2026-02-10T02:16:42,642 Created temporary directory: /tmp/pip-ephem-wheel-cache-wcvkr1by 2026-02-10T02:16:42,644 Created temporary directory: /tmp/pip-build-tracker-i29vtrum 2026-02-10T02:16:42,644 Initialized build tracking at /tmp/pip-build-tracker-i29vtrum 2026-02-10T02:16:42,645 Created build tracker: /tmp/pip-build-tracker-i29vtrum 2026-02-10T02:16:42,645 Entered build tracker: /tmp/pip-build-tracker-i29vtrum 2026-02-10T02:16:42,646 Created temporary directory: /tmp/pip-wheel-capmg_1c 2026-02-10T02:16:42,649 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-10T02:16:42,651 Created temporary directory: /tmp/pip-ephem-wheel-cache-8ezzudpv 2026-02-10T02:16:42,673 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-10T02:16:42,676 2 location(s) to search for versions of mdtraj: 2026-02-10T02:16:42,676 * https://pypi.org/simple/mdtraj/ 2026-02-10T02:16:42,676 * https://www.piwheels.org/simple/mdtraj/ 2026-02-10T02:16:42,677 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2026-02-10T02:16:42,678 Getting page https://pypi.org/simple/mdtraj/ 2026-02-10T02:16:42,679 Found index url https://pypi.org/simple 2026-02-10T02:16:42,926 Fetched page https://pypi.org/simple/mdtraj/ as application/vnd.pypi.simple.v1+json 2026-02-10T02:16:42,958 Found link https://files.pythonhosted.org/packages/cb/82/93ced2a2e5d37f36330fe3e74081fdd4ce8f933ebd16b4fab14cb5c6c29c/mdtraj-0.3.tar.gz (from https://pypi.org/simple/mdtraj/), 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https://files.pythonhosted.org/packages/3c/aa/b344aed2d1ec6bc2ac4e5e897ded78148b51b2ee730c5eaccce851d26082/mdtraj-1.11.1.post1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-10T02:16:43,069 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/92/13/e017236bd57f4564e0b43b9f1783a5c88f329cf7cf4b75076e1a1e37df03/mdtraj-1.11.1.post1-cp312-cp312-win_amd64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-10T02:16:43,070 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/58/94/3b51167be053a4570a323cb032d83914af37db8a5c82afc13cc7bdd5c46a/mdtraj-1.11.1.post1-cp313-cp313-macosx_10_13_universal2.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-10T02:16:43,070 Skipping link: No binaries permitted for mdtraj: 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https://files.pythonhosted.org/packages/3d/4d/372c52d6fb06f87026e3d84469501b8020bf8a7a326d701a17ff1a560b65/mdtraj-1.11.1.post1-cp314-cp314-win_amd64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2026-02-10T02:16:43,074 Found link https://files.pythonhosted.org/packages/66/3b/55f24465b9d5905eea28e14173e0a15c3a24d4e85280073f5062fac0d3b7/mdtraj-1.11.1.post1.tar.gz (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11), version: 1.11.1.post1 2026-02-10T02:16:43,075 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2026-02-10T02:16:43,076 Getting page https://www.piwheels.org/simple/mdtraj/ 2026-02-10T02:16:43,077 Found index url https://www.piwheels.org/simple 2026-02-10T02:16:43,242 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2026-02-10T02:16:43,257 Skipping link: No binaries permitted for mdtraj: 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(from https://www.piwheels.org/simple/mdtraj/) 2026-02-10T02:16:43,280 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/) 2026-02-10T02:16:43,280 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/) 2026-02-10T02:16:43,281 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/) 2026-02-10T02:16:43,282 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv6l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2026-02-10T02:16:43,282 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2026-02-10T02:16:43,283 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2026-02-10T02:16:43,283 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv7l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2026-02-10T02:16:43,284 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv6l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2026-02-10T02:16:43,285 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2026-02-10T02:16:43,286 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2026-02-10T02:16:43,286 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2026-02-10T02:16:43,312 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2026-02-10T02:16:43,330 Collecting mdtraj==1.11.1.post1 2026-02-10T02:16:43,333 Created temporary directory: /tmp/pip-unpack-x_thql1m 2026-02-10T02:16:43,802 Downloading mdtraj-1.11.1.post1.tar.gz (2.7 MB) 2026-02-10T02:16:45,180 Added mdtraj==1.11.1.post1 from https://files.pythonhosted.org/packages/66/3b/55f24465b9d5905eea28e14173e0a15c3a24d4e85280073f5062fac0d3b7/mdtraj-1.11.1.post1.tar.gz to build tracker '/tmp/pip-build-tracker-i29vtrum' 2026-02-10T02:16:45,190 Created temporary directory: /tmp/pip-build-env-8iy54wjl 2026-02-10T02:16:45,195 Installing build dependencies: started 2026-02-10T02:16:45,196 Running command pip subprocess to install build dependencies 2026-02-10T02:16:46,328 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-02-10T02:16:46,935 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-10T02:16:46,958 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-10T02:16:48,713 Collecting setuptools 2026-02-10T02:16:48,732 Using cached setuptools-82.0.0-py3-none-any.whl (1.0 MB) 2026-02-10T02:16:48,942 Collecting versioneer[toml] 2026-02-10T02:16:48,952 Downloading https://www.piwheels.org/simple/versioneer/versioneer-0.29-py3-none-any.whl (46 kB) 2026-02-10T02:16:48,969 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 46.8/46.8 kB 4.4 MB/s eta 0:00:00 2026-02-10T02:16:49,214 Collecting wheel 2026-02-10T02:16:49,228 Using cached https://www.piwheels.org/simple/wheel/wheel-0.46.3-py3-none-any.whl (30 kB) 2026-02-10T02:16:50,225 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-10T02:16:50,233 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-10T02:16:50,239 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-10T02:16:50,247 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-10T02:16:50,254 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-10T02:16:50,954 Collecting numpy~=2.0 2026-02-10T02:16:51,412 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.1-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-02-10T02:16:53,829 Collecting Cython>=3.0.0 2026-02-10T02:16:54,579 Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB) 2026-02-10T02:16:55,069 Collecting packaging>=24.0 2026-02-10T02:16:55,083 Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB) 2026-02-10T02:16:58,155 Installing collected packages: versioneer, setuptools, packaging, numpy, Cython, wheel 2026-02-10T02:16:58,186 Creating /tmp/pip-build-env-8iy54wjl/overlay/local/bin 2026-02-10T02:16:58,188 changing mode of /tmp/pip-build-env-8iy54wjl/overlay/local/bin/versioneer to 755 2026-02-10T02:17:10,156 changing mode of /tmp/pip-build-env-8iy54wjl/overlay/local/bin/f2py to 755 2026-02-10T02:17:10,158 changing mode of /tmp/pip-build-env-8iy54wjl/overlay/local/bin/numpy-config to 755 2026-02-10T02:17:13,861 changing mode of /tmp/pip-build-env-8iy54wjl/overlay/local/bin/cygdb to 755 2026-02-10T02:17:13,863 changing mode of /tmp/pip-build-env-8iy54wjl/overlay/local/bin/cython to 755 2026-02-10T02:17:13,865 changing mode of /tmp/pip-build-env-8iy54wjl/overlay/local/bin/cythonize to 755 2026-02-10T02:17:13,990 changing mode of /tmp/pip-build-env-8iy54wjl/overlay/local/bin/wheel to 755 2026-02-10T02:17:14,039 Successfully installed Cython-3.2.4 numpy-2.4.1 packaging-26.0 setuptools-82.0.0 versioneer-0.29 wheel-0.46.3 2026-02-10T02:17:14,517 Installing build dependencies: finished with status 'done' 2026-02-10T02:17:14,535 Getting requirements to build wheel: started 2026-02-10T02:17:14,536 Running command Getting requirements to build wheel 2026-02-10T02:17:15,338 Using built-in specs. 2026-02-10T02:17:15,338 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-02-10T02:17:15,339 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-02-10T02:17:15,339 Target: arm-linux-gnueabihf 2026-02-10T02:17:15,340 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1+deb12u1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2026-02-10T02:17:15,340 Thread model: posix 2026-02-10T02:17:15,341 Supported LTO compression algorithms: zlib zstd 2026-02-10T02:17:15,341 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-02-10T02:17:19,676 /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T02:17:19,677 !! 2026-02-10T02:17:19,679 ******************************************************************************** 2026-02-10T02:17:19,679 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T02:17:19,681 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-02-10T02:17:19,683 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T02:17:19,684 ******************************************************************************** 2026-02-10T02:17:19,687 !! 2026-02-10T02:17:19,688 self._finalize_license_expression() 2026-02-10T02:17:19,690 C compiler: 2026-02-10T02:17:19,691 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-02-10T02:17:19,692 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-02-10T02:17:19,693 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-02-10T02:17:19,694 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-02-10T02:17:19,694 Attempting to autodetect NEON support... Did not detect NEON support 2026-02-10T02:17:19,695 running egg_info 2026-02-10T02:17:19,696 writing mdtraj.egg-info/PKG-INFO 2026-02-10T02:17:19,700 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2026-02-10T02:17:19,702 writing entry points to mdtraj.egg-info/entry_points.txt 2026-02-10T02:17:19,705 writing requirements to mdtraj.egg-info/requires.txt 2026-02-10T02:17:19,706 writing top-level names to mdtraj.egg-info/top_level.txt 2026-02-10T02:17:19,741 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-02-10T02:17:20,033 reading manifest template 'MANIFEST.in' 2026-02-10T02:17:20,713 no previously-included directories found matching '__pycache__' 2026-02-10T02:17:20,715 no previously-included directories found matching '*.pyc' 2026-02-10T02:17:20,715 adding license file 'LICENSE' 2026-02-10T02:17:20,734 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-02-10T02:17:20,850 Getting requirements to build wheel: finished with status 'done' 2026-02-10T02:17:20,853 Created temporary directory: /tmp/pip-modern-metadata-ybv6rne8 2026-02-10T02:17:20,855 Preparing metadata (pyproject.toml): started 2026-02-10T02:17:20,857 Running command Preparing metadata (pyproject.toml) 2026-02-10T02:17:21,608 Using built-in specs. 