2025-10-16T05:33:46,018 Created temporary directory: /tmp/pip-ephem-wheel-cache-v51rey8b 2025-10-16T05:33:46,020 Created temporary directory: /tmp/pip-build-tracker-4iuttqoe 2025-10-16T05:33:46,021 Initialized build tracking at /tmp/pip-build-tracker-4iuttqoe 2025-10-16T05:33:46,021 Created build tracker: /tmp/pip-build-tracker-4iuttqoe 2025-10-16T05:33:46,022 Entered build tracker: /tmp/pip-build-tracker-4iuttqoe 2025-10-16T05:33:46,023 Created temporary directory: /tmp/pip-wheel-2oghslzf 2025-10-16T05:33:46,026 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 2025-10-16T05:33:46,028 Created temporary directory: /tmp/pip-ephem-wheel-cache-ep_05icm 2025-10-16T05:33:46,055 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-10-16T05:33:46,059 2 location(s) to search for versions of mdtraj: 2025-10-16T05:33:46,059 * https://pypi.org/simple/mdtraj/ 2025-10-16T05:33:46,059 * https://www.piwheels.org/simple/mdtraj/ 2025-10-16T05:33:46,059 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2025-10-16T05:33:46,060 Getting page https://pypi.org/simple/mdtraj/ 2025-10-16T05:33:46,062 Found index url https://pypi.org/simple 2025-10-16T05:33:46,272 Fetched page https://pypi.org/simple/mdtraj/ as application/vnd.pypi.simple.v1+json 2025-10-16T05:33:46,298 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://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv6l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,578 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,578 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv6l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,579 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,580 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv6l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,580 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv7l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,581 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv6l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,582 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,582 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv6l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,582 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,583 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,583 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv7l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,584 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv6l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,585 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2025-10-16T05:33:46,585 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2025-10-16T05:33:46,586 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2025-10-16T05:33:46,612 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2025-10-16T05:33:46,630 Collecting mdtraj==1.11.0 2025-10-16T05:33:46,633 Created temporary directory: /tmp/pip-unpack-b227qc2s 2025-10-16T05:33:46,763 Downloading mdtraj-1.11.0.tar.gz (2.9 MB) 2025-10-16T05:33:48,105 Added mdtraj==1.11.0 from https://files.pythonhosted.org/packages/49/87/04f21b321e7bb6f3e09b5339df51699b8caae4846796175845bbc44f298b/mdtraj-1.11.0.tar.gz to build tracker '/tmp/pip-build-tracker-4iuttqoe' 2025-10-16T05:33:48,114 Created temporary directory: /tmp/pip-build-env-lw424sd7 2025-10-16T05:33:48,118 Installing build dependencies: started 2025-10-16T05:33:48,120 Running command pip subprocess to install build dependencies 2025-10-16T05:33:49,247 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-10-16T05:33:49,832 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 2025-10-16T05:33:49,855 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-10-16T05:33:51,604 Collecting setuptools 2025-10-16T05:33:52,009 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-10-16T05:33:52,315 Collecting versioneer[toml] 2025-10-16T05:33:52,334 Using cached https://www.piwheels.org/simple/versioneer/versioneer-0.29-py3-none-any.whl (46 kB) 2025-10-16T05:33:52,561 Collecting wheel 2025-10-16T05:33:52,577 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2025-10-16T05:33:53,514 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) 2025-10-16T05:33:53,521 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) 2025-10-16T05:33:53,528 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) 2025-10-16T05:33:53,535 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) 2025-10-16T05:33:53,542 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) 2025-10-16T05:33:54,164 Collecting numpy<3,>=2.0.0 2025-10-16T05:33:54,614 Using cached https://www.piwheels.org/simple/numpy/numpy-2.3.3-cp311-cp311-linux_armv7l.whl (6.1 MB) 2025-10-16T05:33:56,599 Collecting Cython>=3.0.0 2025-10-16T05:33:56,621 Using cached cython-3.1.4-py3-none-any.whl (1.2 MB) 2025-10-16T05:33:59,681 Installing collected packages: wheel, versioneer, setuptools, numpy, Cython 2025-10-16T05:33:59,916 Creating /tmp/pip-build-env-lw424sd7/overlay/local/bin 2025-10-16T05:33:59,918 changing mode of /tmp/pip-build-env-lw424sd7/overlay/local/bin/wheel to 755 2025-10-16T05:33:59,954 changing mode of /tmp/pip-build-env-lw424sd7/overlay/local/bin/versioneer to 755 2025-10-16T05:34:12,456 changing mode of /tmp/pip-build-env-lw424sd7/overlay/local/bin/f2py to 755 2025-10-16T05:34:12,459 changing mode of /tmp/pip-build-env-lw424sd7/overlay/local/bin/numpy-config to 755 2025-10-16T05:34:15,450 changing mode of /tmp/pip-build-env-lw424sd7/overlay/local/bin/cygdb to 755 2025-10-16T05:34:15,452 changing mode of /tmp/pip-build-env-lw424sd7/overlay/local/bin/cython to 755 2025-10-16T05:34:15,455 changing mode of /tmp/pip-build-env-lw424sd7/overlay/local/bin/cythonize to 755 2025-10-16T05:34:15,499 Successfully installed Cython-3.1.4 numpy-2.3.3 setuptools-80.9.0 versioneer-0.29 wheel-0.45.1 2025-10-16T05:34:15,937 Installing build dependencies: finished with status 'done' 2025-10-16T05:34:15,953 Getting requirements to build wheel: started 2025-10-16T05:34:15,954 Running command Getting requirements to build wheel 2025-10-16T05:34:16,978 Using built-in specs. 