2026-07-09T08:27:13,541 Created temporary directory: /tmp/pip-ephem-wheel-cache-dn9my5rb 2026-07-09T08:27:13,543 Created temporary directory: /tmp/pip-build-tracker-wewecr3d 2026-07-09T08:27:13,543 Initialized build tracking at /tmp/pip-build-tracker-wewecr3d 2026-07-09T08:27:13,544 Created build tracker: /tmp/pip-build-tracker-wewecr3d 2026-07-09T08:27:13,544 Entered build tracker: /tmp/pip-build-tracker-wewecr3d 2026-07-09T08:27:13,545 Created temporary directory: /tmp/pip-wheel-h09hks37 2026-07-09T08:27:13,548 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 2026-07-09T08:27:13,550 Created temporary directory: /tmp/pip-ephem-wheel-cache-xhg7jnws 2026-07-09T08:27:13,573 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-09T08:27:13,576 2 location(s) to search for versions of mdtraj: 2026-07-09T08:27:13,576 * https://pypi.org/simple/mdtraj/ 2026-07-09T08:27:13,576 * https://www.piwheels.org/simple/mdtraj/ 2026-07-09T08:27:13,577 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2026-07-09T08:27:13,578 Getting page https://pypi.org/simple/mdtraj/ 2026-07-09T08:27:13,579 Found index url https://pypi.org/simple 2026-07-09T08:27:13,756 Fetched page https://pypi.org/simple/mdtraj/ as application/vnd.pypi.simple.v1+json 2026-07-09T08:27:13,791 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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(from https://www.piwheels.org/simple/mdtraj/) 2026-07-09T08:27:14,155 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv7l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2026-07-09T08:27:14,155 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv6l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2026-07-09T08:27:14,155 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2026-07-09T08:27:14,156 Skipping link: No binaries permitted for mdtraj: 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/tmp/pip-unpack-yt2vf8g6 2026-07-09T08:27:14,453 Downloading mdtraj-1.11.1.post2.tar.gz (2.7 MB) 2026-07-09T08:27:16,091 Added mdtraj==1.11.1.post2 from https://files.pythonhosted.org/packages/1a/6e/1e95f2e47056509bd7a4f397b367abbad5741b7cdccd7404b5dcf2d26e60/mdtraj-1.11.1.post2.tar.gz to build tracker '/tmp/pip-build-tracker-wewecr3d' 2026-07-09T08:27:16,107 Created temporary directory: /tmp/pip-build-env-pmfu936n 2026-07-09T08:27:16,112 Installing build dependencies: started 2026-07-09T08:27:16,114 Running command pip subprocess to install build dependencies 2026-07-09T08:27:17,298 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-07-09T08:27:17,785 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 2026-07-09T08:27:17,809 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-07-09T08:27:19,592 Collecting setuptools 2026-07-09T08:27:19,593 Obtaining dependency information for setuptools from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata 2026-07-09T08:27:19,613 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-07-09T08:27:19,719 Collecting versioneer[toml] 2026-07-09T08:27:19,720 Obtaining dependency information for versioneer[toml] from https://www.piwheels.org/simple/versioneer/versioneer-0.29-py3-none-any.whl.metadata 2026-07-09T08:27:19,739 Using cached https://www.piwheels.org/simple/versioneer/versioneer-0.29-py3-none-any.whl.metadata (16 kB) 2026-07-09T08:27:19,974 Collecting wheel 2026-07-09T08:27:19,975 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-07-09T08:27:19,987 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-07-09T08:27:21,062 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) 2026-07-09T08:27:21,069 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) 2026-07-09T08:27:21,076 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) 2026-07-09T08:27:21,082 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) 2026-07-09T08:27:21,089 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) 2026-07-09T08:27:21,535 Link requires a different Python (3.11.2 not in: '>=3.12'): https://files.pythonhosted.org/packages/d3/e1/f2fe8f6113a657a1da83b358b16755e528a602c6976a43724a88f42b482a/numpy-2.5.0rc1.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.12) 2026-07-09T08:27:21,544 Link requires a different Python (3.11.2 not in: '>=3.12'): https://files.pythonhosted.org/packages/e7/05/3d27272d30698dc0ecb7fdfaa41ad70303b444f81722bb99bce1d818638a/numpy-2.5.0.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.12) 2026-07-09T08:27:21,553 Link requires a different Python (3.11.2 not in: '>=3.12'): https://files.pythonhosted.org/packages/22/fd/89965aa4ac08c74998539fcbf24fa3540f3e15237fbeb6bcf9c908f4aade/numpy-2.5.1.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.12) 2026-07-09T08:27:21,895 Collecting numpy<2.5,~=2.0 2026-07-09T08:27:21,896 Obtaining dependency information for numpy<2.5,~=2.0 from https://www.piwheels.org/simple/numpy/numpy-2.4.6-cp311-cp311-linux_armv7l.whl.metadata 2026-07-09T08:27:21,910 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.6-cp311-cp311-linux_armv7l.whl.metadata (6.6 kB) 2026-07-09T08:27:24,072 Collecting Cython>=3.0.0 2026-07-09T08:27:24,073 Obtaining dependency information for Cython>=3.0.0 from https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl.metadata 2026-07-09T08:27:24,087 Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl.metadata (4.2 kB) 2026-07-09T08:27:24,277 Collecting packaging>=24.0 2026-07-09T08:27:24,278 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-07-09T08:27:24,289 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-07-09T08:27:24,501 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-09T08:27:24,938 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.6-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-07-09T08:27:25,822 Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl (11.2 MB) 2026-07-09T08:27:26,022 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-09T08:27:26,044 Using cached https://www.piwheels.org/simple/versioneer/versioneer-0.29-py3-none-any.whl (46 kB) 2026-07-09T08:27:26,122 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-09T08:27:26,154 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-07-09T08:27:26,627 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.6-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-07-09T08:27:27,621 Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl (11.2 MB) 2026-07-09T08:27:27,933 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-07-09T08:27:27,955 Using cached https://www.piwheels.org/simple/versioneer/versioneer-0.29-py3-none-any.whl (46 kB) 2026-07-09T08:27:28,135 Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB) 2026-07-09T08:27:30,963 Installing collected packages: versioneer, setuptools, packaging, numpy, Cython, wheel 2026-07-09T08:27:30,997 Creating /tmp/pip-build-env-pmfu936n/overlay/local/bin 2026-07-09T08:27:30,999 changing mode of /tmp/pip-build-env-pmfu936n/overlay/local/bin/versioneer to 755 2026-07-09T08:27:43,621 changing mode of /tmp/pip-build-env-pmfu936n/overlay/local/bin/f2py to 755 2026-07-09T08:27:43,624 changing mode of /tmp/pip-build-env-pmfu936n/overlay/local/bin/numpy-config to 755 2026-07-09T08:27:47,371 changing mode of /tmp/pip-build-env-pmfu936n/overlay/local/bin/cygdb to 755 2026-07-09T08:27:47,373 changing mode of /tmp/pip-build-env-pmfu936n/overlay/local/bin/cython to 755 2026-07-09T08:27:47,375 changing mode of /tmp/pip-build-env-pmfu936n/overlay/local/bin/cythonize to 755 2026-07-09T08:27:47,508 changing mode of /tmp/pip-build-env-pmfu936n/overlay/local/bin/wheel to 755 2026-07-09T08:27:47,553 Successfully installed Cython-3.2.8 numpy-2.4.6 packaging-26.2 setuptools-83.0.0 versioneer-0.29 wheel-0.47.0 2026-07-09T08:27:48,056 Installing build dependencies: finished with status 'done' 2026-07-09T08:27:48,075 Getting requirements to build wheel: started 2026-07-09T08:27:48,076 Running command Getting requirements to build wheel 2026-07-09T08:27:49,008 Using built-in specs. 2026-07-09T08:27:49,008 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-07-09T08:27:49,009 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-07-09T08:27:49,010 Target: arm-linux-gnueabihf 2026-07-09T08:27:49,010 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 2026-07-09T08:27:49,011 Thread model: posix 2026-07-09T08:27:49,011 Supported LTO compression algorithms: zlib zstd 2026-07-09T08:27:49,012 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-07-09T08:27:53,569 /tmp/pip-build-env-pmfu936n/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-07-09T08:27:53,570 !! 2026-07-09T08:27:53,570 ******************************************************************************** 2026-07-09T08:27:53,571 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-07-09T08:27:53,572 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-07-09T08:27:53,573 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-07-09T08:27:53,573 ******************************************************************************** 2026-07-09T08:27:53,574 !! 2026-07-09T08:27:53,575 self._finalize_license_expression() 2026-07-09T08:27:53,576 C compiler: 2026-07-09T08:27:53,576 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-07-09T08:27:53,577 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-07-09T08:27:53,578 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-07-09T08:27:53,578 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-07-09T08:27:53,579 Attempting to autodetect NEON support... Did not detect NEON support 2026-07-09T08:27:53,580 running egg_info 2026-07-09T08:27:53,587 writing mdtraj.egg-info/PKG-INFO 2026-07-09T08:27:53,593 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2026-07-09T08:27:53,595 writing entry points to mdtraj.egg-info/entry_points.txt 2026-07-09T08:27:53,598 writing requirements to mdtraj.egg-info/requires.txt 2026-07-09T08:27:53,601 writing top-level names to mdtraj.egg-info/top_level.txt 2026-07-09T08:27:53,641 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-07-09T08:27:53,677 reading manifest template 'MANIFEST.in' 2026-07-09T08:27:54,301 no previously-included directories found matching '__pycache__' 2026-07-09T08:27:54,302 no previously-included directories found matching '*.pyc' 2026-07-09T08:27:54,303 adding license file 'LICENSE' 2026-07-09T08:27:54,315 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-07-09T08:27:54,429 Getting requirements to build wheel: finished with status 'done' 2026-07-09T08:27:54,433 Created temporary directory: /tmp/pip-modern-metadata-09_qvexw 2026-07-09T08:27:54,435 Preparing metadata (pyproject.toml): started 2026-07-09T08:27:54,436 Running command Preparing metadata (pyproject.toml) 2026-07-09T08:27:55,408 Using built-in specs. 