06T14:28:51,151 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2026-02-06T14:28:51,152 Getting page https://pypi.org/simple/mdtraj/ 2026-02-06T14:28:51,154 Found index url https://pypi.org/simple 2026-02-06T14:28:51,422 Fetched page https://pypi.org/simple/mdtraj/ as application/vnd.pypi.simple.v1+json 2026-02-06T14:28:51,458 Found link https://files.pythonhosted.org/packages/cb/82/93ced2a2e5d37f36330fe3e74081fdd4ce8f933ebd16b4fab14cb5c6c29c/mdtraj-0.3.tar.gz (from https://pypi.org/simple/mdtraj/), 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https://files.pythonhosted.org/packages/3c/aa/b344aed2d1ec6bc2ac4e5e897ded78148b51b2ee730c5eaccce851d26082/mdtraj-1.11.1.post1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,621 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/92/13/e017236bd57f4564e0b43b9f1783a5c88f329cf7cf4b75076e1a1e37df03/mdtraj-1.11.1.post1-cp312-cp312-win_amd64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,622 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/58/94/3b51167be053a4570a323cb032d83914af37db8a5c82afc13cc7bdd5c46a/mdtraj-1.11.1.post1-cp313-cp313-macosx_10_13_universal2.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,623 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/5b/7a/f719b1921e1941a8eba0e8e9955363db70a321db002c6a4a106f2a3014cf/mdtraj-1.11.1.post1-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,624 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/b9/b8/f935b84d5aaceb9ea7f5d3500dd0459076a5ec167aaf66b75c1ffd1b954e/mdtraj-1.11.1.post1-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,625 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/65/7d/d7382b474ec378380661cb0827b6ccb528d70af8a1b75dc5f3fc753afb0d/mdtraj-1.11.1.post1-cp313-cp313-win_amd64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,626 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/12/f7/959c0448b80344f93c27f364031fceaeedf4ada86d42e2181fa4c0c5545f/mdtraj-1.11.1.post1-cp314-cp314-macosx_10_15_universal2.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,627 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/d5/e7/43a10391774c9c38e192856be775668732043793e29ffae1949823e7f0c6/mdtraj-1.11.1.post1-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,627 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/ac/11/194e3673bbbb7ede3039c8754c37325609b83c9a076b8a13de0156b0aac7/mdtraj-1.11.1.post1-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,628 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/3d/4d/372c52d6fb06f87026e3d84469501b8020bf8a7a326d701a17ff1a560b65/mdtraj-1.11.1.post1-cp314-cp314-win_amd64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-06T14:28:51,629 Found link https://files.pythonhosted.org/packages/66/3b/55f24465b9d5905eea28e14173e0a15c3a24d4e85280073f5062fac0d3b7/mdtraj-1.11.1.post1.tar.gz (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11), version: 1.11.1.post1 2026-02-06T14:28:51,630 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2026-02-06T14:28:51,631 Getting page https://www.piwheels.org/simple/mdtraj/ 2026-02-06T14:28:51,633 Found index url https://www.piwheels.org/simple 2026-02-06T14:28:51,832 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2026-02-06T14:28:51,847 Skipping link: No binaries permitted for mdtraj: 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https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2026-02-06T14:28:51,882 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/) 2026-02-06T14:28:51,883 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/) 2026-02-06T14:28:51,884 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/) 2026-02-06T14:28:51,884 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/) 2026-02-06T14:28:51,885 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2026-02-06T14:28:51,886 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2026-02-06T14:28:51,917 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2026-02-06T14:28:51,938 Collecting mdtraj==1.11.1 2026-02-06T14:28:51,941 Created temporary directory: /tmp/pip-unpack-_jmkvbjs 2026-02-06T14:28:52,209 Downloading mdtraj-1.11.1.tar.gz (2.7 MB) 2026-02-06T14:28:54,132 Added mdtraj==1.11.1 from https://files.pythonhosted.org/packages/f5/75/a17b14d28f1f1f87cfd8b823fc9822c0a4f861ff36f93f22afe8bf1977fa/mdtraj-1.11.1.tar.gz to build tracker '/tmp/pip-build-tracker-96u9uwjt' 2026-02-06T14:28:54,146 Created temporary directory: /tmp/pip-build-env-i6spiuz4 2026-02-06T14:28:54,152 Installing build dependencies: started 2026-02-06T14:28:54,153 Running command pip subprocess to install build dependencies 2026-02-06T14:28:55,538 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-02-06T14:28:56,366 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-06T14:28:56,397 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-06T14:28:58,430 Collecting setuptools 2026-02-06T14:28:58,454 Using cached setuptools-80.10.2-py3-none-any.whl (1.1 MB) 2026-02-06T14:28:58,639 Collecting versioneer[toml] 2026-02-06T14:28:58,664 Using cached https://www.piwheels.org/simple/versioneer/versioneer-0.29-py3-none-any.whl (46 kB) 2026-02-06T14:28:58,934 Collecting wheel 2026-02-06T14:28:58,942 Using cached wheel-0.46.3-py3-none-any.whl (30 kB) 2026-02-06T14:29:00,076 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-06T14:29:00,085 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-06T14:29:00,093 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-06T14:29:00,102 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-06T14:29:00,110 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-06T14:29:00,886 Collecting numpy~=2.0 2026-02-06T14:29:01,606 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.1-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-02-06T14:29:04,695 Collecting Cython>=3.0.0 2026-02-06T14:29:05,741 Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB) 2026-02-06T14:29:06,261 Collecting packaging>=24.0 2026-02-06T14:29:06,268 Using cached packaging-26.0-py3-none-any.whl (74 kB) 2026-02-06T14:29:10,009 Installing collected packages: versioneer, setuptools, packaging, numpy, Cython, wheel 2026-02-06T14:29:10,051 Creating /tmp/pip-build-env-i6spiuz4/overlay/local/bin 2026-02-06T14:29:10,054 changing mode of /tmp/pip-build-env-i6spiuz4/overlay/local/bin/versioneer to 755 2026-02-06T14:29:24,933 changing mode of /tmp/pip-build-env-i6spiuz4/overlay/local/bin/f2py to 755 2026-02-06T14:29:24,936 changing mode of /tmp/pip-build-env-i6spiuz4/overlay/local/bin/numpy-config to 755 2026-02-06T14:29:29,578 changing mode of /tmp/pip-build-env-i6spiuz4/overlay/local/bin/cygdb to 755 2026-02-06T14:29:29,581 changing mode of /tmp/pip-build-env-i6spiuz4/overlay/local/bin/cython to 755 2026-02-06T14:29:29,583 changing mode of /tmp/pip-build-env-i6spiuz4/overlay/local/bin/cythonize to 755 2026-02-06T14:29:29,744 changing mode of /tmp/pip-build-env-i6spiuz4/overlay/local/bin/wheel to 755 2026-02-06T14:29:29,803 Successfully installed Cython-3.2.4 numpy-2.4.1 packaging-26.0 setuptools-80.10.2 versioneer-0.29 wheel-0.46.3 2026-02-06T14:29:30,414 Installing build dependencies: finished with status 'done' 2026-02-06T14:29:30,438 Getting requirements to build wheel: started 2026-02-06T14:29:30,440 Running command Getting requirements to build wheel 2026-02-06T14:29:31,387 Using built-in specs. 2026-02-06T14:29:31,388 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-02-06T14:29:31,388 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-02-06T14:29:31,389 Target: arm-linux-gnueabihf 2026-02-06T14:29:31,390 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1+deb12u1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2026-02-06T14:29:31,390 Thread model: posix 2026-02-06T14:29:31,391 Supported LTO compression algorithms: zlib zstd 2026-02-06T14:29:31,392 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-02-06T14:29:36,758 /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-06T14:29:36,758 !! 2026-02-06T14:29:36,760 ******************************************************************************** 2026-02-06T14:29:36,761 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-06T14:29:36,762 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-02-06T14:29:36,764 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-06T14:29:36,764 ******************************************************************************** 2026-02-06T14:29:36,766 !! 2026-02-06T14:29:36,767 self._finalize_license_expression() 2026-02-06T14:29:36,768 C compiler: 2026-02-06T14:29:36,769 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-02-06T14:29:36,770 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-02-06T14:29:36,770 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-02-06T14:29:36,771 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-02-06T14:29:36,772 Attempting to autodetect NEON support... Did not detect NEON support 2026-02-06T14:29:36,774 running egg_info 2026-02-06T14:29:36,783 writing mdtraj.egg-info/PKG-INFO 2026-02-06T14:29:36,791 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2026-02-06T14:29:36,794 writing entry points to mdtraj.egg-info/entry_points.txt 2026-02-06T14:29:36,798 writing requirements to mdtraj.egg-info/requires.txt 2026-02-06T14:29:36,800 writing top-level names to mdtraj.egg-info/top_level.txt 2026-02-06T14:29:36,847 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-02-06T14:29:36,894 reading manifest template 'MANIFEST.in' 2026-02-06T14:29:37,701 no previously-included directories found matching '__pycache__' 2026-02-06T14:29:37,703 no previously-included directories found matching '*.pyc' 2026-02-06T14:29:37,705 adding license file 'LICENSE' 2026-02-06T14:29:37,720 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-02-06T14:29:37,871 Getting requirements to build wheel: finished with status 'done' 2026-02-06T14:29:37,876 Created temporary directory: /tmp/pip-modern-metadata-oduehj4v 2026-02-06T14:29:37,879 Preparing metadata (pyproject.toml): started 2026-02-06T14:29:37,880 Running command Preparing metadata (pyproject.toml) 2026-02-06T14:29:38,812 Using built-in specs. 