2025-10-16T05:34:16,978 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-10-16T05:34:16,979 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2025-10-16T05:34:16,980 Target: arm-linux-gnueabihf 2025-10-16T05:34:16,980 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 2025-10-16T05:34:16,981 Thread model: posix 2025-10-16T05:34:16,982 Supported LTO compression algorithms: zlib zstd 2025-10-16T05:34:16,982 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2025-10-16T05:34:21,235 /tmp/pip-build-env-lw424sd7/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-10-16T05:34:21,235 !! 2025-10-16T05:34:21,236 ******************************************************************************** 2025-10-16T05:34:21,237 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-10-16T05:34:21,238 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-10-16T05:34:21,239 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-10-16T05:34:21,239 ******************************************************************************** 2025-10-16T05:34:21,240 !! 2025-10-16T05:34:21,241 self._finalize_license_expression() 2025-10-16T05:34:21,242 C compiler: 2025-10-16T05:34:21,242 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2025-10-16T05:34:21,243 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2025-10-16T05:34:21,243 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-10-16T05:34:21,244 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-10-16T05:34:21,245 Attempting to autodetect NEON support... Did not detect NEON support 2025-10-16T05:34:21,246 running egg_info 2025-10-16T05:34:21,249 writing mdtraj.egg-info/PKG-INFO 2025-10-16T05:34:21,257 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2025-10-16T05:34:21,259 writing entry points to mdtraj.egg-info/entry_points.txt 2025-10-16T05:34:21,262 writing requirements to mdtraj.egg-info/requires.txt 2025-10-16T05:34:21,264 writing top-level names to mdtraj.egg-info/top_level.txt 2025-10-16T05:34:21,302 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2025-10-16T05:34:21,335 reading manifest template 'MANIFEST.in' 2025-10-16T05:34:21,957 no previously-included directories found matching '__pycache__' 2025-10-16T05:34:21,958 no previously-included directories found matching '*.pyc' 2025-10-16T05:34:21,958 adding license file 'LICENSE' 2025-10-16T05:34:21,972 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2025-10-16T05:34:22,088 Getting requirements to build wheel: finished with status 'done' 2025-10-16T05:34:22,091 Created temporary directory: /tmp/pip-modern-metadata-hn4u8odl 2025-10-16T05:34:22,094 Preparing metadata (pyproject.toml): started 2025-10-16T05:34:22,095 Running command Preparing metadata (pyproject.toml) 2025-10-16T05:34:22,829 Using built-in specs. 2025-10-16T05:34:22,830 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-10-16T05:34:22,831 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2025-10-16T05:34:22,831 Target: arm-linux-gnueabihf 2025-10-16T05:34:22,832 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 2025-10-16T05:34:22,832 Thread model: posix 2025-10-16T05:34:22,833 Supported LTO compression algorithms: zlib zstd 2025-10-16T05:34:22,834 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2025-10-16T05:34:27,272 /tmp/pip-wheel-2oghslzf/mdtraj_e7cee66d434c4d5dac72e5971504f1ab/basesetup.py:483: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-hn4u8odl --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2025-10-16T05:34:27,272 warnings.warn( 2025-10-16T05:34:31,089 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. 2025-10-16T05:34:31,089 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. 2025-10-16T05:34:31,090 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. 2025-10-16T05:34:52,044 performance hint: mdtraj/geometry/src/image_molecules.pxi:15:0: Exception check on 'make_whole' will always require the GIL to be acquired. 2025-10-16T05:34:52,044 Possible solutions: 2025-10-16T05:34:52,045 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2025-10-16T05:34:52,046 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. 2025-10-16T05:34:52,047 performance hint: mdtraj/geometry/src/image_molecules.pxi:36:0: Exception check on 'anchor_dists' will always require the GIL to be acquired. 2025-10-16T05:34:52,048 Possible solutions: 2025-10-16T05:34:52,048 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2025-10-16T05:34:52,049 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. 2025-10-16T05:34:52,050 performance hint: mdtraj/geometry/src/image_molecules.pxi:68:0: Exception check on 'wrap_mols' will always require the GIL to be acquired. 2025-10-16T05:34:52,050 Possible solutions: 2025-10-16T05:34:52,051 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2025-10-16T05:34:52,051 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. 2025-10-16T05:35:05,102 C compiler: 2025-10-16T05:35:05,102 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2025-10-16T05:35:05,103 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2025-10-16T05:35:05,104 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-10-16T05:35:05,104 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-10-16T05:35:05,105 Attempting to autodetect NEON support... Did not detect NEON support 2025-10-16T05:35:05,106 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2025-10-16T05:35:05,107 [ 2/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2025-10-16T05:35:05,107 [ 3/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2025-10-16T05:35:05,108 [ 4/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2025-10-16T05:35:05,108 [ 5/10] Cythonizing mdtraj/geometry/drid.pyx 2025-10-16T05:35:05,109 [ 6/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2025-10-16T05:35:05,109 [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx 2025-10-16T05:35:05,109 [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2025-10-16T05:35:05,110 [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2025-10-16T05:35:05,110 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2025-10-16T05:35:05,147 /tmp/pip-build-env-lw424sd7/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-10-16T05:35:05,147 !! 