2026-07-09T08:27:55,409 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-07-09T08:27:55,410 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-07-09T08:27:55,410 Target: arm-linux-gnueabihf 2026-07-09T08:27:55,411 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 2026-07-09T08:27:55,411 Thread model: posix 2026-07-09T08:27:55,412 Supported LTO compression algorithms: zlib zstd 2026-07-09T08:27:55,413 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-07-09T08:27:59,657 /tmp/pip-wheel-h09hks37/mdtraj_e4279fdb7475474ba34f89a58225b507/basesetup.py:483: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-09_qvexw --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2026-07-09T08:27:59,658 warnings.warn( 2026-07-09T08:28:02,947 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. 2026-07-09T08:28:02,948 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. 2026-07-09T08:28:02,949 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. 2026-07-09T08:28:23,228 C compiler: 2026-07-09T08:28:23,228 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-07-09T08:28:23,229 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-07-09T08:28:23,230 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-07-09T08:28:23,230 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-07-09T08:28:23,231 Attempting to autodetect NEON support... Did not detect NEON support 2026-07-09T08:28:23,232 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2026-07-09T08:28:23,233 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2026-07-09T08:28:23,233 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2026-07-09T08:28:23,234 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2026-07-09T08:28:23,235 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2026-07-09T08:28:23,235 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2026-07-09T08:28:23,236 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2026-07-09T08:28:23,236 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2026-07-09T08:28:23,237 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2026-07-09T08:28:23,237 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2026-07-09T08:28:23,267 /tmp/pip-build-env-pmfu936n/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-07-09T08:28:23,267 !! 2026-07-09T08:28:23,269 ******************************************************************************** 2026-07-09T08:28:23,269 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-07-09T08:28:23,270 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-07-09T08:28:23,271 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-07-09T08:28:23,272 ******************************************************************************** 2026-07-09T08:28:23,273 !! 2026-07-09T08:28:23,274 self._finalize_license_expression() 2026-07-09T08:28:23,287 running dist_info 2026-07-09T08:28:23,296 creating /tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info 2026-07-09T08:28:23,297 writing /tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info/PKG-INFO 2026-07-09T08:28:23,304 writing dependency_links to /tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info/dependency_links.txt 2026-07-09T08:28:23,306 writing entry points to /tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info/entry_points.txt 2026-07-09T08:28:23,309 writing requirements to /tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info/requires.txt 2026-07-09T08:28:23,311 writing top-level names to /tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info/top_level.txt 2026-07-09T08:28:23,312 writing manifest file '/tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info/SOURCES.txt' 2026-07-09T08:28:23,358 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,358 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,359 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,360 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,360 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,362 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,363 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,364 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,364 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,365 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,367 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,368 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,368 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,369 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,369 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,371 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,372 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,373 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,373 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,373 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,375 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,375 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,376 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,376 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,377 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,378 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,379 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,380 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,380 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,381 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,383 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,383 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,384 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,385 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,385 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:23,400 reading manifest file '/tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info/SOURCES.txt' 2026-07-09T08:28:23,402 reading manifest template 'MANIFEST.in' 2026-07-09T08:28:24,110 no previously-included directories found matching '__pycache__' 2026-07-09T08:28:24,111 no previously-included directories found matching '*.pyc' 2026-07-09T08:28:24,112 adding license file 'LICENSE' 2026-07-09T08:28:24,122 writing manifest file '/tmp/pip-modern-metadata-09_qvexw/mdtraj.egg-info/SOURCES.txt' 2026-07-09T08:28:24,129 creating '/tmp/pip-modern-metadata-09_qvexw/mdtraj-1.11.1.post2.dist-info' 2026-07-09T08:28:25,562 Preparing metadata (pyproject.toml): finished with status 'done' 2026-07-09T08:28:25,566 Source in /tmp/pip-wheel-h09hks37/mdtraj_e4279fdb7475474ba34f89a58225b507 has version 1.11.1.post2, which satisfies requirement mdtraj==1.11.1.post2 from https://files.pythonhosted.org/packages/1a/6e/1e95f2e47056509bd7a4f397b367abbad5741b7cdccd7404b5dcf2d26e60/mdtraj-1.11.1.post2.tar.gz 2026-07-09T08:28:25,568 Removed mdtraj==1.11.1.post2 from https://files.pythonhosted.org/packages/1a/6e/1e95f2e47056509bd7a4f397b367abbad5741b7cdccd7404b5dcf2d26e60/mdtraj-1.11.1.post2.tar.gz from build tracker '/tmp/pip-build-tracker-wewecr3d' 2026-07-09T08:28:25,574 Created temporary directory: /tmp/pip-unpack-81czlkgs 2026-07-09T08:28:25,575 Building wheels for collected packages: mdtraj 2026-07-09T08:28:25,579 Created temporary directory: /tmp/pip-wheel-8ewm6y2o 2026-07-09T08:28:25,579 Destination directory: /tmp/pip-wheel-8ewm6y2o 2026-07-09T08:28:25,582 Building wheel for mdtraj (pyproject.toml): started 2026-07-09T08:28:25,583 Running command Building wheel for mdtraj (pyproject.toml) 2026-07-09T08:28:26,341 Using built-in specs. 2026-07-09T08:28:26,341 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-07-09T08:28:26,342 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-07-09T08:28:26,343 Target: arm-linux-gnueabihf 2026-07-09T08:28:26,343 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 2026-07-09T08:28:26,344 Thread model: posix 2026-07-09T08:28:26,344 Supported LTO compression algorithms: zlib zstd 2026-07-09T08:28:26,345 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-07-09T08:28:33,826 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. 2026-07-09T08:28:33,827 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. 2026-07-09T08:28:33,827 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. 2026-07-09T08:28:53,758 C compiler: 2026-07-09T08:28:53,758 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-07-09T08:28:53,759 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-07-09T08:28:53,759 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-07-09T08:28:53,760 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-07-09T08:28:53,760 Attempting to autodetect NEON support... Did not detect NEON support 2026-07-09T08:28:53,761 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2026-07-09T08:28:53,762 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2026-07-09T08:28:53,762 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2026-07-09T08:28:53,763 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2026-07-09T08:28:53,763 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2026-07-09T08:28:53,764 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2026-07-09T08:28:53,764 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2026-07-09T08:28:53,765 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2026-07-09T08:28:53,765 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2026-07-09T08:28:53,766 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2026-07-09T08:28:53,791 /tmp/pip-build-env-pmfu936n/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-07-09T08:28:53,792 !! 2026-07-09T08:28:53,793 ******************************************************************************** 2026-07-09T08:28:53,793 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-07-09T08:28:53,795 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-07-09T08:28:53,796 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-07-09T08:28:53,796 ******************************************************************************** 2026-07-09T08:28:53,798 !! 