2026-02-06T14:29:38,813 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-02-06T14:29:38,814 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-02-06T14:29:38,815 Target: arm-linux-gnueabihf 2026-02-06T14:29:38,815 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1+deb12u1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2026-02-06T14:29:38,816 Thread model: posix 2026-02-06T14:29:38,818 Supported LTO compression algorithms: zlib zstd 2026-02-06T14:29:38,819 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-02-06T14:29:44,057 /tmp/pip-wheel-up4ec8aj/mdtraj_160d935c08bd413c943605666224f074/basesetup.py:483: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-oduehj4v --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2026-02-06T14:29:44,058 warnings.warn( 2026-02-06T14:29:48,223 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-06T14:29:48,224 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-06T14:29:48,225 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-06T14:30:13,854 C compiler: 2026-02-06T14:30:13,854 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-02-06T14:30:13,855 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-02-06T14:30:13,856 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-02-06T14:30:13,857 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-02-06T14:30:13,857 Attempting to autodetect NEON support... Did not detect NEON support 2026-02-06T14:30:13,859 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2026-02-06T14:30:13,860 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2026-02-06T14:30:13,860 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2026-02-06T14:30:13,861 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2026-02-06T14:30:13,862 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2026-02-06T14:30:13,862 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2026-02-06T14:30:13,863 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2026-02-06T14:30:13,864 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2026-02-06T14:30:13,865 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2026-02-06T14:30:13,866 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2026-02-06T14:30:13,912 /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-06T14:30:13,913 !! 2026-02-06T14:30:13,915 ******************************************************************************** 2026-02-06T14:30:13,915 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-06T14:30:13,916 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-02-06T14:30:13,918 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-06T14:30:13,918 ******************************************************************************** 2026-02-06T14:30:13,920 !! 2026-02-06T14:30:13,920 self._finalize_license_expression() 2026-02-06T14:30:13,938 running dist_info 2026-02-06T14:30:13,950 creating /tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info 2026-02-06T14:30:13,951 writing /tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info/PKG-INFO 2026-02-06T14:30:13,961 writing dependency_links to /tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info/dependency_links.txt 2026-02-06T14:30:13,963 writing entry points to /tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info/entry_points.txt 2026-02-06T14:30:13,967 writing requirements to /tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info/requires.txt 2026-02-06T14:30:13,969 writing top-level names to /tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info/top_level.txt 2026-02-06T14:30:13,972 writing manifest file '/tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info/SOURCES.txt' 2026-02-06T14:30:14,032 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,033 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,034 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,035 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,036 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,038 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,039 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,040 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,041 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,042 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,045 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,046 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,047 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,048 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,049 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,051 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,052 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,053 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,054 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,055 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,057 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,058 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,059 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,060 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,060 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,063 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,064 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,065 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,066 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,066 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,070 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,071 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,072 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,073 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,074 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:30:14,095 reading manifest file '/tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info/SOURCES.txt' 2026-02-06T14:30:14,098 reading manifest template 'MANIFEST.in' 2026-02-06T14:30:14,872 no previously-included directories found matching '__pycache__' 2026-02-06T14:30:14,873 no previously-included directories found matching '*.pyc' 2026-02-06T14:30:14,874 adding license file 'LICENSE' 2026-02-06T14:30:14,887 writing manifest file '/tmp/pip-modern-metadata-oduehj4v/mdtraj.egg-info/SOURCES.txt' 2026-02-06T14:30:14,897 creating '/tmp/pip-modern-metadata-oduehj4v/mdtraj-1.11.1.dist-info' 2026-02-06T14:30:16,818 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-06T14:30:16,824 Source in /tmp/pip-wheel-up4ec8aj/mdtraj_160d935c08bd413c943605666224f074 has version 1.11.1, which satisfies requirement mdtraj==1.11.1 from https://files.pythonhosted.org/packages/f5/75/a17b14d28f1f1f87cfd8b823fc9822c0a4f861ff36f93f22afe8bf1977fa/mdtraj-1.11.1.tar.gz 2026-02-06T14:30:16,825 Removed mdtraj==1.11.1 from https://files.pythonhosted.org/packages/f5/75/a17b14d28f1f1f87cfd8b823fc9822c0a4f861ff36f93f22afe8bf1977fa/mdtraj-1.11.1.tar.gz from build tracker '/tmp/pip-build-tracker-96u9uwjt' 2026-02-06T14:30:16,832 Created temporary directory: /tmp/pip-unpack-dgwoc6f1 2026-02-06T14:30:16,833 Building wheels for collected packages: mdtraj 2026-02-06T14:30:16,838 Created temporary directory: /tmp/pip-wheel-civfdpfv 2026-02-06T14:30:16,839 Destination directory: /tmp/pip-wheel-civfdpfv 2026-02-06T14:30:16,842 Building wheel for mdtraj (pyproject.toml): started 2026-02-06T14:30:16,843 Running command Building wheel for mdtraj (pyproject.toml) 2026-02-06T14:30:17,745 Using built-in specs. 2026-02-06T14:30:17,746 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-02-06T14:30:17,747 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-02-06T14:30:17,749 Target: arm-linux-gnueabihf 2026-02-06T14:30:17,749 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1+deb12u1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2026-02-06T14:30:17,750 Thread model: posix 2026-02-06T14:30:17,751 Supported LTO compression algorithms: zlib zstd 2026-02-06T14:30:17,752 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-02-06T14:30:26,642 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-06T14:30:26,643 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-06T14:30:26,644 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-06T14:30:52,016 C compiler: 2026-02-06T14:30:52,017 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-02-06T14:30:52,018 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-02-06T14:30:52,018 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-02-06T14:30:52,019 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-02-06T14:30:52,020 Attempting to autodetect NEON support... Did not detect NEON support 2026-02-06T14:30:52,021 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2026-02-06T14:30:52,022 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2026-02-06T14:30:52,022 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2026-02-06T14:30:52,023 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2026-02-06T14:30:52,023 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2026-02-06T14:30:52,024 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2026-02-06T14:30:52,025 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2026-02-06T14:30:52,026 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2026-02-06T14:30:52,026 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2026-02-06T14:30:52,027 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2026-02-06T14:30:52,071 /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-06T14:30:52,072 !! 2026-02-06T14:30:52,073 ******************************************************************************** 2026-02-06T14:30:52,074 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-06T14:30:52,075 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-02-06T14:30:52,077 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-06T14:30:52,078 ******************************************************************************** 2026-02-06T14:30:52,079 !! 