2026-02-10T02:17:21,609 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-02-10T02:17:21,609 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-02-10T02:17:21,610 Target: arm-linux-gnueabihf 2026-02-10T02:17:21,610 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1+deb12u1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2026-02-10T02:17:21,611 Thread model: posix 2026-02-10T02:17:21,611 Supported LTO compression algorithms: zlib zstd 2026-02-10T02:17:21,612 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-02-10T02:17:25,838 /tmp/pip-wheel-capmg_1c/mdtraj_c79709dae8874ed9aa7ee053d566bb4b/basesetup.py:483: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-ybv6rne8 --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2026-02-10T02:17:25,838 warnings.warn( 2026-02-10T02:17:29,064 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-10T02:17:29,065 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-10T02:17:29,066 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-10T02:17:49,482 C compiler: 2026-02-10T02:17:49,483 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-02-10T02:17:49,483 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-02-10T02:17:49,484 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-02-10T02:17:49,484 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-02-10T02:17:49,485 Attempting to autodetect NEON support... Did not detect NEON support 2026-02-10T02:17:49,486 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2026-02-10T02:17:49,486 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2026-02-10T02:17:49,487 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2026-02-10T02:17:49,487 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2026-02-10T02:17:49,488 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2026-02-10T02:17:49,488 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2026-02-10T02:17:49,488 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2026-02-10T02:17:49,489 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2026-02-10T02:17:49,489 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2026-02-10T02:17:49,490 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2026-02-10T02:17:49,520 /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T02:17:49,521 !! 2026-02-10T02:17:49,522 ******************************************************************************** 2026-02-10T02:17:49,523 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T02:17:49,524 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-02-10T02:17:49,525 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T02:17:49,526 ******************************************************************************** 2026-02-10T02:17:49,527 !! 2026-02-10T02:17:49,528 self._finalize_license_expression() 2026-02-10T02:17:49,536 running dist_info 2026-02-10T02:17:49,545 creating /tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info 2026-02-10T02:17:49,546 writing /tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info/PKG-INFO 2026-02-10T02:17:49,556 writing dependency_links to /tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info/dependency_links.txt 2026-02-10T02:17:49,558 writing entry points to /tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info/entry_points.txt 2026-02-10T02:17:49,561 writing requirements to /tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info/requires.txt 2026-02-10T02:17:49,562 writing top-level names to /tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info/top_level.txt 2026-02-10T02:17:49,564 writing manifest file '/tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info/SOURCES.txt' 2026-02-10T02:17:49,610 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,611 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,612 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,612 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,613 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,613 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,614 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,615 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,615 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,616 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,616 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,617 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,617 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,617 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,618 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,619 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,619 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,620 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,620 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,621 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,621 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,622 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,623 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,623 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,624 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,625 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,625 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,626 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,626 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,626 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,627 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,627 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,628 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,628 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,629 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:17:49,668 reading manifest file '/tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info/SOURCES.txt' 2026-02-10T02:17:49,671 reading manifest template 'MANIFEST.in' 2026-02-10T02:17:50,268 no previously-included directories found matching '__pycache__' 2026-02-10T02:17:50,269 no previously-included directories found matching '*.pyc' 2026-02-10T02:17:50,270 adding license file 'LICENSE' 2026-02-10T02:17:50,281 writing manifest file '/tmp/pip-modern-metadata-ybv6rne8/mdtraj.egg-info/SOURCES.txt' 2026-02-10T02:17:50,289 creating '/tmp/pip-modern-metadata-ybv6rne8/mdtraj-1.11.1.post1.dist-info' 2026-02-10T02:17:51,691 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-10T02:17:51,696 Source in /tmp/pip-wheel-capmg_1c/mdtraj_c79709dae8874ed9aa7ee053d566bb4b has version 1.11.1.post1, which satisfies requirement mdtraj==1.11.1.post1 from https://files.pythonhosted.org/packages/66/3b/55f24465b9d5905eea28e14173e0a15c3a24d4e85280073f5062fac0d3b7/mdtraj-1.11.1.post1.tar.gz 2026-02-10T02:17:51,697 Removed mdtraj==1.11.1.post1 from https://files.pythonhosted.org/packages/66/3b/55f24465b9d5905eea28e14173e0a15c3a24d4e85280073f5062fac0d3b7/mdtraj-1.11.1.post1.tar.gz from build tracker '/tmp/pip-build-tracker-i29vtrum' 2026-02-10T02:17:51,703 Created temporary directory: /tmp/pip-unpack-e82gkdsg 2026-02-10T02:17:51,703 Building wheels for collected packages: mdtraj 2026-02-10T02:17:51,708 Created temporary directory: /tmp/pip-wheel-9nb2lm0a 2026-02-10T02:17:51,709 Destination directory: /tmp/pip-wheel-9nb2lm0a 2026-02-10T02:17:51,711 Building wheel for mdtraj (pyproject.toml): started 2026-02-10T02:17:51,712 Running command Building wheel for mdtraj (pyproject.toml) 2026-02-10T02:17:52,487 Using built-in specs. 2026-02-10T02:17:52,488 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2026-02-10T02:17:52,488 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2026-02-10T02:17:52,489 Target: arm-linux-gnueabihf 2026-02-10T02:17:52,489 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1+deb12u1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2026-02-10T02:17:52,490 Thread model: posix 2026-02-10T02:17:52,490 Supported LTO compression algorithms: zlib zstd 2026-02-10T02:17:52,491 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2026-02-10T02:17:59,967 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-10T02:17:59,967 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-10T02:17:59,968 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-02-10T02:18:20,440 C compiler: 2026-02-10T02:18:20,440 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2026-02-10T02:18:20,441 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2026-02-10T02:18:20,441 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2026-02-10T02:18:20,442 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2026-02-10T02:18:20,443 Attempting to autodetect NEON support... Did not detect NEON support 2026-02-10T02:18:20,444 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2026-02-10T02:18:20,444 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2026-02-10T02:18:20,445 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2026-02-10T02:18:20,445 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2026-02-10T02:18:20,446 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2026-02-10T02:18:20,446 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2026-02-10T02:18:20,447 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2026-02-10T02:18:20,448 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2026-02-10T02:18:20,448 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2026-02-10T02:18:20,449 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2026-02-10T02:18:20,478 /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-10T02:18:20,478 !! 