2025-10-16T05:35:05,148 ******************************************************************************** 2025-10-16T05:35:05,149 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-10-16T05:35:05,150 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-10-16T05:35:05,151 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-10-16T05:35:05,151 ******************************************************************************** 2025-10-16T05:35:05,153 !! 2025-10-16T05:35:05,153 self._finalize_license_expression() 2025-10-16T05:35:05,166 running dist_info 2025-10-16T05:35:05,175 creating /tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info 2025-10-16T05:35:05,176 writing /tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info/PKG-INFO 2025-10-16T05:35:05,184 writing dependency_links to /tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info/dependency_links.txt 2025-10-16T05:35:05,186 writing entry points to /tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info/entry_points.txt 2025-10-16T05:35:05,189 writing requirements to /tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info/requires.txt 2025-10-16T05:35:05,191 writing top-level names to /tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info/top_level.txt 2025-10-16T05:35:05,192 writing manifest file '/tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info/SOURCES.txt' 2025-10-16T05:35:05,240 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,240 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,241 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,241 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,242 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,243 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,244 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,245 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,245 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,246 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,247 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,247 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,248 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,249 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,249 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,250 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,250 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,251 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,251 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,252 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,252 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,253 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,254 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,254 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,254 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,255 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,256 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,256 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,257 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,257 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,258 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,258 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,259 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,259 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,259 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:35:05,275 reading manifest file '/tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info/SOURCES.txt' 2025-10-16T05:35:05,277 reading manifest template 'MANIFEST.in' 2025-10-16T05:35:05,899 no previously-included directories found matching '__pycache__' 2025-10-16T05:35:05,900 no previously-included directories found matching '*.pyc' 2025-10-16T05:35:05,900 adding license file 'LICENSE' 2025-10-16T05:35:05,911 writing manifest file '/tmp/pip-modern-metadata-hn4u8odl/mdtraj.egg-info/SOURCES.txt' 2025-10-16T05:35:05,919 creating '/tmp/pip-modern-metadata-hn4u8odl/mdtraj-1.11.0.dist-info' 2025-10-16T05:35:07,438 Preparing metadata (pyproject.toml): finished with status 'done' 2025-10-16T05:35:07,442 Source in /tmp/pip-wheel-2oghslzf/mdtraj_e7cee66d434c4d5dac72e5971504f1ab has version 1.11.0, which satisfies requirement mdtraj==1.11.0 from https://files.pythonhosted.org/packages/49/87/04f21b321e7bb6f3e09b5339df51699b8caae4846796175845bbc44f298b/mdtraj-1.11.0.tar.gz 2025-10-16T05:35:07,444 Removed mdtraj==1.11.0 from https://files.pythonhosted.org/packages/49/87/04f21b321e7bb6f3e09b5339df51699b8caae4846796175845bbc44f298b/mdtraj-1.11.0.tar.gz from build tracker '/tmp/pip-build-tracker-4iuttqoe' 2025-10-16T05:35:07,450 Created temporary directory: /tmp/pip-unpack-xjkbrnnz 2025-10-16T05:35:07,450 Building wheels for collected packages: mdtraj 2025-10-16T05:35:07,455 Created temporary directory: /tmp/pip-wheel-_bx5fxrn 2025-10-16T05:35:07,455 Destination directory: /tmp/pip-wheel-_bx5fxrn 2025-10-16T05:35:07,457 Building wheel for mdtraj (pyproject.toml): started 2025-10-16T05:35:07,459 Running command Building wheel for mdtraj (pyproject.toml) 2025-10-16T05:35:08,213 Using built-in specs. 2025-10-16T05:35:08,214 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-10-16T05:35:08,214 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2025-10-16T05:35:08,215 Target: arm-linux-gnueabihf 2025-10-16T05:35:08,215 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 2025-10-16T05:35:08,216 Thread model: posix 2025-10-16T05:35:08,217 Supported LTO compression algorithms: zlib zstd 2025-10-16T05:35:08,217 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1+deb12u1) 2025-10-16T05:35:15,981 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. 