2026-02-06T14:30:52,080 self._finalize_license_expression() 2026-02-06T14:30:52,095 running bdist_wheel 2026-02-06T14:30:52,124 running build 2026-02-06T14:30:52,125 running build_py 2026-02-06T14:30:52,135 creating build/lib.linux-armv7l-cpython-311/mdtraj 2026-02-06T14:30:52,138 copying mdtraj/_version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-02-06T14:30:52,141 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-02-06T14:30:52,144 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-02-06T14:30:52,149 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,151 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,155 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,159 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,163 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,167 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,170 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,173 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,177 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,180 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,184 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,187 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,191 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,195 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,199 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,202 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,206 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,209 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-06T14:30:52,214 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,216 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,220 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,223 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,227 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,230 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,233 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,236 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,240 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-06T14:30:52,244 creating build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,245 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,249 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,252 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,256 copying mdtraj/geometry/pi_stacking.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,259 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,262 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,267 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,271 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,274 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,278 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,508 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,511 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,515 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,518 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,522 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,525 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-06T14:30:52,529 creating build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-06T14:30:52,531 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-06T14:30:52,535 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-06T14:30:52,539 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-06T14:30:52,543 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-06T14:30:52,546 creating build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-02-06T14:30:52,548 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-02-06T14:30:52,551 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-02-06T14:30:52,555 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-02-06T14:30:52,559 creating build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-06T14:30:52,561 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-06T14:30:52,564 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-06T14:30:52,567 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-06T14:30:52,570 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-06T14:30:52,573 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-06T14:30:52,577 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-06T14:30:52,581 creating build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-06T14:30:52,583 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-06T14:30:52,588 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-06T14:30:52,594 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-06T14:30:52,598 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-06T14:30:52,600 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-06T14:30:52,604 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-06T14:30:52,608 creating build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-02-06T14:30:52,610 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-02-06T14:30:52,613 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-02-06T14:30:52,616 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-02-06T14:30:52,620 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-02-06T14:30:52,622 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-02-06T14:30:52,625 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-02-06T14:30:52,630 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-02-06T14:30:52,635 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-06T14:30:52,637 copying mdtraj/formats/pdbx/pdbx.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-06T14:30:52,641 copying mdtraj/formats/pdbx/pdbxfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-06T14:30:52,645 copying mdtraj/formats/pdbx/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-06T14:30:52,648 copying mdtraj/formats/pdbx/PdbxContainers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-06T14:30:52,652 copying mdtraj/formats/pdbx/PdbxReader.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-06T14:30:52,657 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,659 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,663 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,666 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,670 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,673 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,677 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,680 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,684 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,687 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,691 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,694 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,698 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,701 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-06T14:30:52,712 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-02-06T14:30:52,714 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-02-06T14:30:52,719 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-02-06T14:30:52,733 UPDATING build/lib.linux-armv7l-cpython-311/mdtraj/_version.py 2026-02-06T14:30:52,734 set build/lib.linux-armv7l-cpython-311/mdtraj/_version.py to '1.11.1' 2026-02-06T14:30:52,735 running build_ext 2026-02-06T14:30:52,739 building 'mdtraj.formats.xtc' extension 2026-02-06T14:30:52,741 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src 2026-02-06T14:30:52,746 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:30:52,903 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:30:53,101 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2026-02-06T14:30:53,103 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:30:53,104 788 | int smallnum, smaller, larger, i, is_smaller, run; 2026-02-06T14:30:53,105 | ^~~~~~ 2026-02-06T14:30:53,105 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:30:53,106 785 | int smallidx, minidx, maxidx; 2026-02-06T14:30:53,106 | ^~~~~~ 2026-02-06T14:30:53,117 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2026-02-06T14:30:53,118 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:30:53,119 1016 | int errval=1; 2026-02-06T14:30:53,120 | ^~~~~~ 2026-02-06T14:30:53,127 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2026-02-06T14:30:53,128 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:30:53,129 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2026-02-06T14:30:53,130 | ^~~~~~ 2026-02-06T14:30:53,131 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:30:53,132 1302 | int smallidx, minidx, maxidx; 2026-02-06T14:30:53,132 | ^~~~~~ 2026-02-06T14:30:53,144 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2026-02-06T14:30:53,146 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:30:53,147 1509 | int errval=1; 2026-02-06T14:30:53,148 | ^~~~~~ 2026-02-06T14:30:56,271 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:30:56,367 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2026-02-06T14:30:56,368 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 2026-02-06T14:30:56,369 66 | int i,j,result; 2026-02-06T14:30:56,370 | ^ 2026-02-06T14:30:56,370 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 2026-02-06T14:30:56,371 66 | int i,j,result; 2026-02-06T14:30:56,372 | ^ 2026-02-06T14:30:56,373 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2026-02-06T14:30:56,373 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2026-02-06T14:30:56,374 119 | if (NULL == xd) 2026-02-06T14:30:56,375 | ^~ 2026-02-06T14:30:56,376 mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2026-02-06T14:30:56,377 122 | do { 2026-02-06T14:30:56,377 | ^~ 2026-02-06T14:30:56,547 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:31:08,469 In function ‘__Pyx_PyLong_From_int’, 2026-02-06T14:31:08,470 inlined from ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’ at mdtraj/formats/xtc/xtc.c:13181:16, 2026-02-06T14:31:08,471 inlined from ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’ at mdtraj/formats/xtc/xtc.c:12867:13: 2026-02-06T14:31:08,497 mdtraj/formats/xtc/xtc.c:25414:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:08,498 25414 | return PyLong_FromLong((long) value); 2026-02-06T14:31:08,498 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:08,499 