2026-07-09T08:28:53,798 self._finalize_license_expression() 2026-07-09T08:28:53,806 running bdist_wheel 2026-07-09T08:28:53,827 running build 2026-07-09T08:28:53,828 running build_py 2026-07-09T08:28:53,835 creating build/lib.linux-armv7l-cpython-311/mdtraj 2026-07-09T08:28:53,837 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-07-09T08:28:53,840 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-07-09T08:28:53,842 copying mdtraj/_version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-07-09T08:28:53,845 creating build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-07-09T08:28:53,846 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-07-09T08:28:53,850 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-07-09T08:28:53,853 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-07-09T08:28:53,855 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-07-09T08:28:53,858 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-07-09T08:28:53,860 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-07-09T08:28:53,864 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,865 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,867 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,870 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,872 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,875 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,878 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,880 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,883 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,885 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,887 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,889 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,891 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,894 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,896 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,899 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,902 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,905 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-07-09T08:28:53,908 creating build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-07-09T08:28:53,909 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-07-09T08:28:53,912 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-07-09T08:28:53,914 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-07-09T08:28:53,916 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-07-09T08:28:53,919 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,921 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,923 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,925 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,927 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,929 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,932 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,934 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,936 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-07-09T08:28:53,939 creating build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,940 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,943 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,945 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,948 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,950 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,953 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,956 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,958 copying mdtraj/geometry/pi_stacking.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,961 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,963 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,965 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,968 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,970 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,972 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,974 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,976 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-07-09T08:28:53,979 creating build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-07-09T08:28:53,980 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-07-09T08:28:53,983 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-07-09T08:28:53,984 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-07-09T08:28:53,987 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-07-09T08:28:53,988 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-07-09T08:28:53,990 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-07-09T08:28:53,993 creating build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-07-09T08:28:53,994 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-07-09T08:28:53,997 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-07-09T08:28:53,998 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-07-09T08:28:54,001 creating build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-07-09T08:28:54,002 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-07-09T08:28:54,004 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-07-09T08:28:54,007 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-07-09T08:28:54,010 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-07-09T08:28:54,012 copying mdtraj/formats/pdbx/PdbxContainers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-07-09T08:28:54,015 copying mdtraj/formats/pdbx/PdbxReader.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-07-09T08:28:54,017 copying mdtraj/formats/pdbx/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-07-09T08:28:54,019 copying mdtraj/formats/pdbx/pdbxfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-07-09T08:28:54,022 copying mdtraj/formats/pdbx/pdbx.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-07-09T08:28:54,026 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-07-09T08:28:54,027 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-07-09T08:28:54,030 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-07-09T08:28:54,034 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-07-09T08:28:54,036 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,037 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,040 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,042 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,045 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,047 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,050 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,052 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,054 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,056 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,059 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,061 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,064 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,066 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-07-09T08:28:54,076 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-07-09T08:28:54,077 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-07-09T08:28:54,079 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-07-09T08:28:54,089 UPDATING build/lib.linux-armv7l-cpython-311/mdtraj/_version.py 2026-07-09T08:28:54,090 set build/lib.linux-armv7l-cpython-311/mdtraj/_version.py to '1.11.1.post2' 2026-07-09T08:28:54,090 running build_ext 2026-07-09T08:28:54,093 building 'mdtraj.formats.xtc' extension 2026-07-09T08:28:54,094 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src 2026-07-09T08:28:54,098 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:54,219 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:54,369 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2026-07-09T08:28:54,370 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:28:54,371 788 | int smallnum, smaller, larger, i, is_smaller, run; 2026-07-09T08:28:54,371 | ^~~~~~ 2026-07-09T08:28:54,372 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:28:54,373 785 | int smallidx, minidx, maxidx; 2026-07-09T08:28:54,373 | ^~~~~~ 2026-07-09T08:28:54,379 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2026-07-09T08:28:54,380 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:28:54,380 1016 | int errval=1; 2026-07-09T08:28:54,381 | ^~~~~~ 2026-07-09T08:28:54,385 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2026-07-09T08:28:54,386 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:28:54,387 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2026-07-09T08:28:54,388 | ^~~~~~ 2026-07-09T08:28:54,388 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:28:54,389 1302 | int smallidx, minidx, maxidx; 2026-07-09T08:28:54,389 | ^~~~~~ 2026-07-09T08:28:54,397 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2026-07-09T08:28:54,399 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:28:54,399 1509 | int errval=1; 2026-07-09T08:28:54,400 | ^~~~~~ 2026-07-09T08:28:56,951 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:28:57,030 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2026-07-09T08:28:57,030 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 2026-07-09T08:28:57,031 66 | int i,j,result; 2026-07-09T08:28:57,032 | ^ 2026-07-09T08:28:57,032 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 2026-07-09T08:28:57,033 66 | int i,j,result; 2026-07-09T08:28:57,034 | ^ 2026-07-09T08:28:57,035 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2026-07-09T08:28:57,036 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2026-07-09T08:28:57,036 119 | if (NULL == xd) 2026-07-09T08:28:57,037 | ^~ 2026-07-09T08:28:57,038 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’ 2026-07-09T08:28:57,039 122 | do { 2026-07-09T08:28:57,039 | ^~ 2026-07-09T08:28:57,167 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:29:07,272 In function ‘__Pyx_PyLong_From_int’, 2026-07-09T08:29:07,273 inlined from ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’ at mdtraj/formats/xtc/xtc.c:13196:16, 2026-07-09T08:29:07,274 inlined from ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’ at