2025-10-16T05:35:15,982 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. 2025-10-16T05:35:15,982 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. 2025-10-16T05:35:29,280 performance hint: mdtraj/geometry/src/image_molecules.pxi:15:0: Exception check on 'make_whole' will always require the GIL to be acquired. 2025-10-16T05:35:29,280 Possible solutions: 2025-10-16T05:35:29,281 1. Declare 'make_whole' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2025-10-16T05:35:29,282 2. Use an 'int' return type on 'make_whole' to allow an error code to be returned. 2025-10-16T05:35:29,282 performance hint: mdtraj/geometry/src/image_molecules.pxi:36:0: Exception check on 'anchor_dists' will always require the GIL to be acquired. 2025-10-16T05:35:29,283 Possible solutions: 2025-10-16T05:35:29,284 1. Declare 'anchor_dists' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2025-10-16T05:35:29,284 2. Use an 'int' return type on 'anchor_dists' to allow an error code to be returned. 2025-10-16T05:35:29,285 performance hint: mdtraj/geometry/src/image_molecules.pxi:68:0: Exception check on 'wrap_mols' will always require the GIL to be acquired. 2025-10-16T05:35:29,285 Possible solutions: 2025-10-16T05:35:29,286 1. Declare 'wrap_mols' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2025-10-16T05:35:29,287 2. Use an 'int' return type on 'wrap_mols' to allow an error code to be returned. 2025-10-16T05:35:49,476 C compiler: 2025-10-16T05:35:49,477 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2025-10-16T05:35:49,478 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2025-10-16T05:35:49,478 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-10-16T05:35:49,479 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-10-16T05:35:49,480 Attempting to autodetect NEON support... Did not detect NEON support 2025-10-16T05:35:49,482 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2025-10-16T05:35:49,484 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2025-10-16T05:35:49,484 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2025-10-16T05:35:49,489 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2025-10-16T05:35:49,489 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2025-10-16T05:35:49,490 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2025-10-16T05:35:49,491 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2025-10-16T05:35:49,491 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2025-10-16T05:35:49,492 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2025-10-16T05:35:49,492 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2025-10-16T05:35:49,518 /tmp/pip-build-env-lw424sd7/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-10-16T05:35:49,519 !! 2025-10-16T05:35:49,520 ******************************************************************************** 2025-10-16T05:35:49,520 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-10-16T05:35:49,521 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-10-16T05:35:49,522 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-10-16T05:35:49,522 ******************************************************************************** 2025-10-16T05:35:49,523 !! 2025-10-16T05:35:49,524 self._finalize_license_expression() 2025-10-16T05:35:49,538 running bdist_wheel 2025-10-16T05:35:49,564 running build 2025-10-16T05:35:49,564 running build_py 2025-10-16T05:35:49,572 creating build/lib.linux-armv7l-cpython-311/mdtraj 2025-10-16T05:35:49,574 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2025-10-16T05:35:49,578 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2025-10-16T05:35:49,581 copying mdtraj/_version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2025-10-16T05:35:49,583 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2025-10-16T05:35:49,585 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,586 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,589 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,590 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,593 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,595 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,598 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,600 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,603 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,606 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,611 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,616 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,619 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,621 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,623 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,626 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,629 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,632 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2025-10-16T05:35:49,635 creating build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,636 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,639 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,642 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,645 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,647 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,649 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,652 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,657 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,660 copying mdtraj/geometry/pi_stacking.