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’: 2026-02-06T14:31:08,512 mdtraj/formats/xtc/xtc.c:12889:7: note: ‘__pyx_v_status’ was declared here 2026-02-06T14:31:08,513 12889 | int __pyx_v_status; 2026-02-06T14:31:08,513 | ^~~~~~~~~~~~~~ 2026-02-06T14:31:19,833 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2026-02-06T14:31:19,845 mdtraj/formats/xtc/xtc.c:11337:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:19,845 11337 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; 2026-02-06T14:31:19,846 | ^ 2026-02-06T14:31:19,856 mdtraj/formats/xtc/xtc.c:9607:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 2026-02-06T14:31:19,856 9607 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-02-06T14:31:19,857 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:19,868 mdtraj/formats/xtc/xtc.c:11333:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:19,868 11333 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; 2026-02-06T14:31:19,869 | ^ 2026-02-06T14:31:19,878 mdtraj/formats/xtc/xtc.c:9607:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 2026-02-06T14:31:19,879 9607 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-02-06T14:31:19,880 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:19,890 mdtraj/formats/xtc/xtc.c:11329:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:19,891 11329 | } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-06T14:31:19,892 | ^ 2026-02-06T14:31:19,901 mdtraj/formats/xtc/xtc.c:9607:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 2026-02-06T14:31:19,902 9607 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-02-06T14:31:19,903 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:19,913 mdtraj/formats/xtc/xtc.c:11289:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:19,914 11289 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-06T14:31:19,915 | ^ 2026-02-06T14:31:19,924 mdtraj/formats/xtc/xtc.c:9603:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 2026-02-06T14:31:19,925 9603 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; 2026-02-06T14:31:19,926 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:19,936 mdtraj/formats/xtc/xtc.c:11271:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:19,937 11271 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-06T14:31:19,938 | ^ 2026-02-06T14:31:19,947 mdtraj/formats/xtc/xtc.c:9599:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 2026-02-06T14:31:19,948 9599 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; 2026-02-06T14:31:19,949 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:19,959 mdtraj/formats/xtc/xtc.c:11347:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:19,960 11347 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-06T14:31:19,961 | ^ 2026-02-06T14:31:19,970 mdtraj/formats/xtc/xtc.c:9595:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 2026-02-06T14:31:19,971 9595 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; 2026-02-06T14:31:19,971 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:19,982 mdtraj/formats/xtc/xtc.c:11309:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:19,983 11309 | } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; 2026-02-06T14:31:19,983 | ^ 2026-02-06T14:31:19,993 mdtraj/formats/xtc/xtc.c:9589:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 2026-02-06T14:31:19,993 9589 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-02-06T14:31:19,994 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:20,005 mdtraj/formats/xtc/xtc.c:11305:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:20,005 11305 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; 2026-02-06T14:31:20,006 | ^ 2026-02-06T14:31:20,015 mdtraj/formats/xtc/xtc.c:9589:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 2026-02-06T14:31:20,016 9589 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-02-06T14:31:20,017 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:20,027 mdtraj/formats/xtc/xtc.c:11301:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:20,028 11301 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-06T14:31:20,029 | ^ 2026-02-06T14:31:20,038 mdtraj/formats/xtc/xtc.c:9589:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 2026-02-06T14:31:20,039 9589 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-02-06T14:31:20,040 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:20,050 mdtraj/formats/xtc/xtc.c:10959:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:20,051 10959 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; 2026-02-06T14:31:20,051 | ^ 2026-02-06T14:31:20,061 mdtraj/formats/xtc/xtc.c:9591:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 2026-02-06T14:31:20,062 9591 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2026-02-06T14:31:20,062 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:20,072 mdtraj/formats/xtc/xtc.c:10955:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:20,073 10955 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-06T14:31:20,074 | ^ 2026-02-06T14:31:20,084 mdtraj/formats/xtc/xtc.c:9591:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 2026-02-06T14:31:20,084 9591 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2026-02-06T14:31:20,085 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:29,663 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:31:29,885 building 'mdtraj.formats.trr' extension 2026-02-06T14:31:29,885 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:31:30,029 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:31:30,213 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2026-02-06T14:31:30,214 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:31:30,214 788 | int smallnum, smaller, larger, i, is_smaller, run; 2026-02-06T14:31:30,215 | ^~~~~~ 2026-02-06T14:31:30,216 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:31:30,217 785 | int smallidx, minidx, maxidx; 2026-02-06T14:31:30,218 | ^~~~~~ 2026-02-06T14:31:30,227 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2026-02-06T14:31:30,228 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:31:30,228 1016 | int errval=1; 2026-02-06T14:31:30,229 | ^~~~~~ 2026-02-06T14:31:30,235 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2026-02-06T14:31:30,236 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:31:30,237 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2026-02-06T14:31:30,238 | ^~~~~~ 2026-02-06T14:31:30,239 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:31:30,240 1302 | int smallidx, minidx, maxidx; 2026-02-06T14:31:30,240 | ^~~~~~ 2026-02-06T14:31:30,252 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2026-02-06T14:31:30,253 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-02-06T14:31:30,254 1509 | int errval=1; 2026-02-06T14:31:30,255 | ^~~~~~ 2026-02-06T14:31:33,484 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:31:34,457 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:31:47,369 In function ‘__Pyx_PyLong_From_int’, 2026-02-06T14:31:47,370 inlined from ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’ at mdtraj/formats/xtc/trr.c:15162:16, 2026-02-06T14:31:47,371 inlined from ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write’ at mdtraj/formats/xtc/trr.c:14592:13: 2026-02-06T14:31:47,398 mdtraj/formats/xtc/trr.c:27354:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:31:47,399 27354 | return PyLong_FromLong((long) value); 2026-02-06T14:31:47,400 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:31:47,400 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write’: 2026-02-06T14:31:47,414 mdtraj/formats/xtc/trr.c:14622:7: note: ‘__pyx_v_status’ was declared here 2026-02-06T14:31:47,415 14622 | int __pyx_v_status; 2026-02-06T14:31:47,416 | ^~~~~~~~~~~~~~ 2026-02-06T14:32:01,113 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2026-02-06T14:32:01,125 mdtraj/formats/xtc/trr.c:11932:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,126 11932 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_6 = 2; 2026-02-06T14:32:01,127 | ^ 2026-02-06T14:32:01,136 mdtraj/formats/xtc/trr.c:10252:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2026-02-06T14:32:01,137 10252 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-02-06T14:32:01,138 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,148 mdtraj/formats/xtc/trr.c:11928:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,149 11928 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-06T14:32:01,150 | ^ 2026-02-06T14:32:01,160 mdtraj/formats/xtc/trr.c:10252:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2026-02-06T14:32:01,161 10252 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-02-06T14:32:01,162 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,163 mdtraj/formats/xtc/trr.c:2610:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,164 2610 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2026-02-06T14:32:01,165 | ^ 2026-02-06T14:32:01,174 mdtraj/formats/xtc/trr.c:10252:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2026-02-06T14:32:01,175 10252 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-02-06T14:32:01,176 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,186 mdtraj/formats/xtc/trr.c:11922:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,187 11922 | __pyx_t_15 += __pyx_pybuffernd_forces.diminfo[0].shape; 2026-02-06T14:32:01,187 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2026-02-06T14:32:01,197 mdtraj/formats/xtc/trr.c:10252:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2026-02-06T14:32:01,198 10252 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-02-06T14:32:01,198 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,210 mdtraj/formats/xtc/trr.c:11875:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,210 11875 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_6 = 2; 2026-02-06T14:32:01,211 | ^ 2026-02-06T14:32:01,221 mdtraj/formats/xtc/trr.c:10268:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2026-02-06T14:32:01,221 10268 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-02-06T14:32:01,222 