mdtraj/formats/xtc/xtc.c:12882:13: 2026-07-09T08:29:07,298 mdtraj/formats/xtc/xtc.c:25564:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:07,299 25564 | return PyLong_FromLong((long) value); 2026-07-09T08:29:07,299 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:07,300 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’: 2026-07-09T08:29:07,311 mdtraj/formats/xtc/xtc.c:12904:7: note: ‘__pyx_v_status’ was declared here 2026-07-09T08:29:07,312 12904 | int __pyx_v_status; 2026-07-09T08:29:07,312 | ^~~~~~~~~~~~~~ 2026-07-09T08:29:16,429 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2026-07-09T08:29:16,440 mdtraj/formats/xtc/xtc.c:11352:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,441 11352 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; 2026-07-09T08:29:16,442 | ^ 2026-07-09T08:29:16,449 mdtraj/formats/xtc/xtc.c:9622:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 2026-07-09T08:29:16,449 9622 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-07-09T08:29:16,450 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,459 mdtraj/formats/xtc/xtc.c:11348:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,460 11348 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; 2026-07-09T08:29:16,460 | ^ 2026-07-09T08:29:16,468 mdtraj/formats/xtc/xtc.c:9622:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 2026-07-09T08:29:16,469 9622 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-07-09T08:29:16,470 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,479 mdtraj/formats/xtc/xtc.c:11344:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,479 11344 | } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-07-09T08:29:16,480 | ^ 2026-07-09T08:29:16,488 mdtraj/formats/xtc/xtc.c:9622:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 2026-07-09T08:29:16,488 9622 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-07-09T08:29:16,489 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,498 mdtraj/formats/xtc/xtc.c:11304:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,499 11304 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-07-09T08:29:16,499 | ^ 2026-07-09T08:29:16,507 mdtraj/formats/xtc/xtc.c:9618:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 2026-07-09T08:29:16,508 9618 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; 2026-07-09T08:29:16,508 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,517 mdtraj/formats/xtc/xtc.c:11286:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,518 11286 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-07-09T08:29:16,518 | ^ 2026-07-09T08:29:16,526 mdtraj/formats/xtc/xtc.c:9614:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 2026-07-09T08:29:16,527 9614 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; 2026-07-09T08:29:16,527 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,536 mdtraj/formats/xtc/xtc.c:11362:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,537 11362 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-07-09T08:29:16,537 | ^ 2026-07-09T08:29:16,545 mdtraj/formats/xtc/xtc.c:9610:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 2026-07-09T08:29:16,546 9610 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; 2026-07-09T08:29:16,547 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,555 mdtraj/formats/xtc/xtc.c:11324:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,556 11324 | } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; 2026-07-09T08:29:16,557 | ^ 2026-07-09T08:29:16,565 mdtraj/formats/xtc/xtc.c:9604:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 2026-07-09T08:29:16,565 9604 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-07-09T08:29:16,566 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,575 mdtraj/formats/xtc/xtc.c:11320:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,575 11320 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; 2026-07-09T08:29:16,576 | ^ 2026-07-09T08:29:16,584 mdtraj/formats/xtc/xtc.c:9604:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 2026-07-09T08:29:16,584 9604 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-07-09T08:29:16,585 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,594 mdtraj/formats/xtc/xtc.c:11316:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,594 11316 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-07-09T08:29:16,595 | ^ 2026-07-09T08:29:16,603 mdtraj/formats/xtc/xtc.c:9604:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 2026-07-09T08:29:16,603 9604 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-07-09T08:29:16,604 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,613 mdtraj/formats/xtc/xtc.c:10974:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,613 10974 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; 2026-07-09T08:29:16,614 | ^ 2026-07-09T08:29:16,622 mdtraj/formats/xtc/xtc.c:9606:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 2026-07-09T08:29:16,622 9606 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2026-07-09T08:29:16,623 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:16,631 mdtraj/formats/xtc/xtc.c:10970:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:16,632 10970 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0; 2026-07-09T08:29:16,633 | ^ 2026-07-09T08:29:16,640 mdtraj/formats/xtc/xtc.c:9606:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 2026-07-09T08:29:16,641 9606 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2026-07-09T08:29:16,642 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:24,682 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 2026-07-09T08:29:24,853 building 'mdtraj.formats.trr' extension 2026-07-09T08:29:24,854 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:29:24,967 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:29:25,112 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2026-07-09T08:29:25,112 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:29:25,113 788 | int smallnum, smaller, larger, i, is_smaller, run; 2026-07-09T08:29:25,113 | ^~~~~~ 2026-07-09T08:29:25,114 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:29:25,114 785 | int smallidx, minidx, maxidx; 2026-07-09T08:29:25,115 | ^~~~~~ 2026-07-09T08:29:25,121 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2026-07-09T08:29:25,122 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:29:25,122 1016 | int errval=1; 2026-07-09T08:29:25,123 | ^~~~~~ 2026-07-09T08:29:25,127 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2026-07-09T08:29:25,128 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:29:25,129 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2026-07-09T08:29:25,130 | ^~~~~~ 2026-07-09T08:29:25,130 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:29:25,131 1302 | int smallidx, minidx, maxidx; 2026-07-09T08:29:25,132 | ^~~~~~ 2026-07-09T08:29:25,140 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2026-07-09T08:29:25,141 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-07-09T08:29:25,142 1509 | int errval=1; 2026-07-09T08:29:25,142 | ^~~~~~ 2026-07-09T08:29:27,662 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:29:28,476 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:29:39,465 In function ‘__Pyx_PyLong_From_int’, 2026-07-09T08:29:39,465 inlined from ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’ at mdtraj/formats/xtc/trr.c:15177:16, 2026-07-09T08:29:39,466 inlined from ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write’ at mdtraj/formats/xtc/trr.c:14607:13: 2026-07-09T08:29:39,494 mdtraj/formats/xtc/trr.c:27504:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:39,495 27504 | return PyLong_FromLong((long) value); 2026-07-09T08:29:39,495 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:39,496 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write’: 2026-07-09T08:29:39,509 mdtraj/formats/xtc/trr.c:14637:7: note: ‘__pyx_v_status’ was declared here 2026-07-09T08:29:39,510 14637 | int __pyx_v_status; 2026-07-09T08:29:39,510 | ^~~~~~~~~~~~~~ 2026-07-09T08:29:50,647 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2026-07-09T08:29:50,658 mdtraj/formats/xtc/trr.c:11947:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,659 11947 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_6 = 2; 2026-07-09T08:29:50,659 | ^ 2026-07-09T08:29:50,668 mdtraj/formats/xtc/trr.c:10267:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2026-07-09T08:29:50,669 10267 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-07-09T08:29:50,669 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,680 mdtraj/formats/xtc/trr.c:11943:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,680 11943 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_6 = 1; 2026-07-09T08:29:50,681 | ^ 2026-07-09T08:29:50,690 mdtraj/formats/xtc/trr.c:10267:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2026-07-09T08:29:50,691 10267 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-07-09T08:29:50,691 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,692 mdtraj/formats/xtc/trr.c:2610:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,693 2610 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2026-07-09T08:29:50,693 | ^ 2026-07-09T08:29:50,702 mdtraj/formats/xtc/trr.c:10267:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2026-07-09T08:29:50,703 10267 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-07-09T08:29:50,703 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,714 mdtraj/formats/xtc/trr.c:11937:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,714 11937 | __pyx_t_15 += __pyx_pybuffernd_forces.diminfo[0].shape; 2026-07-09T08:29:50,715 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2026-07-09T08:29:50,724 mdtraj/formats/xtc/trr.c:10267:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2026-07-09T08:29:50,724 10267 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-07-09T08:29:50,725 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,735 mdtraj/formats/xtc/trr.c:11890:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,736 11890 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_6 = 2; 2026-07-09T08:29:50,736 | ^ 2026-07-09T08:29:50,745 