2026-02-10T02:18:20,480 ******************************************************************************** 2026-02-10T02:18:20,480 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-10T02:18:20,481 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2026-02-10T02:18:20,482 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-10T02:18:20,483 ******************************************************************************** 2026-02-10T02:18:20,484 !! 2026-02-10T02:18:20,484 self._finalize_license_expression() 2026-02-10T02:18:20,493 running bdist_wheel 2026-02-10T02:18:20,515 running build 2026-02-10T02:18:20,515 running build_py 2026-02-10T02:18:20,522 creating build/lib.linux-armv7l-cpython-311/mdtraj 2026-02-10T02:18:20,524 copying mdtraj/_version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-02-10T02:18:20,526 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-02-10T02:18:20,528 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2026-02-10T02:18:20,531 creating build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-10T02:18:20,532 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-10T02:18:20,536 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-10T02:18:20,539 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-10T02:18:20,541 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-10T02:18:20,545 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-10T02:18:20,548 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2026-02-10T02:18:20,551 creating build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-02-10T02:18:20,552 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-02-10T02:18:20,553 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-02-10T02:18:20,556 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2026-02-10T02:18:20,559 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,561 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,563 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,566 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,568 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,571 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,573 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,575 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,578 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,581 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,584 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,587 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,589 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,591 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,594 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,597 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,600 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,602 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2026-02-10T02:18:20,606 creating build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-10T02:18:20,607 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-10T02:18:20,610 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-10T02:18:20,612 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-10T02:18:20,614 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2026-02-10T02:18:20,617 creating build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-10T02:18:20,618 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-10T02:18:20,621 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-10T02:18:20,622 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-10T02:18:20,624 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-10T02:18:20,626 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-10T02:18:20,629 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2026-02-10T02:18:20,631 creating build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-02-10T02:18:20,632 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-02-10T02:18:20,635 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-02-10T02:18:20,637 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2026-02-10T02:18:20,640 creating build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,641 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,644 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,646 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,649 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,651 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,653 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,656 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,658 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,661 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,663 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,666 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,668 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,670 copying mdtraj/geometry/pi_stacking.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,673 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,675 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,677 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2026-02-10T02:18:20,680 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,681 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,683 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,685 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,688 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,689 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,692 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,694 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,696 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2026-02-10T02:18:20,699 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-10T02:18:20,700 copying mdtraj/formats/pdbx/PdbxReader.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-10T02:18:20,702 copying mdtraj/formats/pdbx/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-10T02:18:20,704 copying mdtraj/formats/pdbx/pdbxfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-10T02:18:20,707 copying mdtraj/formats/pdbx/pdbx.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-10T02:18:20,710 copying mdtraj/formats/pdbx/PdbxContainers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2026-02-10T02:18:20,713 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-02-10T02:18:20,714 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-02-10T02:18:20,716 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-02-10T02:18:20,719 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2026-02-10T02:18:20,723 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,724 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,726 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,728 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,731 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,733 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,735 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,738 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,740 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,742 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,745 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,748 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,750 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,753 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2026-02-10T02:18:20,761 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-02-10T02:18:20,762 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-02-10T02:18:20,766 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2026-02-10T02:18:20,775 UPDATING build/lib.linux-armv7l-cpython-311/mdtraj/_version.py 2026-02-10T02:18:20,776 set build/lib.linux-armv7l-cpython-311/mdtraj/_version.py to '1.11.1.post1' 2026-02-10T02:18:20,777 running build_ext 2026-02-10T02:18:20,780 building 'mdtraj.formats.xtc' extension 2026-02-10T02:18:20,781 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src 2026-02-10T02:18:20,785 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:18:20,902 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:18:21,054 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2026-02-10T02:18:21,055 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:21,055 788 | int smallnum, smaller, larger, i, is_smaller, run; 2026-02-10T02:18:21,056 | ^~~~~~ 2026-02-10T02:18:21,056 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:21,057 785 | int smallidx, minidx, maxidx; 2026-02-10T02:18:21,058 | ^~~~~~ 2026-02-10T02:18:21,066 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2026-02-10T02:18:21,067 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:21,068 1016 | int errval=1; 2026-02-10T02:18:21,068 | ^~~~~~ 2026-02-10T02:18:21,074 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2026-02-10T02:18:21,075 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:21,075 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2026-02-10T02:18:21,076 | ^~~~~~ 2026-02-10T02:18:21,077 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:21,077 1302 | int smallidx, minidx, maxidx; 2026-02-10T02:18:21,078 | ^~~~~~ 2026-02-10T02:18:21,088 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2026-02-10T02:18:21,090 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:21,090 1509 | int errval=1; 2026-02-10T02:18:21,091 | ^~~~~~ 2026-02-10T02:18:23,698 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:18:23,776 