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,232 mdtraj/formats/xtc/trr.c:11871:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,233 11871 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-06T14:32:01,234 | ^ 2026-02-06T14:32:01,243 mdtraj/formats/xtc/trr.c:10268:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2026-02-06T14:32:01,244 10268 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-02-06T14:32:01,245 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,246 mdtraj/formats/xtc/trr.c:2610:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,247 2610 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2026-02-06T14:32:01,248 | ^ 2026-02-06T14:32:01,257 mdtraj/formats/xtc/trr.c:10268:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2026-02-06T14:32:01,258 10268 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-02-06T14:32:01,258 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,269 mdtraj/formats/xtc/trr.c:11865:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,269 11865 | __pyx_t_15 += __pyx_pybuffernd_vel.diminfo[0].shape; 2026-02-06T14:32:01,270 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2026-02-06T14:32:01,280 mdtraj/formats/xtc/trr.c:10268:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2026-02-06T14:32:01,280 10268 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-02-06T14:32:01,281 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,292 mdtraj/formats/xtc/trr.c:12264:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,293 12264 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-06T14:32:01,293 | ^ 2026-02-06T14:32:01,303 mdtraj/formats/xtc/trr.c:10274:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2026-02-06T14:32:01,304 10274 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2026-02-06T14:32:01,305 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,315 mdtraj/formats/xtc/trr.c:12260:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,317 12260 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-02-06T14:32:01,317 | ^ 2026-02-06T14:32:01,327 mdtraj/formats/xtc/trr.c:10274:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2026-02-06T14:32:01,327 10274 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2026-02-06T14:32:01,328 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,339 mdtraj/formats/xtc/trr.c:12105:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,339 12105 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-06T14:32:01,340 | ^ 2026-02-06T14:32:01,349 mdtraj/formats/xtc/trr.c:10270:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2026-02-06T14:32:01,350 10270 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2026-02-06T14:32:01,351 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,361 mdtraj/formats/xtc/trr.c:12101:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,362 12101 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-02-06T14:32:01,363 | ^ 2026-02-06T14:32:01,372 mdtraj/formats/xtc/trr.c:10270:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2026-02-06T14:32:01,373 10270 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2026-02-06T14:32:01,374 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,385 mdtraj/formats/xtc/trr.c:12157:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,385 12157 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-06T14:32:01,386 | ^ 2026-02-06T14:32:01,396 mdtraj/formats/xtc/trr.c:10254:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2026-02-06T14:32:01,396 10254 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2026-02-06T14:32:01,397 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:01,408 mdtraj/formats/xtc/trr.c:12153:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:01,409 12153 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-02-06T14:32:01,409 | ^ 2026-02-06T14:32:01,419 mdtraj/formats/xtc/trr.c:10254:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2026-02-06T14:32:01,420 10254 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2026-02-06T14:32:01,421 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:11,229 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:32:11,419 building 'mdtraj.formats.dcd' extension 2026-02-06T14:32:11,420 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd 2026-02-06T14:32:11,422 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src 2026-02-06T14:32:11,423 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:32:25,146 In function ‘__Pyx_PyLong_From_int’, 2026-02-06T14:32:25,146 inlined from ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’ at mdtraj/formats/dcd/dcd.c:9971:19: 2026-02-06T14:32:25,166 mdtraj/formats/dcd/dcd.c:19224:22: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:32:25,167 19224 | return PyLong_FromLong((long) value); 2026-02-06T14:32:25,168 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:25,168 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2026-02-06T14:32:25,175 mdtraj/formats/dcd/dcd.c:8619:7: note: ‘__pyx_v_i’ was declared here 2026-02-06T14:32:25,176 8619 | int __pyx_v_i; 2026-02-06T14:32:25,177 | ^~~~~~~~~ 2026-02-06T14:32:30,060 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:32:30,363 mdtraj/formats/dcd/src/dcdplugin.c: In function ‘open_dcd_read’: 2026-02-06T14:32:30,364 mdtraj/formats/dcd/src/dcdplugin.c:903:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘fio_size_t’ {aka ‘long long int’} [-Wformat=] 2026-02-06T14:32:30,365 903 | printf("dcdplugin) Warning: DCD header claims %d frames, but \n" 2026-02-06T14:32:30,366 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:30,366 ...... 2026-02-06T14:32:30,367 906 | dcd->nsets, trjsize, newnsets, framesize); 2026-02-06T14:32:30,368 | ~~~~~~~ 2026-02-06T14:32:30,369 | | 2026-02-06T14:32:30,370 | fio_size_t {aka long long int} 2026-02-06T14:32:30,371 mdtraj/formats/dcd/src/dcdplugin.c:904:39: note: format string is defined here 2026-02-06T14:32:30,371 904 | "dcdplugin) file size (%ld) indicates there are actually \n" 2026-02-06T14:32:30,372 | ~~^ 2026-02-06T14:32:30,373 | | 2026-02-06T14:32:30,374 | long int 2026-02-06T14:32:30,375 | %lld 2026-02-06T14:32:30,376 mdtraj/formats/dcd/src/dcdplugin.c:903:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘fio_size_t’ {aka ‘long long int’} [-Wformat=] 2026-02-06T14:32:30,377 903 | printf("dcdplugin) Warning: DCD header claims %d frames, but \n" 2026-02-06T14:32:30,379 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:32:30,380 ...... 2026-02-06T14:32:30,381 906 | dcd->nsets, trjsize, newnsets, framesize); 2026-02-06T14:32:30,382 | ~~~~~~~~~ 2026-02-06T14:32:30,382 | | 2026-02-06T14:32:30,383 | fio_size_t {aka long long int} 2026-02-06T14:32:30,384 mdtraj/formats/dcd/src/dcdplugin.c:905:36: note: format string is defined here 2026-02-06T14:32:30,385 905 | "%d frames of size (%ld)\n", 2026-02-06T14:32:30,386 | ~~^ 2026-02-06T14:32:30,387 | | 2026-02-06T14:32:30,387 | long int 2026-02-06T14:32:30,388 | %lld 2026-02-06T14:32:32,042 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:32:32,207 building 'mdtraj.formats.dtr' extension 2026-02-06T14:32:32,208 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr 2026-02-06T14:32:32,210 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src 2026-02-06T14:32:32,211 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:32:54,423 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:32:57,677 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2026-02-06T14:32:57,678 mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-02-06T14:32:57,679 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2026-02-06T14:32:57,680 | ~~^ ~ 2026-02-06T14:32:57,681 | | | 2026-02-06T14:32:57,682 | | size_t {aka unsigned int} 2026-02-06T14:32:57,683 | long int 2026-02-06T14:32:57,683 | %d 2026-02-06T14:32:57,684 mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-06T14:32:57,685 487 | printf("size %d framesize %d\n\n", 2026-02-06T14:32:57,686 | ~^ 2026-02-06T14:32:57,687 | | 2026-02-06T14:32:57,688 | int 2026-02-06T14:32:57,689 | %lld 2026-02-06T14:32:57,690 488 | keys[i].size(), m_framesize); 2026-02-06T14:32:57,691 | ~~~~~~~~~~~~~~ 2026-02-06T14:32:57,692 | | 2026-02-06T14:32:57,693 | uint64_t {aka long long unsigned int} 2026-02-06T14:32:57,694 mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-06T14:32:57,695 487 | printf("size %d framesize %d\n\n", 2026-02-06T14:32:57,695 | ~^ 2026-02-06T14:32:57,696 | | 2026-02-06T14:32:57,697 | int 2026-02-06T14:32:57,698 | %lld 2026-02-06T14:32:57,698 488 | keys[i].size(), m_framesize); 2026-02-06T14:32:57,699 | ~~~~~~~~~~~ 2026-02-06T14:32:57,700 | | 2026-02-06T14:32:57,701 | uint64_t {aka long long unsigned int} 2026-02-06T14:32:57,701 mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-02-06T14:32:57,702 494 | "non-constant time interval at frame %ld\n", i); 2026-02-06T14:32:57,703 | ~~^ ~ 2026-02-06T14:32:57,703 | | | 2026-02-06T14:32:57,704 | | size_t {aka unsigned int} 2026-02-06T14:32:57,705 | long int 2026-02-06T14:32:57,706 | %d 2026-02-06T14:32:57,706 mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-02-06T14:32:57,707 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2026-02-06T14:32:57,708 | ~~^ ~ 2026-02-06T14:32:57,709 | | | 2026-02-06T14:32:57,710 | | size_t {aka unsigned int} 2026-02-06T14:32:57,711 | long int 2026-02-06T14:32:57,712 | %d 2026-02-06T14:32:57,915 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2026-02-06T14:32:57,916 mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-06T14:32:57,917 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2026-02-06T14:32:57,918 | ~~^ 2026-02-06T14:32:57,919 | | 2026-02-06T14:32:57,919 | long int 2026-02-06T14:32:57,920 | %lld 2026-02-06T14:32:57,921 1302 | 3*natoms, pos.count); 2026-02-06T14:32:57,922 | ~~~~~~~~~ 2026-02-06T14:32:57,923 | | 2026-02-06T14:32:57,924 | uint64_t {aka long long unsigned int} 2026-02-06T14:32:57,925 mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-06T14:32:57,926 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2026-02-06T14:32:57,927 | ~~^ 