mdtraj/formats/xtc/trr.c:10283:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2026-07-09T08:29:50,746 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-07-09T08:29:50,747 | ^~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,757 mdtraj/formats/xtc/trr.c:11886:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,757 11886 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_6 = 1; 2026-07-09T08:29:50,758 | ^ 2026-07-09T08:29:50,767 mdtraj/formats/xtc/trr.c:10283:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2026-07-09T08:29:50,767 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-07-09T08:29:50,768 | ^~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,769 mdtraj/formats/xtc/trr.c:2610:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,769 2610 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2026-07-09T08:29:50,770 | ^ 2026-07-09T08:29:50,779 mdtraj/formats/xtc/trr.c:10283:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2026-07-09T08:29:50,780 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-07-09T08:29:50,780 | ^~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,790 mdtraj/formats/xtc/trr.c:11880:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,791 11880 | __pyx_t_15 += __pyx_pybuffernd_vel.diminfo[0].shape; 2026-07-09T08:29:50,791 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2026-07-09T08:29:50,800 mdtraj/formats/xtc/trr.c:10283:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2026-07-09T08:29:50,801 10283 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-07-09T08:29:50,802 | ^~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,813 mdtraj/formats/xtc/trr.c:12279:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,813 12279 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-07-09T08:29:50,814 | ^ 2026-07-09T08:29:50,823 mdtraj/formats/xtc/trr.c:10289:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2026-07-09T08:29:50,823 10289 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2026-07-09T08:29:50,824 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,835 mdtraj/formats/xtc/trr.c:12275:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,835 12275 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-07-09T08:29:50,836 | ^ 2026-07-09T08:29:50,845 mdtraj/formats/xtc/trr.c:10289:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2026-07-09T08:29:50,846 10289 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2026-07-09T08:29:50,846 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,857 mdtraj/formats/xtc/trr.c:12120:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,858 12120 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-07-09T08:29:50,858 | ^ 2026-07-09T08:29:50,867 mdtraj/formats/xtc/trr.c:10285:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2026-07-09T08:29:50,868 10285 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2026-07-09T08:29:50,869 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,879 mdtraj/formats/xtc/trr.c:12116:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,880 12116 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-07-09T08:29:50,881 | ^ 2026-07-09T08:29:50,889 mdtraj/formats/xtc/trr.c:10285:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2026-07-09T08:29:50,890 10285 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2026-07-09T08:29:50,891 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,902 mdtraj/formats/xtc/trr.c:12172:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,902 12172 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-07-09T08:29:50,902 | ^ 2026-07-09T08:29:50,912 mdtraj/formats/xtc/trr.c:10269:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2026-07-09T08:29:50,912 10269 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2026-07-09T08:29:50,913 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:50,923 mdtraj/formats/xtc/trr.c:12168:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:29:50,924 12168 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-07-09T08:29:50,924 | ^ 2026-07-09T08:29:50,933 mdtraj/formats/xtc/trr.c:10269:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2026-07-09T08:29:50,934 10269 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2026-07-09T08:29:50,934 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:29:58,970 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 2026-07-09T08:29:59,136 building 'mdtraj.formats.dcd' extension 2026-07-09T08:29:59,137 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd 2026-07-09T08:29:59,138 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src 2026-07-09T08:29:59,138 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:30:10,596 In function ‘__Pyx_PyLong_From_int’, 2026-07-09T08:30:10,598 inlined from ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’ at mdtraj/formats/dcd/dcd.c:9986:19: 2026-07-09T08:30:10,616 mdtraj/formats/dcd/dcd.c:19373:22: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:30:10,617 19373 | return PyLong_FromLong((long) value); 2026-07-09T08:30:10,618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:10,618 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2026-07-09T08:30:10,625 mdtraj/formats/dcd/dcd.c:8634:7: note: ‘__pyx_v_i’ was declared here 2026-07-09T08:30:10,626 8634 | int __pyx_v_i; 2026-07-09T08:30:10,626 | ^~~~~~~~~ 2026-07-09T08:30:14,463 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:30:14,706 mdtraj/formats/dcd/src/dcdplugin.c: In function ‘open_dcd_read’: 2026-07-09T08:30:14,707 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=] 2026-07-09T08:30:14,708 903 | printf("dcdplugin) Warning: DCD header claims %d frames, but \n" 2026-07-09T08:30:14,708 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:14,708 ...... 2026-07-09T08:30:14,709 906 | dcd->nsets, trjsize, newnsets, framesize); 2026-07-09T08:30:14,709 | ~~~~~~~ 2026-07-09T08:30:14,709 | | 2026-07-09T08:30:14,710 | fio_size_t {aka long long int} 2026-07-09T08:30:14,710 mdtraj/formats/dcd/src/dcdplugin.c:904:39: note: format string is defined here 2026-07-09T08:30:14,711 904 | "dcdplugin) file size (%ld) indicates there are actually \n" 2026-07-09T08:30:14,711 | ~~^ 2026-07-09T08:30:14,712 | | 2026-07-09T08:30:14,712 | long int 2026-07-09T08:30:14,713 | %lld 2026-07-09T08:30:14,713 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=] 2026-07-09T08:30:14,714 903 | printf("dcdplugin) Warning: DCD header claims %d frames, but \n" 2026-07-09T08:30:14,715 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:14,715 ...... 2026-07-09T08:30:14,716 906 | dcd->nsets, trjsize, newnsets, framesize); 2026-07-09T08:30:14,717 | ~~~~~~~~~ 2026-07-09T08:30:14,718 | | 2026-07-09T08:30:14,719 | fio_size_t {aka long long int} 2026-07-09T08:30:14,720 mdtraj/formats/dcd/src/dcdplugin.c:905:36: note: format string is defined here 2026-07-09T08:30:14,721 905 | "%d frames of size (%ld)\n", 2026-07-09T08:30:14,721 | ~~^ 2026-07-09T08:30:14,722 | | 2026-07-09T08:30:14,723 | long int 2026-07-09T08:30:14,723 | %lld 2026-07-09T08:30:16,061 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 2026-07-09T08:30:16,195 building 'mdtraj.formats.dtr' extension 2026-07-09T08:30:16,196 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr 2026-07-09T08:30:16,197 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src 2026-07-09T08:30:16,198 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:30:34,113 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:30:36,461 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2026-07-09T08:30:36,462 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=] 2026-07-09T08:30:36,463 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2026-07-09T08:30:36,464 | ~~^ ~ 2026-07-09T08:30:36,464 | | | 2026-07-09T08:30:36,465 | | size_t {aka unsigned int} 2026-07-09T08:30:36,466 | long int 2026-07-09T08:30:36,466 | %d 2026-07-09T08:30:36,467 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=] 2026-07-09T08:30:36,468 487 | printf("size %d framesize %d\n\n", 2026-07-09T08:30:36,468 | ~^ 2026-07-09T08:30:36,469 | | 2026-07-09T08:30:36,470 | int 2026-07-09T08:30:36,470 | %lld 2026-07-09T08:30:36,471 488 | keys[i].size(), m_framesize); 2026-07-09T08:30:36,472 | ~~~~~~~~~~~~~~ 2026-07-09T08:30:36,472 | | 2026-07-09T08:30:36,473 | uint64_t {aka long long unsigned int} 2026-07-09T08:30:36,474 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=] 2026-07-09T08:30:36,475 487 | printf("size %d framesize %d\n\n", 2026-07-09T08:30:36,475 | ~^ 2026-07-09T08:30:36,476 | | 2026-07-09T08:30:36,477 | int 2026-07-09T08:30:36,478 | %lld 2026-07-09T08:30:36,478 488 | keys[i].size(), m_framesize); 2026-07-09T08:30:36,479 | ~~~~~~~~~~~ 2026-07-09T08:30:36,480 | | 2026-07-09T08:30:36,480 | uint64_t {aka long long unsigned int} 2026-07-09T08:30:36,481 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=] 2026-07-09T08:30:36,482 494 | "non-constant time interval at frame %ld\n", i); 2026-07-09T08:30:36,482 | ~~^ ~ 2026-07-09T08:30:36,483 | | | 2026-07-09T08:30:36,484 | | size_t {aka unsigned int} 2026-07-09T08:30:36,485 | long int 2026-07-09T08:30:36,485 | %d 2026-07-09T08:30:36,486 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=] 2026-07-09T08:30:36,487 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2026-07-09T08:30:36,488 | ~~^ ~ 2026-07-09T08:30:36,489 | | | 2026-07-09T08:30:36,489 | | size_t {aka unsigned int} 2026-07-09T08:30:36,490 | long int 2026-07-09T08:30:36,491 | %d 2026-07-09T08:30:36,628 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2026-07-09T08:30:36,629 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=] 2026-07-09T08:30:36,629 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2026-07-09T08:30:36,630 | ~~^ 2026-07-09T08:30:36,631 | | 2026-07-09T08:30:36,631 | long int 2026-07-09T08:30:36,632 | %lld 2026-07-09T08:30:36,633 1302 | 3*natoms, pos.count); 2026-07-09T08:30:36,633 | ~~~~~~~~~ 2026-07-09T08:30:36,634 | | 2026-07-09T08:30:36,635 | uint64_t {aka long long unsigned int} 2026-07-09T08:30:36,635 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=] 2026-07-09T08:30:36,636 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2026-07-09T08:30:36,637 | ~~^ 2026-07-09T08:30:36,638 | | 2026-07-09T08:30:36,638 | long int 2026-07-09T08:30:36,639 | %lld 2026-07-09T08:30:36,640 