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,662 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,665 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,666 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,669 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,671 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,673 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,675 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2025-10-16T05:35:49,678 creating build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2025-10-16T05:35:49,679 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2025-10-16T05:35:49,681 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2025-10-16T05:35:49,683 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2025-10-16T05:35:49,686 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2025-10-16T05:35:49,688 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2025-10-16T05:35:49,690 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2025-10-16T05:35:49,693 creating build/lib.linux-armv7l-cpython-311/mdtraj/testing 2025-10-16T05:35:49,694 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2025-10-16T05:35:49,696 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2025-10-16T05:35:49,698 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2025-10-16T05:35:49,701 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2025-10-16T05:35:49,703 creating build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2025-10-16T05:35:49,705 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2025-10-16T05:35:49,708 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2025-10-16T05:35:49,710 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2025-10-16T05:35:49,713 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,715 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,717 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,719 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,721 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,724 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,726 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,728 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,730 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2025-10-16T05:35:49,733 creating build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2025-10-16T05:35:49,734 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2025-10-16T05:35:49,737 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2025-10-16T05:35:49,739 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2025-10-16T05:35:49,741 creating build/lib.linux-armv7l-cpython-311/mdtraj/core 2025-10-16T05:35:49,742 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2025-10-16T05:35:49,746 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2025-10-16T05:35:49,751 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2025-10-16T05:35:49,755 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2025-10-16T05:35:49,760 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2025-10-16T05:35:49,764 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2025-10-16T05:35:49,766 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2025-10-16T05:35:49,767 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2025-10-16T05:35:49,770 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2025-10-16T05:35:49,773 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2025-10-16T05:35:49,775 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2025-10-16T05:35:49,776 copying mdtraj/formats/pdbx/pdbx.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2025-10-16T05:35:49,779 copying mdtraj/formats/pdbx/pdbxfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2025-10-16T05:35:49,782 copying mdtraj/formats/pdbx/PdbxReader.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2025-10-16T05:35:49,784 copying mdtraj/formats/pdbx/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2025-10-16T05:35:49,786 copying mdtraj/formats/pdbx/PdbxContainers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx 2025-10-16T05:35:49,790 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,791 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,794 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,797 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,800 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,802 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,804 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,807 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,809 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,812 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,814 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,816 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,819 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,822 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2025-10-16T05:35:49,831 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2025-10-16T05:35:49,832 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2025-10-16T05:35:49,835 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2025-10-16T05:35:49,845 UPDATING build/lib.linux-armv7l-cpython-311/mdtraj/_version.py 2025-10-16T05:35:49,845 set build/lib.linux-armv7l-cpython-311/mdtraj/_version.py to '1.11.0' 2025-10-16T05:35:49,846 running build_ext 2025-10-16T05:35:49,849 building 'mdtraj.formats.xtc' extension 2025-10-16T05:35:49,850 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src 2025-10-16T05:35:49,854 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-lw424sd7/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 2025-10-16T05:35:49,978 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-lw424sd7/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 2025-10-16T05:35:50,407 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2025-10-16T05:35:50,408 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:35:50,408 788 | int smallnum, smaller, larger, i, is_smaller, run; 2025-10-16T05:35:50,409 | ^~~~~~ 2025-10-16T05:35:50,410 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:35:50,411 785 | int smallidx, minidx, maxidx; 2025-10-16T05:35:50,412 | ^~~~~~ 2025-10-16T05:35:50,417 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2025-10-16T05:35:50,417 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:35:50,418 1016 | int errval=1; 2025-10-16T05:35:50,419 | ^~~~~~ 2025-10-16T05:35:50,423 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2025-10-16T05:35:50,424 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:35:50,424 