2026-02-06T14:32:57,928 | | 2026-02-06T14:32:57,928 | long int 2026-02-06T14:32:57,929 | %lld 2026-02-06T14:32:57,930 1311 | 3*natoms, vel.count); 2026-02-06T14:32:57,930 | ~~~~~~~~~ 2026-02-06T14:32:57,931 | | 2026-02-06T14:32:57,932 | uint64_t {aka long long unsigned int} 2026-02-06T14:32:57,963 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2026-02-06T14:32:57,964 mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-06T14:32:57,965 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2026-02-06T14:32:57,966 | ~~^ 2026-02-06T14:32:57,966 | | 2026-02-06T14:32:57,967 | long int 2026-02-06T14:32:57,968 | %lld 2026-02-06T14:32:57,968 1573 | velblob.count, 3*natoms); 2026-02-06T14:32:57,969 | ~~~~~~~~~~~~~ 2026-02-06T14:32:57,970 | | 2026-02-06T14:32:57,971 | uint64_t {aka long long unsigned int} 2026-02-06T14:32:59,755 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2026-02-06T14:32:59,756 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2026-02-06T14:32:59,757 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2026-02-06T14:32:59,757 | ~~~~~~~~^~~~~ 2026-02-06T14:33:03,312 In file included from /usr/include/c++/12/map:60, 2026-02-06T14:33:03,313 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2026-02-06T14:33:03,313 /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2026-02-06T14:33:03,314 /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-06T14:33:03,315 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2026-02-06T14:33:03,316 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:03,402 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2026-02-06T14:33:03,403 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-06T14:33:03,404 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2026-02-06T14:33:03,405 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:03,477 In file included from /usr/include/c++/12/map:61: 2026-02-06T14:33:03,478 /usr/include/c++/12/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2026-02-06T14:33:03,479 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-06T14:33:03,480 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-02-06T14:33:03,480 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:03,481 531 | std::forward_as_tuple(std::move(__k)), 2026-02-06T14:33:03,482 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:03,483 532 | std::tuple<>()); 2026-02-06T14:33:03,484 | ~~~~~~~~~~~~~~~ 2026-02-06T14:33:03,600 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’, 2026-02-06T14:33:03,601 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28: 2026-02-06T14:33:03,602 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-06T14:33:03,603 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-02-06T14:33:03,604 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:03,605 531 | std::forward_as_tuple(std::move(__k)), 2026-02-06T14:33:03,606 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:03,607 532 | std::tuple<>()); 2026-02-06T14:33:03,607 | ~~~~~~~~~~~~~~~ 2026-02-06T14:33:04,646 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2026-02-06T14:33:04,647 mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2026-02-06T14:33:04,647 706 | sprintf(sub, "%03x/", i); 2026-02-06T14:33:04,648 | ^~~~ 2026-02-06T14:33:04,649 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2026-02-06T14:33:04,650 706 | sprintf(sub, "%03x/", i); 2026-02-06T14:33:04,650 | ^~~~~~~ 2026-02-06T14:33:04,651 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2026-02-06T14:33:04,652 706 | sprintf(sub, "%03x/", i); 2026-02-06T14:33:04,653 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2026-02-06T14:33:04,653 mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2026-02-06T14:33:04,654 714 | sprintf(subsub, "%03x", j); 2026-02-06T14:33:04,655 | ^~~~ 2026-02-06T14:33:04,655 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2026-02-06T14:33:04,656 714 | sprintf(subsub, "%03x", j); 2026-02-06T14:33:04,657 | ^~~~~~ 2026-02-06T14:33:04,658 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2026-02-06T14:33:04,659 714 | sprintf(subsub, "%03x", j); 2026-02-06T14:33:04,660 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:05,153 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2026-02-06T14:33:05,154 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-06T14:33:05,155 667 | sprintf(answer, "%03x/", d1); 2026-02-06T14:33:05,155 | ^ 2026-02-06T14:33:05,156 In function ‘std::string DDreldir(const std::string&, int, int)’, 2026-02-06T14:33:05,157 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2026-02-06T14:33:05,158 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2026-02-06T14:33:05,159 667 | sprintf(answer, "%03x/", d1); 2026-02-06T14:33:05,160 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:05,161 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2026-02-06T14:33:05,162 mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 2026-02-06T14:33:05,162 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-02-06T14:33:05,163 | ^~~~ 2026-02-06T14:33:05,164 In function ‘std::string DDreldir(const std::string&, int, int)’, 2026-02-06T14:33:05,165 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2026-02-06T14:33:05,166 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2026-02-06T14:33:05,167 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-02-06T14:33:05,168 | ^~~~~~~~~~~~ 2026-02-06T14:33:05,169 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2026-02-06T14:33:05,169 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-02-06T14:33:05,170 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:09,113 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’, 2026-02-06T14:33:09,114 inlined from ‘int desres::molfile::DtrReader::frame_from_bytes(const void*, uint64_t, molfile_timestep_t*) const’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1735:38: 2026-02-06T14:33:09,115 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-06T14:33:09,116 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-02-06T14:33:09,117 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:09,118 531 | std::forward_as_tuple(std::move(__k)), 2026-02-06T14:33:09,119 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-06T14:33:09,120 532 | std::tuple<>()); 2026-02-06T14:33:09,120 | ~~~~~~~~~~~~~~~ 2026-02-06T14:33:15,119 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:33:15,559 building 'mdtraj._rmsd' extension 2026-02-06T14:33:15,560 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd 2026-02-06T14:33:15,561 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src 2026-02-06T14:33:15,563 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:13,475 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:13,723 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:14,038 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:14,956 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:34:15,586 building 'mdtraj._lprmsd' extension 2026-02-06T14:34:15,588 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:49,259 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:52,953 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:53,194 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:54,837 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:55,219 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:55,528 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:34:56,442 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:34:56,812 building 'mdtraj.core.lib.libtheobald' extension 2026-02-06T14:34:56,813 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2026-02-06T14:34:57,726 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2026-02-06T14:34:57,967 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o 2026-02-06T14:34:58,008 building 'mdtraj.geometry._geometry' extension 2026-02-06T14:34:58,009 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src 2026-02-06T14:34:58,012 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:35:45,961 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:36:03,329 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:36:08,427 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:36:09,840 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:36:10,302 building 'mdtraj.geometry.drid' extension 2026-02-06T14:36:10,303 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:36:49,641 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:36:50,487 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:36:50,618 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:36:50,985 building 'mdtraj.geometry.neighbors' extension 2026-02-06T14:36:50,986 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:37:27,991 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:37:29,722 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:37:30,114 building 'mdtraj.geometry.neighborlist' extension 2026-02-06T14:37:30,115 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:38:04,210 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-06T14:38:09,824 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2026-02-06T14:38:09,825 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2026-02-06T14:38:09,826 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:38:09,826 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2026-02-06T14:38:09,827 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-02-06T14:38:09,828 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2026-02-06T14:38:09,829 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-02-06T14:38:09,830 341 | float periodicBoxVectors[3][3]; 2026-02-06T14:38:09,831 | ^~~~~~~~~~~~~~~~~~ 2026-02-06T14:38:09,832 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2026-02-06T14:38:09,833 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2026-02-06T14:38:09,834 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:38:09,834 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2026-02-06T14:38:09,835 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-02-06T14:38:09,836 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2026-02-06T14:38:09,836 