1311 | 3*natoms, vel.count); 2026-07-09T08:30:36,640 | ~~~~~~~~~ 2026-07-09T08:30:36,641 | | 2026-07-09T08:30:36,642 | uint64_t {aka long long unsigned int} 2026-07-09T08:30:36,662 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2026-07-09T08:30:36,662 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=] 2026-07-09T08:30:36,663 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2026-07-09T08:30:36,664 | ~~^ 2026-07-09T08:30:36,664 | | 2026-07-09T08:30:36,665 | long int 2026-07-09T08:30:36,666 | %lld 2026-07-09T08:30:36,667 1573 | velblob.count, 3*natoms); 2026-07-09T08:30:36,668 | ~~~~~~~~~~~~~ 2026-07-09T08:30:36,669 | | 2026-07-09T08:30:36,669 | uint64_t {aka long long unsigned int} 2026-07-09T08:30:37,967 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2026-07-09T08:30:37,968 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2026-07-09T08:30:37,969 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2026-07-09T08:30:37,969 | ~~~~~~~~^~~~~ 2026-07-09T08:30:40,729 In file included from /usr/include/c++/12/map:60, 2026-07-09T08:30:40,729 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2026-07-09T08:30:40,730 /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> >]’: 2026-07-09T08:30:40,731 /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 2026-07-09T08:30:40,731 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2026-07-09T08:30:40,732 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:40,798 /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> >]’: 2026-07-09T08:30:40,799 /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 2026-07-09T08:30:40,800 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2026-07-09T08:30:40,800 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:40,857 In file included from /usr/include/c++/12/map:61: 2026-07-09T08:30:40,858 /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> >]’: 2026-07-09T08:30:40,858 /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 2026-07-09T08:30:40,859 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-07-09T08:30:40,860 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:40,861 531 | std::forward_as_tuple(std::move(__k)), 2026-07-09T08:30:40,861 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:40,862 532 | std::tuple<>()); 2026-07-09T08:30:40,862 | ~~~~~~~~~~~~~~~ 2026-07-09T08:30:40,948 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> >]’, 2026-07-09T08:30:40,949 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28: 2026-07-09T08:30:40,949 /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 2026-07-09T08:30:40,950 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-07-09T08:30:40,951 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:40,952 531 | std::forward_as_tuple(std::move(__k)), 2026-07-09T08:30:40,952 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:40,953 532 | std::tuple<>()); 2026-07-09T08:30:40,954 | ~~~~~~~~~~~~~~~ 2026-07-09T08:30:41,774 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2026-07-09T08:30:41,775 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=] 2026-07-09T08:30:41,776 706 | sprintf(sub, "%03x/", i); 2026-07-09T08:30:41,776 | ^~~~ 2026-07-09T08:30:41,777 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2026-07-09T08:30:41,778 706 | sprintf(sub, "%03x/", i); 2026-07-09T08:30:41,778 | ^~~~~~~ 2026-07-09T08:30:41,779 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2026-07-09T08:30:41,780 706 | sprintf(sub, "%03x/", i); 2026-07-09T08:30:41,781 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2026-07-09T08:30:41,782 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=] 2026-07-09T08:30:41,782 714 | sprintf(subsub, "%03x", j); 2026-07-09T08:30:41,783 | ^~~~ 2026-07-09T08:30:41,784 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2026-07-09T08:30:41,785 714 | sprintf(subsub, "%03x", j); 2026-07-09T08:30:41,786 | ^~~~~~ 2026-07-09T08:30:41,786 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2026-07-09T08:30:41,787 714 | sprintf(subsub, "%03x", j); 2026-07-09T08:30:41,788 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:42,179 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2026-07-09T08:30:42,180 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-07-09T08:30:42,180 667 | sprintf(answer, "%03x/", d1); 2026-07-09T08:30:42,181 | ^ 2026-07-09T08:30:42,181 In function ‘std::string DDreldir(const std::string&, int, int)’, 2026-07-09T08:30:42,182 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2026-07-09T08:30:42,183 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2026-07-09T08:30:42,183 667 | sprintf(answer, "%03x/", d1); 2026-07-09T08:30:42,184 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:42,185 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2026-07-09T08:30:42,185 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=] 2026-07-09T08:30:42,186 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-07-09T08:30:42,187 | ^~~~ 2026-07-09T08:30:42,188 In function ‘std::string DDreldir(const std::string&, int, int)’, 2026-07-09T08:30:42,189 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2026-07-09T08:30:42,190 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2026-07-09T08:30:42,191 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-07-09T08:30:42,192 | ^~~~~~~~~~~~ 2026-07-09T08:30:42,193 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2026-07-09T08:30:42,194 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-07-09T08:30:42,195 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:45,309 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> >]’, 2026-07-09T08:30:45,309 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: 2026-07-09T08:30:45,310 /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 2026-07-09T08:30:45,311 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-07-09T08:30:45,312 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:45,313 531 | std::forward_as_tuple(std::move(__k)), 2026-07-09T08:30:45,313 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-07-09T08:30:45,314 532 | std::tuple<>()); 2026-07-09T08:30:45,314 | ~~~~~~~~~~~~~~~ 2026-07-09T08:30:50,234 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -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 2026-07-09T08:30:50,599 building 'mdtraj._rmsd' extension 2026-07-09T08:30:50,600 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd 2026-07-09T08:30:50,601 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src 2026-07-09T08:30:50,603 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:31:37,794 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:31:38,004 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:31:38,264 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:31:39,003 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -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 2026-07-09T08:31:39,368 building 'mdtraj._lprmsd' extension 2026-07-09T08:31:39,368 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:06,433 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:09,245 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:09,448 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:10,694 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:10,997 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:11,255 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:12,029 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -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 2026-07-09T08:32:12,376 building 'mdtraj.core.lib.libtheobald' extension 2026-07-09T08:32:12,383 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:13,128 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:13,331 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 2026-07-09T08:32:13,358 building 'mdtraj.geometry._geometry' extension 2026-07-09T08:32:13,360 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src 2026-07-09T08:32:13,362 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:32:52,443 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:33:06,560 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:33:10,546 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:33:11,683 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -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 2026-07-09T08:33:12,100 building 'mdtraj.geometry.drid' extension 2026-07-09T08:33:12,103 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:33:44,399 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:33:45,042 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:33:45,151 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -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 2026-07-09T08:33:45,483 building 'mdtraj.geometry.neighbors' extension 2026-07-09T08:33:45,484 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:15,724 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:17,032 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -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 2026-07-09T08:34:17,354 building 'mdtraj.geometry.neighborlist' extension 2026-07-09T08:34:17,355 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:44,867 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:49,267 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2026-07-09T08:34:49,268 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2026-07-09T08:34:49,268 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:34:49,269 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2026-07-09T08:34:49,270 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-07-09T08:34:49,271 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2026-07-09T08:34:49,271 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-07-09T08:34:49,272 341 | float periodicBoxVectors[3][3]; 2026-07-09T08:34:49,272 | ^~~~~~~~~~~~~~~~~~ 2026-07-09T08:34:49,273 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2026-07-09T08:34:49,273 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2026-07-09T08:34:49,274 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:34:49,274 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2026-07-09T08:34:49,275 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-07-09T08:34:49,275 