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2025-10-16T05:35:50,425 | ^~~~~~ 2025-10-16T05:35:50,426 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:35:50,426 1302 | int smallidx, minidx, maxidx; 2025-10-16T05:35:50,427 | ^~~~~~ 2025-10-16T05:35:50,435 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2025-10-16T05:35:50,436 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:35:50,437 1509 | int errval=1; 2025-10-16T05:35:50,438 | ^~~~~~ 2025-10-16T05:35:53,001 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-lw424sd7/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 2025-10-16T05:35:53,078 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2025-10-16T05:35:53,079 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 2025-10-16T05:35:53,079 66 | int i,j,result; 2025-10-16T05:35:53,080 | ^ 2025-10-16T05:35:53,080 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 2025-10-16T05:35:53,081 66 | int i,j,result; 2025-10-16T05:35:53,081 | ^ 2025-10-16T05:35:53,082 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2025-10-16T05:35:53,082 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-10-16T05:35:53,083 119 | if (NULL == xd) 2025-10-16T05:35:53,083 | ^~ 2025-10-16T05:35:53,084 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’ 2025-10-16T05:35:53,084 122 | do { 2025-10-16T05:35:53,085 | ^~ 2025-10-16T05:35:53,228 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-lw424sd7/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 2025-10-16T05:36:03,367 In function ‘__Pyx_PyLong_From_int’, 2025-10-16T05:36:03,368 inlined from ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’ at mdtraj/formats/xtc/xtc.c:13447:16, 2025-10-16T05:36:03,369 inlined from ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’ at mdtraj/formats/xtc/xtc.c:13129:13: 2025-10-16T05:36:03,395 mdtraj/formats/xtc/xtc.c:25758:20: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:03,396 25758 | return PyLong_FromLong((long) value); 2025-10-16T05:36:03,397 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:03,397 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’: 2025-10-16T05:36:03,410 mdtraj/formats/xtc/xtc.c:13151:7: note: ‘__pyx_v_status’ was declared here 2025-10-16T05:36:03,411 13151 | int __pyx_v_status; 2025-10-16T05:36:03,411 | ^~~~~~~~~~~~~~ 2025-10-16T05:36:12,798 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2025-10-16T05:36:12,809 mdtraj/formats/xtc/xtc.c:11586:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,810 11586 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_5 = 2; 2025-10-16T05:36:12,811 | ^ 2025-10-16T05:36:12,820 mdtraj/formats/xtc/xtc.c:9804:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 2025-10-16T05:36:12,821 9804 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2025-10-16T05:36:12,821 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:12,832 mdtraj/formats/xtc/xtc.c:11582:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,833 11582 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_5 = 1; 2025-10-16T05:36:12,833 | ^ 2025-10-16T05:36:12,843 mdtraj/formats/xtc/xtc.c:9804:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 2025-10-16T05:36:12,843 9804 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2025-10-16T05:36:12,844 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:12,855 mdtraj/formats/xtc/xtc.c:11578:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,855 11578 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2025-10-16T05:36:12,856 | ^ 2025-10-16T05:36:12,865 mdtraj/formats/xtc/xtc.c:9804:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 2025-10-16T05:36:12,866 9804 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2025-10-16T05:36:12,866 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:12,877 mdtraj/formats/xtc/xtc.c:11538:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,877 11538 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2025-10-16T05:36:12,878 | ^ 2025-10-16T05:36:12,887 mdtraj/formats/xtc/xtc.c:9800:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 2025-10-16T05:36:12,888 9800 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; 2025-10-16T05:36:12,889 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:12,899 mdtraj/formats/xtc/xtc.c:11520:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,900 11520 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2025-10-16T05:36:12,901 | ^ 2025-10-16T05:36:12,910 mdtraj/formats/xtc/xtc.c:9796:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 2025-10-16T05:36:12,911 9796 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; 2025-10-16T05:36:12,911 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:12,922 mdtraj/formats/xtc/xtc.c:11596:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,923 11596 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2025-10-16T05:36:12,923 | ^ 2025-10-16T05:36:12,933 mdtraj/formats/xtc/xtc.c:9792:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 2025-10-16T05:36:12,933 9792 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; 2025-10-16T05:36:12,934 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:12,944 mdtraj/formats/xtc/xtc.c:11558:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,945 11558 | } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_5 = 2; 2025-10-16T05:36:12,946 | ^ 2025-10-16T05:36:12,955 mdtraj/formats/xtc/xtc.c:9786:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 2025-10-16T05:36:12,956 9786 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2025-10-16T05:36:12,957 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:12,967 mdtraj/formats/xtc/xtc.c:11554:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,968 11554 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_5 = 1; 2025-10-16T05:36:12,968 | ^ 2025-10-16T05:36:12,978 mdtraj/formats/xtc/xtc.c:9786:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 2025-10-16T05:36:12,978 9786 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2025-10-16T05:36:12,979 