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-02-06T14:38:09,837 341 | float periodicBoxVectors[3][3]; 2026-02-06T14:38:09,838 | ^~~~~~~~~~~~~~~~~~ 2026-02-06T14:38:09,839 mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:38:09,839 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); 2026-02-06T14:38:09,840 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-02-06T14:38:09,841 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-02-06T14:38:09,842 341 | float periodicBoxVectors[3][3]; 2026-02-06T14:38:09,842 | ^~~~~~~~~~~~~~~~~~ 2026-02-06T14:38:09,843 mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-06T14:38:09,844 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); 2026-02-06T14:38:09,845 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-02-06T14:38:09,845 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-02-06T14:38:09,846 341 | float periodicBoxVectors[3][3]; 2026-02-06T14:38:09,847 | ^~~~~~~~~~~~~~~~~~ 2026-02-06T14:38:10,859 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so 2026-02-06T14:38:11,289 installing to build/bdist.linux-armv7l/wheel 2026-02-06T14:38:11,290 running install 2026-02-06T14:38:11,318 running install_lib 2026-02-06T14:38:11,333 creating build/bdist.linux-armv7l/wheel 2026-02-06T14:38:11,337 creating build/bdist.linux-armv7l/wheel/mdtraj 2026-02-06T14:38:11,340 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2026-02-06T14:38:11,343 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,427 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,431 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,435 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,488 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,492 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,496 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,499 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,502 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,507 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,510 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,515 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2026-02-06T14:38:11,518 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2026-02-06T14:38:11,520 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb/data 2026-02-06T14:38:11,524 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb/data 2026-02-06T14:38:11,529 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-02-06T14:38:11,532 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-02-06T14:38:11,537 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-02-06T14:38:11,542 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,546 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdbx 2026-02-06T14:38:11,548 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/pdbx.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-06T14:38:11,552 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/pdbxfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-06T14:38:11,556 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-06T14:38:11,559 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/PdbxContainers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-06T14:38:11,563 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/PdbxReader.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-06T14:38:11,567 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,623 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,628 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,632 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,636 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,639 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,643 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,646 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,709 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-06T14:38:11,716 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2026-02-06T14:38:11,718 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-06T14:38:11,722 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2026-02-06T14:38:11,724 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,728 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,732 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,736 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,740 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,744 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,748 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,751 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,755 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,759 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,762 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,766 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,769 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-06T14:38:11,772 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-06T14:38:11,776 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-06T14:38:11,780 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-06T14:38:11,784 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-06T14:38:11,787 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-06T14:38:11,790 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-06T14:38:11,793 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-06T14:38:11,798 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2026-02-06T14:38:11,799 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,803 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,807 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,811 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,962 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/pi_stacking.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,967 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,970 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,974 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,978 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,982 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,985 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:11,989 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,055 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,113 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,116 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,119 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,124 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,128 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,131 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,239 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-06T14:38:12,242 copying build/lib.linux-armv7l-cpython-311/mdtraj/_version.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-06T14:38:12,246 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2026-02-06T14:38:12,248 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-02-06T14:38:12,252 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-02-06T14:38:12,256 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-02-06T14:38:12,260 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-02-06T14:38:12,263 copying build/lib.linux-armv7l-cpython-311/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-06T14:38:12,267 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2026-02-06T14:38:12,269 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-02-06T14:38:12,272 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-02-06T14:38:12,276 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-02-06T14:38:12,280 copying build/lib.linux-armv7l-cpython-311/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-06T14:38:12,284 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2026-02-06T14:38:12,286 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-06T14:38:12,290 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-06T14:38:12,293 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-06T14:38:12,296 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-06T14:38:12,299 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-06T14:38:12,303 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-06T14:38:12,308 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2026-02-06T14:38:12,310 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-06T14:38:12,316 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-06T14:38:12,323 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-06T14:38:12,328 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-06T14:38:12,331 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-06T14:38:12,335 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-06T14:38:12,340 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2026-02-06T14:38:12,341 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-02-06T14:38:12,347 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-02-06T14:38:12,350 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-02-06T14:38:12,365 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2026-02-06T14:38:12,367 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-02-06T14:38:12,371 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-02-06T14:38:12,374 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-02-06T14:38:12,378 copying build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-06T14:38:12,524 copying build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-06T14:38:12,571 running install_egg_info 2026-02-06T14:38:12,600 running egg_info 2026-02-06T14:38:12,611 writing mdtraj.egg-info/PKG-INFO 2026-02-06T14:38:12,619 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2026-02-06T14:38:12,622 writing entry points to mdtraj.egg-info/entry_points.txt 2026-02-06T14:38:12,626 writing requirements to mdtraj.egg-info/requires.txt 2026-02-06T14:38:12,628 writing top-level names to mdtraj.egg-info/top_level.txt 2026-02-06T14:38:12,679 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,680 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,681 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,682 