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2026-02-10T02:18:23,777 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 2026-02-10T02:18:23,778 66 | int i,j,result; 2026-02-10T02:18:23,779 | ^ 2026-02-10T02:18:23,779 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 2026-02-10T02:18:23,780 66 | int i,j,result; 2026-02-10T02:18:23,780 | ^ 2026-02-10T02:18:23,781 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2026-02-10T02:18:23,781 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2026-02-10T02:18:23,782 119 | if (NULL == xd) 2026-02-10T02:18:23,782 | ^~ 2026-02-10T02:18:23,783 mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2026-02-10T02:18:23,784 122 | do { 2026-02-10T02:18:23,784 | ^~ 2026-02-10T02:18:23,924 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:18:33,855 In function ‘__Pyx_PyLong_From_int’, 2026-02-10T02:18:33,855 inlined from ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’ at mdtraj/formats/xtc/xtc.c:13181:16, 2026-02-10T02:18:33,856 inlined from ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’ at mdtraj/formats/xtc/xtc.c:12867:13: 2026-02-10T02:18:33,881 mdtraj/formats/xtc/xtc.c:25414:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:33,881 25414 | return PyLong_FromLong((long) value); 2026-02-10T02:18:33,882 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:33,882 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’: 2026-02-10T02:18:33,893 mdtraj/formats/xtc/xtc.c:12889:7: note: ‘__pyx_v_status’ was declared here 2026-02-10T02:18:33,894 12889 | int __pyx_v_status; 2026-02-10T02:18:33,895 | ^~~~~~~~~~~~~~ 2026-02-10T02:18:43,097 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2026-02-10T02:18:43,108 mdtraj/formats/xtc/xtc.c:11337:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,108 11337 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; 2026-02-10T02:18:43,109 | ^ 2026-02-10T02:18:43,117 mdtraj/formats/xtc/xtc.c:9607:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 2026-02-10T02:18:43,117 9607 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-02-10T02:18:43,118 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,127 mdtraj/formats/xtc/xtc.c:11333:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,128 11333 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; 2026-02-10T02:18:43,128 | ^ 2026-02-10T02:18:43,136 mdtraj/formats/xtc/xtc.c:9607:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 2026-02-10T02:18:43,137 9607 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-02-10T02:18:43,137 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,146 mdtraj/formats/xtc/xtc.c:11329:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,147 11329 | } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-10T02:18:43,148 | ^ 2026-02-10T02:18:43,155 mdtraj/formats/xtc/xtc.c:9607:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 2026-02-10T02:18:43,156 9607 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2026-02-10T02:18:43,156 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,165 mdtraj/formats/xtc/xtc.c:11289:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,166 11289 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-10T02:18:43,166 | ^ 2026-02-10T02:18:43,174 mdtraj/formats/xtc/xtc.c:9603:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 2026-02-10T02:18:43,175 9603 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; 2026-02-10T02:18:43,175 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,184 mdtraj/formats/xtc/xtc.c:11271:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,185 11271 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-10T02:18:43,185 | ^ 2026-02-10T02:18:43,193 mdtraj/formats/xtc/xtc.c:9599:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 2026-02-10T02:18:43,194 9599 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; 2026-02-10T02:18:43,195 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,204 mdtraj/formats/xtc/xtc.c:11347:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,204 11347 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-10T02:18:43,205 | ^ 2026-02-10T02:18:43,213 mdtraj/formats/xtc/xtc.c:9595:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 2026-02-10T02:18:43,213 9595 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; 2026-02-10T02:18:43,214 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,223 mdtraj/formats/xtc/xtc.c:11309:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,223 11309 | } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; 2026-02-10T02:18:43,224 | ^ 2026-02-10T02:18:43,232 mdtraj/formats/xtc/xtc.c:9589:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 2026-02-10T02:18:43,232 9589 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-02-10T02:18:43,233 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,242 mdtraj/formats/xtc/xtc.c:11305:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,243 11305 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; 2026-02-10T02:18:43,243 | ^ 2026-02-10T02:18:43,251 mdtraj/formats/xtc/xtc.c:9589:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 2026-02-10T02:18:43,251 9589 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-02-10T02:18:43,252 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,261 mdtraj/formats/xtc/xtc.c:11301:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,262 11301 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-10T02:18:43,262 | ^ 2026-02-10T02:18:43,270 mdtraj/formats/xtc/xtc.c:9589:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 2026-02-10T02:18:43,270 9589 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2026-02-10T02:18:43,271 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,280 mdtraj/formats/xtc/xtc.c:10959:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,280 10959 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; 2026-02-10T02:18:43,281 | ^ 2026-02-10T02:18:43,289 mdtraj/formats/xtc/xtc.c:9591:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 2026-02-10T02:18:43,289 9591 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2026-02-10T02:18:43,290 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:43,299 mdtraj/formats/xtc/xtc.c:10955:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:18:43,299 10955 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0; 2026-02-10T02:18:43,300 | ^ 2026-02-10T02:18:43,308 mdtraj/formats/xtc/xtc.c:9591:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 2026-02-10T02:18:43,308 9591 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2026-02-10T02:18:43,309 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:18:51,460 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:18:51,687 building 'mdtraj.formats.trr' extension 2026-02-10T02:18:51,688 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:18:51,802 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:18:51,947 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2026-02-10T02:18:51,948 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:51,949 788 | int smallnum, smaller, larger, i, is_smaller, run; 2026-02-10T02:18:51,949 | ^~~~~~ 2026-02-10T02:18:51,950 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:51,951 785 | int smallidx, minidx, maxidx; 2026-02-10T02:18:51,952 | ^~~~~~ 2026-02-10T02:18:51,959 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2026-02-10T02:18:51,960 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:51,961 1016 | int errval=1; 2026-02-10T02:18:51,962 | ^~~~~~ 2026-02-10T02:18:51,967 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2026-02-10T02:18:51,968 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:51,969 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2026-02-10T02:18:51,969 | ^~~~~~ 2026-02-10T02:18:51,970 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:51,971 1302 | int smallidx, minidx, maxidx; 2026-02-10T02:18:51,971 | ^~~~~~ 2026-02-10T02:18:51,981 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2026-02-10T02:18:51,983 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2026-02-10T02:18:51,983 1509 | int errval=1; 2026-02-10T02:18:51,984 | ^~~~~~ 2026-02-10T02:18:54,554 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:18:55,344 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:19:06,197 In function ‘__Pyx_PyLong_From_int’, 2026-02-10T02:19:06,198 inlined from ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’ at mdtraj/formats/xtc/trr.c:15162:16, 2026-02-10T02:19:06,198 inlined from ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write’ at mdtraj/formats/xtc/trr.c:14592:13: 2026-02-10T02:19:06,227 mdtraj/formats/xtc/trr.c:27354:22: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:06,228 27354 | return PyLong_FromLong((long) value); 2026-02-10T02:19:06,228 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:06,229 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write’: 2026-02-10T02:19:06,244 mdtraj/formats/xtc/trr.c:14622:7: note: ‘__pyx_v_status’ was declared here 2026-02-10T02:19:06,244 14622 | int __pyx_v_status; 2026-02-10T02:19:06,245 | ^~~~~~~~~~~~~~ 2026-02-10T02:19:17,428 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2026-02-10T02:19:17,439 mdtraj/formats/xtc/trr.c:11932:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,440 11932 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_6 = 2; 2026-02-10T02:19:17,440 | ^ 2026-02-10T02:19:17,449 mdtraj/formats/xtc/trr.c:10252:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2026-02-10T02:19:17,449 10252 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-02-10T02:19:17,450 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,460 mdtraj/formats/xtc/trr.c:11928:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,671 11928 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-10T02:19:17,672 | ^ 2026-02-10T02:19:17,672 