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:12,989 mdtraj/formats/xtc/xtc.c:11550:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:12,990 11550 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_5 = 0; 2025-10-16T05:36:12,990 | ^ 2025-10-16T05:36:13,000 mdtraj/formats/xtc/xtc.c:9786:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 2025-10-16T05:36:13,000 9786 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2025-10-16T05:36:13,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:13,011 mdtraj/formats/xtc/xtc.c:11169:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:13,012 11169 | } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; 2025-10-16T05:36:13,012 | ^ 2025-10-16T05:36:13,022 mdtraj/formats/xtc/xtc.c:9788:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 2025-10-16T05:36:13,022 9788 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2025-10-16T05:36:13,023 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:13,033 mdtraj/formats/xtc/xtc.c:11165:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:13,034 11165 | } else if (unlikely(__pyx_t_21 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0; 2025-10-16T05:36:13,034 | ^ 2025-10-16T05:36:13,044 mdtraj/formats/xtc/xtc.c:9788:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 2025-10-16T05:36:13,045 9788 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2025-10-16T05:36:13,045 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:21,165 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 2025-10-16T05:36:21,326 building 'mdtraj.formats.trr' extension 2025-10-16T05:36:21,328 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-lw424sd7/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 2025-10-16T05:36:21,438 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-lw424sd7/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 2025-10-16T05:36:21,587 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2025-10-16T05:36:21,588 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:36:21,589 788 | int smallnum, smaller, larger, i, is_smaller, run; 2025-10-16T05:36:21,590 | ^~~~~~ 2025-10-16T05:36:21,590 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:36:21,591 785 | int smallidx, minidx, maxidx; 2025-10-16T05:36:21,591 | ^~~~~~ 2025-10-16T05:36:21,601 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2025-10-16T05:36:21,602 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:36:21,603 1016 | int errval=1; 2025-10-16T05:36:21,603 | ^~~~~~ 2025-10-16T05:36:21,610 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2025-10-16T05:36:21,611 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:36:21,612 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2025-10-16T05:36:21,613 | ^~~~~~ 2025-10-16T05:36:21,613 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:36:21,614 1302 | int smallidx, minidx, maxidx; 2025-10-16T05:36:21,614 | ^~~~~~ 2025-10-16T05:36:21,628 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2025-10-16T05:36:21,629 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2025-10-16T05:36:21,630 1509 | int errval=1; 2025-10-16T05:36:21,631 | ^~~~~~ 2025-10-16T05:36:24,249 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-lw424sd7/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 2025-10-16T05:36:25,044 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-lw424sd7/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 2025-10-16T05:36:36,107 In function ‘__Pyx_PyLong_From_int’, 2025-10-16T05:36:36,108 inlined from ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’ at mdtraj/formats/xtc/trr.c:15464:16, 2025-10-16T05:36:36,109 inlined from ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write’ at mdtraj/formats/xtc/trr.c:14890:13: 2025-10-16T05:36:36,135 mdtraj/formats/xtc/trr.c:27767:20: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:36,136 27767 | return PyLong_FromLong((long) value); 2025-10-16T05:36:36,137 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:36,137 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_19_write’: 2025-10-16T05:36:36,150 mdtraj/formats/xtc/trr.c:14920:7: note: ‘__pyx_v_status’ was declared here 2025-10-16T05:36:36,151 14920 | int __pyx_v_status; 2025-10-16T05:36:36,152 | ^~~~~~~~~~~~~~ 2025-10-16T05:36:47,741 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2025-10-16T05:36:47,753 mdtraj/formats/xtc/trr.c:12178:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,753 12178 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_7 = 2; 2025-10-16T05:36:47,754 | ^ 2025-10-16T05:36:47,763 mdtraj/formats/xtc/trr.c:10479:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2025-10-16T05:36:47,763 10479 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2025-10-16T05:36:47,764 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,774 mdtraj/formats/xtc/trr.c:12174:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,775 12174 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_7 = 1; 2025-10-16T05:36:47,775 | ^ 2025-10-16T05:36:47,784 mdtraj/formats/xtc/trr.c:10479:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2025-10-16T05:36:47,785 10479 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2025-10-16T05:36:47,785 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,786 mdtraj/formats/xtc/trr.c:2541:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,787 2541 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2025-10-16T05:36:47,787 | ^ 2025-10-16T05:36:47,796 mdtraj/formats/xtc/trr.c:10479:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2025-10-16T05:36:47,797 10479 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2025-10-16T05:36:47,797 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,807 mdtraj/formats/xtc/trr.c:12168:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,808 12168 | __pyx_t_15 += __pyx_pybuffernd_forces.diminfo[0].shape; 2025-10-16T05:36:47,809 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2025-10-16T05:36:47,817 