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,683 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,686 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,687 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,688 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,689 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,690 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,694 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,695 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,696 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,696 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,697 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,700 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,701 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,702 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,703 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,704 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,706 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,708 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,708 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,709 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,710 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,713 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,714 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,715 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,716 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,717 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,721 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,722 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,723 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,724 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,724 dependency /tmp/pip-build-env-i6spiuz4/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-06T14:38:12,745 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-02-06T14:38:12,778 reading manifest template 'MANIFEST.in' 2026-02-06T14:38:13,626 no previously-included directories found matching '__pycache__' 2026-02-06T14:38:13,628 no previously-included directories found matching '*.pyc' 2026-02-06T14:38:13,630 adding license file 'LICENSE' 2026-02-06T14:38:13,647 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-02-06T14:38:13,657 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/./mdtraj-1.11.1-py3.11.egg-info 2026-02-06T14:38:13,676 running install_scripts 2026-02-06T14:38:13,742 creating build/bdist.linux-armv7l/wheel/mdtraj-1.11.1.dist-info/WHEEL 2026-02-06T14:38:13,747 creating '/tmp/pip-wheel-civfdpfv/.tmp-o394_djn/mdtraj-1.11.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-06T14:38:13,752 adding 'mdtraj/__init__.py' 2026-02-06T14:38:14,031 adding 'mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:14,495 adding 'mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:14,510 adding 'mdtraj/_version.py' 2026-02-06T14:38:14,513 adding 'mdtraj/io.py' 2026-02-06T14:38:14,516 adding 'mdtraj/core/__init__.py' 2026-02-06T14:38:14,519 adding 'mdtraj/core/element.py' 2026-02-06T14:38:14,523 adding 'mdtraj/core/residue_names.py' 2026-02-06T14:38:14,527 adding 'mdtraj/core/selection.py' 2026-02-06T14:38:14,537 adding 'mdtraj/core/topology.py' 2026-02-06T14:38:14,548 adding 'mdtraj/core/trajectory.py' 2026-02-06T14:38:14,552 adding 'mdtraj/core/lib/center.h' 2026-02-06T14:38:14,561 adding 'mdtraj/core/lib/libtheobald.a' 2026-02-06T14:38:14,564 adding 'mdtraj/core/lib/theobald_rmsd.h' 2026-02-06T14:38:14,567 adding 'mdtraj/formats/__init__.py' 2026-02-06T14:38:14,571 adding 'mdtraj/formats/amberrst.py' 2026-02-06T14:38:14,575 adding 'mdtraj/formats/arc.py' 2026-02-06T14:38:14,771 adding 'mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:15,253 adding 'mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:15,270 adding 'mdtraj/formats/gro.py' 2026-02-06T14:38:15,273 adding 'mdtraj/formats/gsd.py' 2026-02-06T14:38:15,280 adding 'mdtraj/formats/hdf5.py' 2026-02-06T14:38:15,282 adding 'mdtraj/formats/hoomdxml.py' 2026-02-06T14:38:15,286 adding 'mdtraj/formats/lammpstrj.py' 2026-02-06T14:38:15,290 adding 'mdtraj/formats/lh5.py' 2026-02-06T14:38:15,294 adding 'mdtraj/formats/mdcrd.py' 2026-02-06T14:38:15,297 adding 'mdtraj/formats/mol2.py' 2026-02-06T14:38:15,301 adding 'mdtraj/formats/netcdf.py' 2026-02-06T14:38:15,304 adding 'mdtraj/formats/openmmxml.py' 2026-02-06T14:38:15,306 adding 'mdtraj/formats/prmtop.py' 2026-02-06T14:38:15,309 adding 'mdtraj/formats/psf.py' 2026-02-06T14:38:15,312 adding 'mdtraj/formats/registry.py' 2026-02-06T14:38:15,645 adding 'mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:15,970 adding 'mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:15,981 adding 'mdtraj/formats/xyzfile.py' 2026-02-06T14:38:15,984 adding 'mdtraj/formats/pdb/__init__.py' 2026-02-06T14:38:15,990 adding 'mdtraj/formats/pdb/pdbfile.py' 2026-02-06T14:38:15,997 adding 'mdtraj/formats/pdb/pdbstructure.py' 2026-02-06T14:38:16,000 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2026-02-06T14:38:16,003 adding 'mdtraj/formats/pdb/data/residues.xml' 2026-02-06T14:38:16,009 adding 'mdtraj/formats/pdbx/PdbxContainers.py' 2026-02-06T14:38:16,013 adding 'mdtraj/formats/pdbx/PdbxReader.py' 2026-02-06T14:38:16,015 adding 'mdtraj/formats/pdbx/__init__.py' 2026-02-06T14:38:16,018 adding 'mdtraj/formats/pdbx/pdbx.py' 2026-02-06T14:38:16,023 adding 'mdtraj/formats/pdbx/pdbxfile.py' 2026-02-06T14:38:16,026 adding 'mdtraj/geometry/__init__.py' 2026-02-06T14:38:16,594 adding 'mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:16,613 adding 'mdtraj/geometry/alignment.py' 2026-02-06T14:38:16,616 adding 'mdtraj/geometry/angle.py' 2026-02-06T14:38:16,619 adding 'mdtraj/geometry/contact.py' 2026-02-06T14:38:16,623 adding 'mdtraj/geometry/dihedral.py' 2026-02-06T14:38:16,626 adding 'mdtraj/geometry/distance.py' 2026-02-06T14:38:16,976 adding 'mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:16,987 adding 'mdtraj/geometry/dssp.py' 2026-02-06T14:38:16,990 adding 'mdtraj/geometry/hbond.py' 2026-02-06T14:38:16,994 adding 'mdtraj/geometry/internal.py' 2026-02-06T14:38:17,343 adding 'mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:17,719 adding 'mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so' 2026-02-06T14:38:17,731 adding 'mdtraj/geometry/order.py' 2026-02-06T14:38:17,735 adding 'mdtraj/geometry/pi_stacking.py' 2026-02-06T14:38:17,738 adding 'mdtraj/geometry/rdf.py' 2026-02-06T14:38:17,740 adding 'mdtraj/geometry/rg.py' 2026-02-06T14:38:17,743 adding 'mdtraj/geometry/sasa.py' 2026-02-06T14:38:17,746 adding 'mdtraj/geometry/shape.py' 2026-02-06T14:38:17,748 adding 'mdtraj/geometry/thermodynamic_properties.py' 2026-02-06T14:38:17,751 adding 'mdtraj/nmr/__init__.py' 2026-02-06T14:38:17,754 adding 'mdtraj/nmr/scalar_couplings.py' 2026-02-06T14:38:17,757 adding 'mdtraj/nmr/shift_wrappers.py' 2026-02-06T14:38:17,760 adding 'mdtraj/reporters/__init__.py' 2026-02-06T14:38:17,762 adding 'mdtraj/reporters/basereporter.py' 2026-02-06T14:38:17,765 adding 'mdtraj/reporters/dcdreporter.py' 2026-02-06T14:38:17,768 adding 'mdtraj/reporters/hdf5reporter.py' 2026-02-06T14:38:17,770 adding 'mdtraj/reporters/netcdfreporter.py' 2026-02-06T14:38:17,773 adding 'mdtraj/reporters/xtcreporter.py' 2026-02-06T14:38:17,776 adding 'mdtraj/scripts/__init__.py' 2026-02-06T14:38:17,779 adding 'mdtraj/scripts/mdconvert.py' 2026-02-06T14:38:17,782 adding 'mdtraj/scripts/mdinspect.py' 2026-02-06T14:38:17,785 adding 'mdtraj/testing/__init__.py' 2026-02-06T14:38:17,789 adding 'mdtraj/testing/docscrape.py' 2026-02-06T14:38:17,791 adding 'mdtraj/testing/docstrings.py' 2026-02-06T14:38:17,794 adding 'mdtraj/testing/testing.py' 2026-02-06T14:38:17,797 adding 'mdtraj/utils/__init__.py' 2026-02-06T14:38:17,799 adding 'mdtraj/utils/contextmanagers.py' 2026-02-06T14:38:17,802 adding 'mdtraj/utils/delay_import.py' 2026-02-06T14:38:17,805 adding 'mdtraj/utils/rotation.py' 2026-02-06T14:38:17,807 adding 'mdtraj/utils/singleton.py' 2026-02-06T14:38:17,809 adding 'mdtraj/utils/unitcell.py' 2026-02-06T14:38:17,812 adding 'mdtraj/utils/validation.py' 2026-02-06T14:38:17,815 adding 'mdtraj/utils/zipped.py' 2026-02-06T14:38:17,818 adding 'mdtraj/utils/unit/__init__.py' 2026-02-06T14:38:17,821 adding 'mdtraj/utils/unit/basedimension.py' 2026-02-06T14:38:17,823 adding 'mdtraj/utils/unit/baseunit.py' 2026-02-06T14:38:17,826 adding 'mdtraj/utils/unit/constants.py' 2026-02-06T14:38:17,830 adding 'mdtraj/utils/unit/doctests.py' 2026-02-06T14:38:17,833 adding 'mdtraj/utils/unit/mymatrix.py' 2026-02-06T14:38:17,836 adding 'mdtraj/utils/unit/prefix.py' 2026-02-06T14:38:17,841 adding 'mdtraj/utils/unit/quantity.py' 2026-02-06T14:38:17,843 adding 'mdtraj/utils/unit/standard_dimensions.py' 2026-02-06T14:38:17,848 adding 'mdtraj/utils/unit/unit.py' 2026-02-06T14:38:17,851 adding 'mdtraj/utils/unit/unit_definitions.py' 2026-02-06T14:38:17,854 adding 'mdtraj/utils/unit/unit_math.py' 2026-02-06T14:38:17,857 adding 'mdtraj/utils/unit/unit_operators.py' 2026-02-06T14:38:17,864 adding 'mdtraj-1.11.1.dist-info/licenses/LICENSE' 2026-02-06T14:38:17,866 adding 'mdtraj-1.11.1.dist-info/METADATA' 2026-02-06T14:38:17,869 adding 'mdtraj-1.11.1.dist-info/WHEEL' 2026-02-06T14:38:17,871 adding 'mdtraj-1.11.1.dist-info/entry_points.txt' 2026-02-06T14:38:17,873 adding 'mdtraj-1.11.1.dist-info/top_level.txt' 2026-02-06T14:38:17,876 adding 'mdtraj-1.11.1.dist-info/RECORD' 2026-02-06T14:38:18,073 removing build/bdist.linux-armv7l/wheel 2026-02-06T14:38:20,032 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2026-02-06T14:38:20,422 Created wheel for mdtraj: filename=mdtraj-1.11.1-cp311-cp311-linux_armv7l.whl size=7021357 sha256=89d53c41aa8fac26da343918adc645291b034dc308db026e47c9396cded47e96 2026-02-06T14:38:20,423 Stored in directory: /tmp/pip-ephem-wheel-cache-l2gxfpp5/wheels/00/76/5a/328f54eceb2d93ac37767a157d7e9ecd4527f7f22a58f72ba1 2026-02-06T14:38:20,444 Successfully built mdtraj 2026-02-06T14:38:20,696 Removed build tracker: '/tmp/pip-build-tracker-96u9uwjt'