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2026-07-09T08:34:49,276 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-07-09T08:34:49,277 341 | float periodicBoxVectors[3][3]; 2026-07-09T08:34:49,277 | ^~~~~~~~~~~~~~~~~~ 2026-07-09T08:34:49,278 mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:34:49,278 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); 2026-07-09T08:34:49,279 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-07-09T08:34:49,280 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-07-09T08:34:49,280 341 | float periodicBoxVectors[3][3]; 2026-07-09T08:34:49,281 | ^~~~~~~~~~~~~~~~~~ 2026-07-09T08:34:49,282 mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-07-09T08:34:49,283 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); 2026-07-09T08:34:49,284 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-07-09T08:34:49,284 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-07-09T08:34:49,285 341 | float periodicBoxVectors[3][3]; 2026-07-09T08:34:49,286 | ^~~~~~~~~~~~~~~~~~ 2026-07-09T08:34:50,103 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -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 2026-07-09T08:34:50,502 installing to build/bdist.linux-armv7l/wheel 2026-07-09T08:34:50,503 running install 2026-07-09T08:34:50,527 running install_lib 2026-07-09T08:34:50,540 creating build/bdist.linux-armv7l/wheel 2026-07-09T08:34:50,543 creating build/bdist.linux-armv7l/wheel/mdtraj 2026-07-09T08:34:50,545 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2026-07-09T08:34:50,547 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2026-07-09T08:34:50,549 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-07-09T08:34:50,553 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-07-09T08:34:50,555 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-07-09T08:34:50,559 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-07-09T08:34:50,563 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-07-09T08:34:50,568 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-07-09T08:34:50,570 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-07-09T08:34:50,573 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-07-09T08:34:50,576 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-07-09T08:34:50,579 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2026-07-09T08:34:50,581 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,583 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,586 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,590 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdbx 2026-07-09T08:34:50,591 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/PdbxContainers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-07-09T08:34:50,595 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/PdbxReader.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-07-09T08:34:50,597 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-07-09T08:34:50,599 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/pdbxfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-07-09T08:34:50,603 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/pdbx.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-07-09T08:34:50,605 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,636 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,639 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,643 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,647 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,651 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,653 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,656 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,658 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,660 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,663 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,666 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,669 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,709 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,712 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,725 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,727 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,730 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2026-07-09T08:34:50,731 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-07-09T08:34:50,734 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-07-09T08:34:50,737 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-07-09T08:34:50,740 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2026-07-09T08:34:50,741 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb/data 2026-07-09T08:34:50,743 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb/data 2026-07-09T08:34:50,746 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-07-09T08:34:50,770 copying build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-07-09T08:34:50,802 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2026-07-09T08:34:50,803 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-07-09T08:34:50,806 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-07-09T08:34:50,808 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-07-09T08:34:50,811 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-07-09T08:34:50,814 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2026-07-09T08:34:50,814 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-07-09T08:34:50,817 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-07-09T08:34:50,819 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-07-09T08:34:50,821 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-07-09T08:34:50,823 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-07-09T08:34:50,827 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2026-07-09T08:34:50,828 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,830 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,832 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,834 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,836 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,838 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,840 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,843 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,845 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,847 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,850 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,852 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,855 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-07-09T08:34:50,857 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-07-09T08:34:50,859 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-07-09T08:34:50,861 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-07-09T08:34:50,864 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2026-07-09T08:34:50,865 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,867 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,869 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,871 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,914 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,916 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,918 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,921 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,923 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/pi_stacking.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,926 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,928 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,930 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,932 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,955 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,957 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,959 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,961 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,993 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:50,995 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:51,022 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-07-09T08:34:51,025 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2026-07-09T08:34:51,027 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-07-09T08:34:51,029 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-07-09T08:34:51,031 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-07-09T08:34:51,034 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-07-09T08:34:51,036 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-07-09T08:34:51,038 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-07-09T08:34:51,041 copying build/lib.linux-armv7l-cpython-311/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-07-09T08:34:51,044 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2026-07-09T08:34:51,045 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-07-09T08:34:51,048 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-07-09T08:34:51,050 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-07-09T08:34:51,053 copying build/lib.linux-armv7l-cpython-311/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-07-09T08:34:51,055 copying build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-07-09T08:34:51,082 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2026-07-09T08:34:51,083 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-07-09T08:34:51,084 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-07-09T08:34:51,087 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-07-09T08:34:51,089 copying build/lib.linux-armv7l-cpython-311/mdtraj/_version.