mdtraj/formats/xtc/trr.c:10252:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2026-02-10T02:19:17,673 10252 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-02-10T02:19:17,673 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,673 mdtraj/formats/xtc/trr.c:2610:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,674 2610 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2026-02-10T02:19:17,674 | ^ 2026-02-10T02:19:17,675 mdtraj/formats/xtc/trr.c:10252:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2026-02-10T02:19:17,675 10252 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-02-10T02:19:17,676 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,676 mdtraj/formats/xtc/trr.c:11922:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,677 11922 | __pyx_t_15 += __pyx_pybuffernd_forces.diminfo[0].shape; 2026-02-10T02:19:17,677 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2026-02-10T02:19:17,678 mdtraj/formats/xtc/trr.c:10252:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2026-02-10T02:19:17,678 10252 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2026-02-10T02:19:17,679 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,679 mdtraj/formats/xtc/trr.c:11875:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,680 11875 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_6 = 2; 2026-02-10T02:19:17,680 | ^ 2026-02-10T02:19:17,681 mdtraj/formats/xtc/trr.c:10268:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2026-02-10T02:19:17,682 10268 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-02-10T02:19:17,682 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,683 mdtraj/formats/xtc/trr.c:11871:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,683 11871 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-10T02:19:17,684 | ^ 2026-02-10T02:19:17,684 mdtraj/formats/xtc/trr.c:10268:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2026-02-10T02:19:17,685 10268 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-02-10T02:19:17,685 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,686 mdtraj/formats/xtc/trr.c:2610:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,687 2610 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2026-02-10T02:19:17,687 | ^ 2026-02-10T02:19:17,688 mdtraj/formats/xtc/trr.c:10268:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2026-02-10T02:19:17,688 10268 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-02-10T02:19:17,689 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,689 mdtraj/formats/xtc/trr.c:11865:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,690 11865 | __pyx_t_15 += __pyx_pybuffernd_vel.diminfo[0].shape; 2026-02-10T02:19:17,690 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2026-02-10T02:19:17,691 mdtraj/formats/xtc/trr.c:10268:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2026-02-10T02:19:17,691 10268 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2026-02-10T02:19:17,691 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,692 mdtraj/formats/xtc/trr.c:12264:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,692 12264 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-10T02:19:17,693 | ^ 2026-02-10T02:19:17,693 mdtraj/formats/xtc/trr.c:10274:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2026-02-10T02:19:17,694 10274 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2026-02-10T02:19:17,694 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,695 mdtraj/formats/xtc/trr.c:12260:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,695 12260 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-02-10T02:19:17,696 | ^ 2026-02-10T02:19:17,696 mdtraj/formats/xtc/trr.c:10274:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2026-02-10T02:19:17,697 10274 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2026-02-10T02:19:17,698 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,698 mdtraj/formats/xtc/trr.c:12105:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,699 12105 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-10T02:19:17,700 | ^ 2026-02-10T02:19:17,700 mdtraj/formats/xtc/trr.c:10270:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2026-02-10T02:19:17,701 10270 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2026-02-10T02:19:17,702 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,703 mdtraj/formats/xtc/trr.c:12101:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,703 12101 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-02-10T02:19:17,704 | ^ 2026-02-10T02:19:17,704 mdtraj/formats/xtc/trr.c:10270:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2026-02-10T02:19:17,705 10270 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2026-02-10T02:19:17,705 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,706 mdtraj/formats/xtc/trr.c:12157:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,707 12157 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_6 = 1; 2026-02-10T02:19:17,708 | ^ 2026-02-10T02:19:17,709 mdtraj/formats/xtc/trr.c:10254:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2026-02-10T02:19:17,709 10254 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2026-02-10T02:19:17,710 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:17,711 mdtraj/formats/xtc/trr.c:12153:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:17,712 12153 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_6 = 0; 2026-02-10T02:19:17,712 | ^ 2026-02-10T02:19:17,713 mdtraj/formats/xtc/trr.c:10254:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2026-02-10T02:19:17,714 10254 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2026-02-10T02:19:17,714 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:26,042 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:19:26,198 building 'mdtraj.formats.dcd' extension 2026-02-10T02:19:26,199 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd 2026-02-10T02:19:26,200 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src 2026-02-10T02:19:26,201 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:19:37,709 In function ‘__Pyx_PyLong_From_int’, 2026-02-10T02:19:37,710 inlined from ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’ at mdtraj/formats/dcd/dcd.c:9971:19: 2026-02-10T02:19:37,730 mdtraj/formats/dcd/dcd.c:19224:22: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:19:37,731 19224 | return PyLong_FromLong((long) value); 2026-02-10T02:19:37,731 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:37,732 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2026-02-10T02:19:37,740 mdtraj/formats/dcd/dcd.c:8619:7: note: ‘__pyx_v_i’ was declared here 2026-02-10T02:19:37,741 8619 | int __pyx_v_i; 2026-02-10T02:19:37,742 | ^~~~~~~~~ 2026-02-10T02:19:41,583 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:19:41,838 mdtraj/formats/dcd/src/dcdplugin.c: In function ‘open_dcd_read’: 2026-02-10T02:19:41,839 mdtraj/formats/dcd/src/dcdplugin.c:903:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘fio_size_t’ {aka ‘long long int’} [-Wformat=] 2026-02-10T02:19:41,840 903 | printf("dcdplugin) Warning: DCD header claims %d frames, but \n" 2026-02-10T02:19:41,840 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:41,841 ...... 2026-02-10T02:19:41,841 906 | dcd->nsets, trjsize, newnsets, framesize); 2026-02-10T02:19:41,842 | ~~~~~~~ 2026-02-10T02:19:41,843 | | 2026-02-10T02:19:41,843 | fio_size_t {aka long long int} 2026-02-10T02:19:41,843 mdtraj/formats/dcd/src/dcdplugin.c:904:39: note: format string is defined here 2026-02-10T02:19:41,844 904 | "dcdplugin) file size (%ld) indicates there are actually \n" 2026-02-10T02:19:41,844 | ~~^ 2026-02-10T02:19:41,845 | | 2026-02-10T02:19:41,845 | long int 2026-02-10T02:19:41,846 | %lld 2026-02-10T02:19:41,846 mdtraj/formats/dcd/src/dcdplugin.c:903:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘fio_size_t’ {aka ‘long long int’} [-Wformat=] 2026-02-10T02:19:41,847 903 | printf("dcdplugin) Warning: DCD header claims %d frames, but \n" 2026-02-10T02:19:41,847 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:19:41,848 ...... 2026-02-10T02:19:41,848 906 | dcd->nsets, trjsize, newnsets, framesize); 2026-02-10T02:19:41,849 | ~~~~~~~~~ 2026-02-10T02:19:41,849 | | 2026-02-10T02:19:41,850 | fio_size_t {aka long long int} 2026-02-10T02:19:41,850 mdtraj/formats/dcd/src/dcdplugin.c:905:36: note: format string is defined here 2026-02-10T02:19:41,851 905 | "%d frames of size (%ld)\n", 2026-02-10T02:19:41,852 | ~~^ 2026-02-10T02:19:41,853 | | 2026-02-10T02:19:41,854 | long int 2026-02-10T02:19:41,855 | %lld 2026-02-10T02:19:43,242 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:19:43,418 building 'mdtraj.formats.dtr' extension 2026-02-10T02:19:43,419 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr 2026-02-10T02:19:43,420 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src 2026-02-10T02:19:43,421 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:20:01,446 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:20:03,846 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2026-02-10T02:20:03,847 mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-02-10T02:20:03,847 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2026-02-10T02:20:03,848 | ~~^ ~ 2026-02-10T02:20:03,848 | | | 2026-02-10T02:20:03,849 | | size_t {aka unsigned int} 2026-02-10T02:20:03,849 | long int 2026-02-10T02:20:03,850 | %d 2026-02-10T02:20:03,850 mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-10T02:20:03,851 487 | printf("size %d framesize %d\n\n", 2026-02-10T02:20:03,851 | ~^ 2026-02-10T02:20:03,852 | | 2026-02-10T02:20:03,852 | int 2026-02-10T02:20:03,853 | %lld 2026-02-10T02:20:03,853 488 | keys[i].size(), m_framesize); 2026-02-10T02:20:03,854 | ~~~~~~~~~~~~~~ 2026-02-10T02:20:03,854 | | 2026-02-10T02:20:03,855 | uint64_t {aka long long unsigned int} 2026-02-10T02:20:03,855 mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-10T02:20:03,856 487 | printf("size %d framesize %d\n\n", 2026-02-10T02:20:03,856 | ~^ 2026-02-10T02:20:03,857 | | 2026-02-10T02:20:03,858 | int 2026-02-10T02:20:03,858 | %lld 2026-02-10T02:20:03,859 488 | keys[i].size(), m_framesize); 2026-02-10T02:20:03,859 | ~~~~~~~~~~~ 2026-02-10T02:20:03,860 | | 2026-02-10T02:20:03,860 | uint64_t {aka long long unsigned int} 2026-02-10T02:20:03,861 mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-02-10T02:20:03,861 494 | "non-constant time interval at frame %ld\n", i); 2026-02-10T02:20:03,862 | ~~^ ~ 2026-02-10T02:20:03,863 | | | 2026-02-10T02:20:03,863 | | size_t {aka unsigned int} 2026-02-10T02:20:03,864 | long int 2026-02-10T02:20:03,864 | %d 2026-02-10T02:20:03,865 mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-02-10T02:20:03,865 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2026-02-10T02:20:03,866 | ~~^ ~ 2026-02-10T02:20:03,866 | | | 2026-02-10T02:20:03,867 | | size_t {aka unsigned int} 2026-02-10T02:20:03,868 | long int 2026-02-10T02:20:03,868 | %d 2026-02-10T02:20:04,026 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2026-02-10T02:20:04,027 mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-10T02:20:04,027 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2026-02-10T02:20:04,028 | ~~^ 2026-02-10T02:20:04,029 | | 2026-02-10T02:20:04,029 | long int 2026-02-10T02:20:04,030 | %lld 2026-02-10T02:20:04,030 1302 | 3*natoms, pos.count); 2026-02-10T02:20:04,031 | ~~~~~~~~~ 2026-02-10T02:20:04,031 | | 2026-02-10T02:20:04,032 | uint64_t {aka long long unsigned int} 2026-02-10T02:20:04,033 mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-10T02:20:04,034 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2026-02-10T02:20:04,034 | ~~^ 2026-02-10T02:20:04,035 | | 2026-02-10T02:20:04,036 | long int 2026-02-10T02:20:04,036 | %lld 2026-02-10T02:20:04,037 1311 | 3*natoms, vel.count); 2026-02-10T02:20:04,037 | ~~~~~~~~~ 2026-02-10T02:20:04,038 | | 2026-02-10T02:20:04,038 | uint64_t {aka long long unsigned int} 2026-02-10T02:20:04,067 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2026-02-10T02:20:04,068 mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2026-02-10T02:20:04,069 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2026-02-10T02:20:04,069 | ~~^ 2026-02-10T02:20:04,070 | | 2026-02-10T02:20:04,071 | long int 2026-02-10T02:20:04,071 | %lld 2026-02-10T02:20:04,072 1573 | velblob.count, 3*natoms); 2026-02-10T02:20:04,072 | ~~~~~~~~~~~~~ 2026-02-10T02:20:04,073 | | 2026-02-10T02:20:04,073 | uint64_t {aka long long unsigned int} 2026-02-10T02:20:05,384 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2026-02-10T02:20:05,385 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2026-02-10T02:20:05,386 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2026-02-10T02:20:05,386 | ~~~~~~~~^~~~~ 2026-02-10T02:20:08,173 In file included from /usr/include/c++/12/map:60, 2026-02-10T02:20:08,174 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2026-02-10T02:20:08,175 /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2026-02-10T02:20:08,176 /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-10T02:20:08,176 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2026-02-10T02:20:08,177 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:08,245 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2026-02-10T02:20:08,245 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-10T02:20:08,246 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2026-02-10T02:20:08,247 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:08,306 In file included from /usr/include/c++/12/map:61: 2026-02-10T02:20:08,306 /usr/include/c++/12/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2026-02-10T02:20:08,307 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-10T02:20:08,308 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-02-10T02:20:08,308 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:08,309 531 | std::forward_as_tuple(std::move(__k)), 2026-02-10T02:20:08,310 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:08,311 532 | std::tuple<>()); 2026-02-10T02:20:08,311 | ~~~~~~~~~~~~~~~ 2026-02-10T02:20:08,399 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’, 2026-02-10T02:20:08,399 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28: 2026-02-10T02:20:08,400 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-10T02:20:08,400 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-02-10T02:20:08,401 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:08,402 531 | std::forward_as_tuple(std::move(__k)), 2026-02-10T02:20:08,402 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:08,403 532 | std::tuple<>()); 2026-02-10T02:20:08,404 | ~~~~~~~~~~~~~~~ 2026-02-10T02:20:09,249 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2026-02-10T02:20:09,250 mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2026-02-10T02:20:09,251 706 | sprintf(sub, "%03x/", i); 2026-02-10T02:20:09,251 | ^~~~ 2026-02-10T02:20:09,252 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2026-02-10T02:20:09,252 706 | sprintf(sub, "%03x/", i); 2026-02-10T02:20:09,253 | ^~~~~~~ 2026-02-10T02:20:09,254 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2026-02-10T02:20:09,254 706 | sprintf(sub, "%03x/", i); 2026-02-10T02:20:09,255 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2026-02-10T02:20:09,255 mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2026-02-10T02:20:09,256 714 | sprintf(subsub, "%03x", j); 2026-02-10T02:20:09,257 | ^~~~ 2026-02-10T02:20:09,257 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2026-02-10T02:20:09,258 714 | sprintf(subsub, "%03x", j); 2026-02-10T02:20:09,259 | ^~~~~~ 2026-02-10T02:20:09,259 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2026-02-10T02:20:09,260 714 | sprintf(subsub, "%03x", j); 2026-02-10T02:20:09,260 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:09,655 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2026-02-10T02:20:09,656 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-10T02:20:09,657 667 | sprintf(answer, "%03x/", d1); 2026-02-10T02:20:09,657 | ^ 2026-02-10T02:20:09,658 In function ‘std::string DDreldir(const std::string&, int, int)’, 2026-02-10T02:20:09,659 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2026-02-10T02:20:09,659 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2026-02-10T02:20:09,660 667 | sprintf(answer, "%03x/", d1); 2026-02-10T02:20:09,660 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:09,661 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2026-02-10T02:20:09,661 mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 2026-02-10T02:20:09,662 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-02-10T02:20:09,662 | ^~~~ 2026-02-10T02:20:09,663 In function ‘std::string DDreldir(const std::string&, int, int)’, 2026-02-10T02:20:09,663 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2026-02-10T02:20:09,664 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2026-02-10T02:20:09,665 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-02-10T02:20:09,665 | ^~~~~~~~~~~~ 2026-02-10T02:20:09,666 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2026-02-10T02:20:09,666 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2026-02-10T02:20:09,667 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:12,817 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’, 2026-02-10T02:20:12,817 inlined from ‘int desres::molfile::DtrReader::frame_from_bytes(const void*, uint64_t, molfile_timestep_t*) const’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1735:38: 2026-02-10T02:20:12,818 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2026-02-10T02:20:12,819 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2026-02-10T02:20:12,819 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:12,820 531 | std::forward_as_tuple(std::move(__k)), 2026-02-10T02:20:12,821 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-10T02:20:12,822 532 | std::tuple<>()); 2026-02-10T02:20:12,822 | ~~~~~~~~~~~~~~~ 2026-02-10T02:20:17,789 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:20:18,141 building 'mdtraj._rmsd' extension 2026-02-10T02:20:18,143 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd 2026-02-10T02:20:18,144 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src 2026-02-10T02:20:18,145 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:05,667 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:05,873 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:06,133 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:06,913 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:21:07,242 building 'mdtraj._lprmsd' extension 2026-02-10T02:21:07,243 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:33,987 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:36,797 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:37,001 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:38,256 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:38,561 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:38,824 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:21:39,616 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:21:39,925 building 'mdtraj.core.lib.libtheobald' extension 2026-02-10T02:21:39,926 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2026-02-10T02:21:40,676 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2026-02-10T02:21:40,879 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o 2026-02-10T02:21:40,908 building 'mdtraj.geometry._geometry' extension 2026-02-10T02:21:40,909 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src 2026-02-10T02:21:40,911 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:22:19,884 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:22:34,082 