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-07-09T08:34:51,091 running install_egg_info 2026-07-09T08:34:51,106 running egg_info 2026-07-09T08:34:51,114 writing mdtraj.egg-info/PKG-INFO 2026-07-09T08:34:51,121 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2026-07-09T08:34:51,122 writing entry points to mdtraj.egg-info/entry_points.txt 2026-07-09T08:34:51,125 writing requirements to mdtraj.egg-info/requires.txt 2026-07-09T08:34:51,126 writing top-level names to mdtraj.egg-info/top_level.txt 2026-07-09T08:34:51,173 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,173 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,174 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,175 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,175 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,176 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,177 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,178 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,178 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,179 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,180 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,181 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,182 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,182 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,183 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,184 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,184 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,185 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,186 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,187 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,187 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,188 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,188 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,189 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,189 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,190 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,191 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,192 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,192 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,193 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,195 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,196 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,196 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,197 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,198 dependency /tmp/pip-build-env-pmfu936n/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 2026-07-09T08:34:51,217 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-07-09T08:34:51,244 reading manifest template 'MANIFEST.in' 2026-07-09T08:34:51,847 no previously-included directories found matching '__pycache__' 2026-07-09T08:34:51,849 no previously-included directories found matching '*.pyc' 2026-07-09T08:34:51,850 adding license file 'LICENSE' 2026-07-09T08:34:51,863 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-07-09T08:34:51,871 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/./mdtraj-1.11.1.post2-py3.11.egg-info 2026-07-09T08:34:51,885 running install_scripts 2026-07-09T08:34:51,940 creating build/bdist.linux-armv7l/wheel/mdtraj-1.11.1.post2.dist-info/WHEEL 2026-07-09T08:34:51,943 creating '/tmp/pip-wheel-8ewm6y2o/.tmp-81pvjv6m/mdtraj-1.11.1.post2-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-07-09T08:34:51,946 adding 'mdtraj/__init__.py' 2026-07-09T08:34:52,203 adding 'mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:52,618 adding 'mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:52,632 adding 'mdtraj/_version.py' 2026-07-09T08:34:52,634 adding 'mdtraj/io.py' 2026-07-09T08:34:52,636 adding 'mdtraj/core/__init__.py' 2026-07-09T08:34:52,638 adding 'mdtraj/core/element.py' 2026-07-09T08:34:52,641 adding 'mdtraj/core/residue_names.py' 2026-07-09T08:34:52,644 adding 'mdtraj/core/selection.py' 2026-07-09T08:34:52,652 adding 'mdtraj/core/topology.py' 2026-07-09T08:34:52,662 adding 'mdtraj/core/trajectory.py' 2026-07-09T08:34:52,664 adding 'mdtraj/core/lib/center.h' 2026-07-09T08:34:52,672 adding 'mdtraj/core/lib/libtheobald.a' 2026-07-09T08:34:52,674 adding 'mdtraj/core/lib/theobald_rmsd.h' 2026-07-09T08:34:52,675 adding 'mdtraj/formats/__init__.py' 2026-07-09T08:34:52,679 adding 'mdtraj/formats/amberrst.py' 2026-07-09T08:34:52,681 adding 'mdtraj/formats/arc.py' 2026-07-09T08:34:52,854 adding 'mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:53,291 adding 'mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:53,308 adding 'mdtraj/formats/gro.py' 2026-07-09T08:34:53,310 adding 'mdtraj/formats/gsd.py' 2026-07-09T08:34:53,315 adding 'mdtraj/formats/hdf5.py' 2026-07-09T08:34:53,316 adding 'mdtraj/formats/hoomdxml.py' 2026-07-09T08:34:53,319 adding 'mdtraj/formats/lammpstrj.py' 2026-07-09T08:34:53,322 adding 'mdtraj/formats/lh5.py' 2026-07-09T08:34:53,324 adding 'mdtraj/formats/mdcrd.py' 2026-07-09T08:34:53,326 adding 'mdtraj/formats/mol2.py' 2026-07-09T08:34:53,329 adding 'mdtraj/formats/netcdf.py' 2026-07-09T08:34:53,331 adding 'mdtraj/formats/openmmxml.py' 2026-07-09T08:34:53,333 adding 'mdtraj/formats/prmtop.py' 2026-07-09T08:34:53,335 adding 'mdtraj/formats/psf.py' 2026-07-09T08:34:53,336 adding 'mdtraj/formats/registry.py' 2026-07-09T08:34:53,632 adding 'mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:53,923 adding 'mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:53,933 adding 'mdtraj/formats/xyzfile.py' 2026-07-09T08:34:53,935 adding 'mdtraj/formats/pdb/__init__.py' 2026-07-09T08:34:53,939 adding 'mdtraj/formats/pdb/pdbfile.py' 2026-07-09T08:34:53,945 adding 'mdtraj/formats/pdb/pdbstructure.py' 2026-07-09T08:34:53,947 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2026-07-09T08:34:53,949 adding 'mdtraj/formats/pdb/data/residues.xml' 2026-07-09T08:34:53,953 adding 'mdtraj/formats/pdbx/PdbxContainers.py' 2026-07-09T08:34:53,955 adding 'mdtraj/formats/pdbx/PdbxReader.py' 2026-07-09T08:34:53,957 adding 'mdtraj/formats/pdbx/__init__.py' 2026-07-09T08:34:53,959 adding 'mdtraj/formats/pdbx/pdbx.py' 2026-07-09T08:34:53,962 adding 'mdtraj/formats/pdbx/pdbxfile.py' 2026-07-09T08:34:53,965 adding 'mdtraj/geometry/__init__.py' 2026-07-09T08:34:54,482 adding 'mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:54,502 adding 'mdtraj/geometry/alignment.py' 2026-07-09T08:34:54,504 adding 'mdtraj/geometry/angle.py' 2026-07-09T08:34:54,506 adding 'mdtraj/geometry/contact.py' 2026-07-09T08:34:54,509 adding 'mdtraj/geometry/dihedral.py' 2026-07-09T08:34:54,511 adding 'mdtraj/geometry/distance.py' 2026-07-09T08:34:54,822 adding 'mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:54,832 adding 'mdtraj/geometry/dssp.py' 2026-07-09T08:34:54,834 adding 'mdtraj/geometry/hbond.py' 2026-07-09T08:34:54,837 adding 'mdtraj/geometry/internal.py' 2026-07-09T08:34:55,153 adding 'mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:55,458 adding 'mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so' 2026-07-09T08:34:55,469 adding 'mdtraj/geometry/order.py' 2026-07-09T08:34:55,471 adding 'mdtraj/geometry/pi_stacking.py' 2026-07-09T08:34:55,473 adding 'mdtraj/geometry/rdf.py' 2026-07-09T08:34:55,474 adding 'mdtraj/geometry/rg.py' 2026-07-09T08:34:55,476 adding 'mdtraj/geometry/sasa.py' 2026-07-09T08:34:55,478 adding 'mdtraj/geometry/shape.py' 2026-07-09T08:34:55,479 adding 'mdtraj/geometry/thermodynamic_properties.py' 2026-07-09T08:34:55,481 adding 'mdtraj/nmr/__init__.py' 2026-07-09T08:34:55,483 adding 'mdtraj/nmr/scalar_couplings.py' 2026-07-09T08:34:55,485 adding 'mdtraj/nmr/shift_wrappers.py' 2026-07-09T08:34:55,486 adding 'mdtraj/reporters/__init__.py' 2026-07-09T08:34:55,488 adding 'mdtraj/reporters/basereporter.py' 2026-07-09T08:34:55,490 adding 'mdtraj/reporters/dcdreporter.py' 2026-07-09T08:34:55,491 adding 'mdtraj/reporters/hdf5reporter.py' 2026-07-09T08:34:55,492 adding 'mdtraj/reporters/netcdfreporter.py' 2026-07-09T08:34:55,494 adding 'mdtraj/reporters/xtcreporter.py' 2026-07-09T08:34:55,496 adding 'mdtraj/scripts/__init__.py' 2026-07-09T08:34:55,498 adding 'mdtraj/scripts/mdconvert.py' 2026-07-09T08:34:55,500 adding 'mdtraj/scripts/mdinspect.py' 2026-07-09T08:34:55,502 adding 'mdtraj/testing/__init__.py' 2026-07-09T08:34:55,505 adding 'mdtraj/testing/docscrape.py' 2026-07-09T08:34:55,506 adding 'mdtraj/testing/docstrings.py' 2026-07-09T08:34:55,508 adding 'mdtraj/testing/testing.py' 2026-07-09T08:34:55,510 adding 'mdtraj/utils/__init__.py' 2026-07-09T08:34:55,512 adding 'mdtraj/utils/contextmanagers.py' 2026-07-09T08:34:55,513 adding 'mdtraj/utils/delay_import.py' 2026-07-09T08:34:55,515 adding 'mdtraj/utils/rotation.py' 2026-07-09T08:34:55,516 adding 'mdtraj/utils/singleton.py' 2026-07-09T08:34:55,518 adding 'mdtraj/utils/unitcell.py' 2026-07-09T08:34:55,520 adding 'mdtraj/utils/validation.py' 2026-07-09T08:34:55,521 adding 'mdtraj/utils/zipped.py' 2026-07-09T08:34:55,524 adding 'mdtraj/utils/unit/__init__.py' 2026-07-09T08:34:55,525 adding 'mdtraj/utils/unit/basedimension.py' 2026-07-09T08:34:55,527 adding 'mdtraj/utils/unit/baseunit.py' 2026-07-09T08:34:55,528 adding 'mdtraj/utils/unit/constants.py' 2026-07-09T08:34:55,531 adding 'mdtraj/utils/unit/doctests.py' 2026-07-09T08:34:55,533 adding 'mdtraj/utils/unit/mymatrix.py' 2026-07-09T08:34:55,535 adding 'mdtraj/utils/unit/prefix.py' 2026-07-09T08:34:55,538 adding 'mdtraj/utils/unit/quantity.py' 2026-07-09T08:34:55,540 adding 'mdtraj/utils/unit/standard_dimensions.py' 2026-07-09T08:34:55,543 adding 'mdtraj/utils/unit/unit.py' 2026-07-09T08:34:55,546 adding 'mdtraj/utils/unit/unit_definitions.py' 2026-07-09T08:34:55,547 adding 'mdtraj/utils/unit/unit_math.py' 2026-07-09T08:34:55,549 adding 'mdtraj/utils/unit/unit_operators.py' 2026-07-09T08:34:55,554 adding 'mdtraj-1.11.1.post2.dist-info/licenses/LICENSE' 2026-07-09T08:34:55,556 adding 'mdtraj-1.11.1.post2.dist-info/METADATA' 2026-07-09T08:34:55,557 adding 'mdtraj-1.11.1.post2.dist-info/WHEEL' 2026-07-09T08:34:55,558 adding 'mdtraj-1.11.1.post2.dist-info/entry_points.txt' 2026-07-09T08:34:55,559 adding 'mdtraj-1.11.1.post2.dist-info/top_level.txt' 2026-07-09T08:34:55,561 adding 'mdtraj-1.11.1.post2.dist-info/RECORD' 2026-07-09T08:34:55,637 removing build/bdist.linux-armv7l/wheel 2026-07-09T08:34:57,030 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2026-07-09T08:34:57,182 Created wheel for mdtraj: filename=mdtraj-1.11.1.post2-cp311-cp311-linux_armv7l.whl size=7014977 sha256=82b6f526adbecbdda86bc3cc5fb7c892f5cad08bff5f1eefc407258358ea8cf8 2026-07-09T08:34:57,183 Stored in directory: /tmp/pip-ephem-wheel-cache-xhg7jnws/wheels/4b/b8/2f/6d1a570f769afbeab08cf24108eb719c2bc59cb2ddcd42da62 2026-07-09T08:34:57,202 Successfully built mdtraj 2026-07-09T08:34:57,381 Removed build tracker: '/tmp/pip-build-tracker-wewecr3d'