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:22:38,142 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:22:39,268 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:22:39,633 building 'mdtraj.geometry.drid' extension 2026-02-10T02:22:39,635 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:23:11,955 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:23:12,596 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:23:12,704 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:23:12,999 building 'mdtraj.geometry.neighbors' extension 2026-02-10T02:23:13,000 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:23:43,167 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:23:44,470 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:23:44,760 building 'mdtraj.geometry.neighborlist' extension 2026-02-10T02:23:44,761 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:24:12,149 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2026-02-10T02:24:16,638 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2026-02-10T02:24:16,639 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2026-02-10T02:24:16,639 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:24:16,640 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2026-02-10T02:24:16,640 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-02-10T02:24:16,641 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2026-02-10T02:24:16,641 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-02-10T02:24:16,642 341 | float periodicBoxVectors[3][3]; 2026-02-10T02:24:16,643 | ^~~~~~~~~~~~~~~~~~ 2026-02-10T02:24:16,643 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2026-02-10T02:24:16,644 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2026-02-10T02:24:16,644 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:24:16,645 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2026-02-10T02:24:16,646 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-02-10T02:24:16,646 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2026-02-10T02:24:16,647 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-02-10T02:24:16,648 341 | float periodicBoxVectors[3][3]; 2026-02-10T02:24:16,648 | ^~~~~~~~~~~~~~~~~~ 2026-02-10T02:24:16,649 mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:24:16,650 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); 2026-02-10T02:24:16,651 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-02-10T02:24:16,651 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-02-10T02:24:16,652 341 | float periodicBoxVectors[3][3]; 2026-02-10T02:24:16,653 | ^~~~~~~~~~~~~~~~~~ 2026-02-10T02:24:16,653 mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-10T02:24:16,654 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); 2026-02-10T02:24:16,654 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2026-02-10T02:24:16,655 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2026-02-10T02:24:16,656 341 | float periodicBoxVectors[3][3]; 2026-02-10T02:24:16,656 | ^~~~~~~~~~~~~~~~~~ 2026-02-10T02:24:17,472 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so 2026-02-10T02:24:17,890 installing to build/bdist.linux-armv7l/wheel 2026-02-10T02:24:17,890 running install 2026-02-10T02:24:17,915 running install_lib 2026-02-10T02:24:17,927 creating build/bdist.linux-armv7l/wheel 2026-02-10T02:24:17,930 creating build/bdist.linux-armv7l/wheel/mdtraj 2026-02-10T02:24:17,931 copying build/lib.linux-armv7l-cpython-311/mdtraj/_version.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-10T02:24:17,933 copying build/lib.linux-armv7l-cpython-311/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-10T02:24:17,936 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2026-02-10T02:24:17,937 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-10T02:24:17,941 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-10T02:24:17,944 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-10T02:24:17,945 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-10T02:24:17,949 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-10T02:24:17,952 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2026-02-10T02:24:17,953 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-02-10T02:24:17,955 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-02-10T02:24:17,956 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2026-02-10T02:24:17,959 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2026-02-10T02:24:17,962 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2026-02-10T02:24:17,963 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-02-10T02:24:17,965 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-02-10T02:24:17,967 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2026-02-10T02:24:17,971 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2026-02-10T02:24:17,972 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:17,975 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,000 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,003 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,005 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,007 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,010 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,023 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,026 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,028 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,031 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,033 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,055 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,057 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,059 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,061 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,065 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdbx 2026-02-10T02:24:18,066 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/PdbxReader.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-10T02:24:18,069 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-10T02:24:18,071 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/pdbxfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-10T02:24:18,073 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/pdbx.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-10T02:24:18,076 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/PdbxContainers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2026-02-10T02:24:18,079 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,082 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2026-02-10T02:24:18,083 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-02-10T02:24:18,085 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2026-02-10T02:24:18,086 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb/data 2026-02-10T02:24:18,089 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb/data 2026-02-10T02:24:18,091 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-02-10T02:24:18,094 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2026-02-10T02:24:18,097 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,183 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,187 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,190 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2026-02-10T02:24:18,193 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2026-02-10T02:24:18,194 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-02-10T02:24:18,196 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-02-10T02:24:18,199 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-02-10T02:24:18,201 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2026-02-10T02:24:18,204 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2026-02-10T02:24:18,205 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-10T02:24:18,208 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-10T02:24:18,210 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-10T02:24:18,212 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-10T02:24:18,213 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-10T02:24:18,216 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2026-02-10T02:24:18,218 copying build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-10T02:24:18,239 copying build/lib.linux-armv7l-cpython-311/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-10T02:24:18,241 copying build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj 2026-02-10T02:24:18,275 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2026-02-10T02:24:18,276 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-02-10T02:24:18,278 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-02-10T02:24:18,280 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2026-02-10T02:24:18,283 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2026-02-10T02:24:18,284 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,286 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,289 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,292 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,294 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,296 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,298 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,321 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,324 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,326 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,329 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,332 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,335 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,338 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,380 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/pi_stacking.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,382 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,384 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,386 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,409 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,506 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2026-02-10T02:24:18,509 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2026-02-10T02:24:18,510 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-10T02:24:18,512 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-10T02:24:18,514 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-10T02:24:18,517 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-10T02:24:18,518 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-10T02:24:18,521 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-10T02:24:18,524 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-10T02:24:18,526 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2026-02-10T02:24:18,529 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2026-02-10T02:24:18,530 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,533 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,535 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,538 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,540 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,543 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,546 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,549 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,551 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,554 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,557 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,560 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,562 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2026-02-10T02:24:18,564 running install_egg_info 2026-02-10T02:24:18,581 running egg_info 2026-02-10T02:24:18,590 writing mdtraj.egg-info/PKG-INFO 2026-02-10T02:24:18,596 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2026-02-10T02:24:18,598 writing entry points to mdtraj.egg-info/entry_points.txt 2026-02-10T02:24:18,601 writing requirements to mdtraj.egg-info/requires.txt 2026-02-10T02:24:18,602 writing top-level names to mdtraj.egg-info/top_level.txt 2026-02-10T02:24:18,638 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,638 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,639 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,639 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,640 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,642 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,642 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,643 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,643 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,644 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,646 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,646 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,647 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,648 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,648 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,650 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,650 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,651 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,651 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,651 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,653 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,653 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,654 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,655 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,655 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,657 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,657 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,658 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,658 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,659 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,661 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,662 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,662 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,663 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,663 dependency /tmp/pip-build-env-8iy54wjl/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-10T02:24:18,678 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-02-10T02:24:18,701 reading manifest template 'MANIFEST.in' 2026-02-10T02:24:19,332 no previously-included directories found matching '__pycache__' 2026-02-10T02:24:19,334 no previously-included directories found matching '*.pyc' 2026-02-10T02:24:19,335 adding license file 'LICENSE' 2026-02-10T02:24:19,349 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2026-02-10T02:24:19,357 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/./mdtraj-1.11.1.post1-py3.11.egg-info 2026-02-10T02:24:19,371 running install_scripts 2026-02-10T02:24:19,424 creating build/bdist.linux-armv7l/wheel/mdtraj-1.11.1.post1.dist-info/WHEEL 2026-02-10T02:24:19,428 creating '/tmp/pip-wheel-9nb2lm0a/.tmp-hc_0cagr/mdtraj-1.11.1.post1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-10T02:24:19,430 adding 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'mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so' 2026-02-10T02:24:22,071 adding 'mdtraj/geometry/alignment.py' 2026-02-10T02:24:22,073 adding 'mdtraj/geometry/angle.py' 2026-02-10T02:24:22,075 adding 'mdtraj/geometry/contact.py' 2026-02-10T02:24:22,078 adding 'mdtraj/geometry/dihedral.py' 2026-02-10T02:24:22,080 adding 'mdtraj/geometry/distance.py' 2026-02-10T02:24:22,390 adding 'mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so' 2026-02-10T02:24:22,401 adding 'mdtraj/geometry/dssp.py' 2026-02-10T02:24:22,404 adding 'mdtraj/geometry/hbond.py' 2026-02-10T02:24:22,406 adding 'mdtraj/geometry/internal.py' 2026-02-10T02:24:22,721 adding 'mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so' 2026-02-10T02:24:23,024 adding 'mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so' 2026-02-10T02:24:23,034 adding 'mdtraj/geometry/order.py' 2026-02-10T02:24:23,037 adding 'mdtraj/geometry/pi_stacking.py' 2026-02-10T02:24:23,039 adding 'mdtraj/geometry/rdf.py' 2026-02-10T02:24:23,040 adding 'mdtraj/geometry/rg.py' 2026-02-10T02:24:23,042 adding 'mdtraj/geometry/sasa.py' 2026-02-10T02:24:23,044 adding 'mdtraj/geometry/shape.py' 2026-02-10T02:24:23,046 adding 'mdtraj/geometry/thermodynamic_properties.py' 2026-02-10T02:24:23,048 adding 'mdtraj/nmr/__init__.py' 2026-02-10T02:24:23,049 adding 'mdtraj/nmr/scalar_couplings.py' 2026-02-10T02:24:23,051 adding 'mdtraj/nmr/shift_wrappers.py' 2026-02-10T02:24:23,053 adding 'mdtraj/reporters/__init__.py' 2026-02-10T02:24:23,055 adding 'mdtraj/reporters/basereporter.py' 2026-02-10T02:24:23,056 adding 'mdtraj/reporters/dcdreporter.py' 2026-02-10T02:24:23,058 adding 'mdtraj/reporters/hdf5reporter.py' 2026-02-10T02:24:23,059 adding 'mdtraj/reporters/netcdfreporter.py' 2026-02-10T02:24:23,061 adding 'mdtraj/reporters/xtcreporter.py' 2026-02-10T02:24:23,063 adding 'mdtraj/scripts/__init__.py' 2026-02-10T02:24:23,065 adding 'mdtraj/scripts/mdconvert.py' 2026-02-10T02:24:23,069 adding 'mdtraj/scripts/mdinspect.py' 2026-02-10T02:24:23,070 adding 'mdtraj/testing/__init__.py' 2026-02-10T02:24:23,073 adding 'mdtraj/testing/docscrape.py' 2026-02-10T02:24:23,075 adding 'mdtraj/testing/docstrings.py' 2026-02-10T02:24:23,076 adding 'mdtraj/testing/testing.py' 2026-02-10T02:24:23,078 adding 'mdtraj/utils/__init__.py' 2026-02-10T02:24:23,080 adding 'mdtraj/utils/contextmanagers.py' 2026-02-10T02:24:23,081 adding 'mdtraj/utils/delay_import.py' 2026-02-10T02:24:23,083 adding 'mdtraj/utils/rotation.py' 2026-02-10T02:24:23,084 adding 'mdtraj/utils/singleton.py' 2026-02-10T02:24:23,086 adding 'mdtraj/utils/unitcell.py' 2026-02-10T02:24:23,088 adding 'mdtraj/utils/validation.py' 2026-02-10T02:24:23,089 adding 'mdtraj/utils/zipped.py' 2026-02-10T02:24:23,092 adding 'mdtraj/utils/unit/__init__.py' 2026-02-10T02:24:23,093 adding 'mdtraj/utils/unit/basedimension.py' 2026-02-10T02:24:23,095 adding 'mdtraj/utils/unit/baseunit.py' 2026-02-10T02:24:23,097 adding 'mdtraj/utils/unit/constants.py' 2026-02-10T02:24:23,099 adding 'mdtraj/utils/unit/doctests.py' 2026-02-10T02:24:23,102 adding 'mdtraj/utils/unit/mymatrix.py' 2026-02-10T02:24:23,103 adding 'mdtraj/utils/unit/prefix.py' 2026-02-10T02:24:23,107 adding 'mdtraj/utils/unit/quantity.py' 2026-02-10T02:24:23,109 adding 'mdtraj/utils/unit/standard_dimensions.py' 2026-02-10T02:24:23,112 adding 'mdtraj/utils/unit/unit.py' 2026-02-10T02:24:23,114 adding 'mdtraj/utils/unit/unit_definitions.py' 2026-02-10T02:24:23,116 adding 'mdtraj/utils/unit/unit_math.py' 2026-02-10T02:24:23,117 adding 'mdtraj/utils/unit/unit_operators.py' 2026-02-10T02:24:23,123 adding 'mdtraj-1.11.1.post1.dist-info/licenses/LICENSE' 2026-02-10T02:24:23,124 adding 'mdtraj-1.11.1.post1.dist-info/METADATA' 2026-02-10T02:24:23,125 adding 'mdtraj-1.11.1.post1.dist-info/WHEEL' 2026-02-10T02:24:23,126 adding 'mdtraj-1.11.1.post1.dist-info/entry_points.txt' 2026-02-10T02:24:23,127 adding 'mdtraj-1.11.1.post1.dist-info/top_level.txt' 2026-02-10T02:24:23,129 adding 'mdtraj-1.11.1.post1.dist-info/RECORD' 2026-02-10T02:24:23,215 removing build/bdist.linux-armv7l/wheel 2026-02-10T02:24:24,622 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2026-02-10T02:24:24,776 Created wheel for mdtraj: filename=mdtraj-1.11.1.post1-cp311-cp311-linux_armv7l.whl size=7021525 sha256=f4d25f27c5416d8636c7ba05aedc53e20985c10a0ffaf5d864e9541c5fea1733 2026-02-10T02:24:24,778 Stored in directory: /tmp/pip-ephem-wheel-cache-8ezzudpv/wheels/4f/26/74/7f4d1ac7a1da2cb07a297808f3eab65f5fa5c44b1d6c1d13e0 2026-02-10T02:24:24,796 Successfully built mdtraj 2026-02-10T02:24:24,979 Removed build tracker: '/tmp/pip-build-tracker-i29vtrum'