mdtraj/formats/xtc/trr.c:10479:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2025-10-16T05:36:47,818 10479 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2025-10-16T05:36:47,818 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,828 mdtraj/formats/xtc/trr.c:12121:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,829 12121 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_7 = 2; 2025-10-16T05:36:47,829 | ^ 2025-10-16T05:36:47,838 mdtraj/formats/xtc/trr.c:10495:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2025-10-16T05:36:47,839 10495 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2025-10-16T05:36:47,839 | ^~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,849 mdtraj/formats/xtc/trr.c:12117:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,850 12117 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_7 = 1; 2025-10-16T05:36:47,850 | ^ 2025-10-16T05:36:47,859 mdtraj/formats/xtc/trr.c:10495:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2025-10-16T05:36:47,860 10495 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2025-10-16T05:36:47,860 | ^~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,861 mdtraj/formats/xtc/trr.c:2541:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,861 2541 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2025-10-16T05:36:47,862 | ^ 2025-10-16T05:36:47,871 mdtraj/formats/xtc/trr.c:10495:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2025-10-16T05:36:47,871 10495 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2025-10-16T05:36:47,872 | ^~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,882 mdtraj/formats/xtc/trr.c:12111:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,882 12111 | __pyx_t_15 += __pyx_pybuffernd_vel.diminfo[0].shape; 2025-10-16T05:36:47,883 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2025-10-16T05:36:47,892 mdtraj/formats/xtc/trr.c:10495:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2025-10-16T05:36:47,892 10495 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2025-10-16T05:36:47,893 | ^~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,903 mdtraj/formats/xtc/trr.c:12510:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,904 12510 | } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_7 = 1; 2025-10-16T05:36:47,904 | ^ 2025-10-16T05:36:47,913 mdtraj/formats/xtc/trr.c:10501:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2025-10-16T05:36:47,914 10501 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2025-10-16T05:36:47,915 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,925 mdtraj/formats/xtc/trr.c:12506:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,925 12506 | } else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_7 = 0; 2025-10-16T05:36:47,926 | ^ 2025-10-16T05:36:47,935 mdtraj/formats/xtc/trr.c:10501:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2025-10-16T05:36:47,935 10501 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2025-10-16T05:36:47,936 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,946 mdtraj/formats/xtc/trr.c:12351:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,946 12351 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_7 = 1; 2025-10-16T05:36:47,947 | ^ 2025-10-16T05:36:47,956 mdtraj/formats/xtc/trr.c:10497:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2025-10-16T05:36:47,956 10497 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2025-10-16T05:36:47,957 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,967 mdtraj/formats/xtc/trr.c:12347:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,968 12347 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_7 = 0; 2025-10-16T05:36:47,968 | ^ 2025-10-16T05:36:47,977 mdtraj/formats/xtc/trr.c:10497:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2025-10-16T05:36:47,978 10497 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2025-10-16T05:36:47,979 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:47,988 mdtraj/formats/xtc/trr.c:12403:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:47,989 12403 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_7 = 1; 2025-10-16T05:36:47,989 | ^ 2025-10-16T05:36:47,998 mdtraj/formats/xtc/trr.c:10481:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2025-10-16T05:36:47,999 10481 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2025-10-16T05:36:47,999 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:48,010 mdtraj/formats/xtc/trr.c:12399:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:36:48,010 12399 | } else if (unlikely(__pyx_t_22 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_7 = 0; 2025-10-16T05:36:48,011 | ^ 2025-10-16T05:36:48,020 mdtraj/formats/xtc/trr.c:10481:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2025-10-16T05:36:48,020 10481 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2025-10-16T05:36:48,021 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:36:56,104 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 2025-10-16T05:36:56,270 building 'mdtraj.formats.dcd' extension 2025-10-16T05:36:56,270 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd 2025-10-16T05:36:56,271 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src 2025-10-16T05:36:56,272 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-lw424sd7/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 2025-10-16T05:37:07,971 In function ‘__Pyx_PyLong_From_int’, 2025-10-16T05:37:07,972 inlined from ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’ at mdtraj/formats/dcd/dcd.c:10161:19: 2025-10-16T05:37:07,992 mdtraj/formats/dcd/dcd.c:19434:20: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:37:07,993 19434 | return PyLong_FromLong((long) value); 2025-10-16T05:37:07,994 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:07,994 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2025-10-16T05:37:08,002 mdtraj/formats/dcd/dcd.c:8790:7: note: ‘__pyx_v_i’ was declared here 2025-10-16T05:37:08,003 8790 | int __pyx_v_i; 2025-10-16T05:37:08,004 | ^~~~~~~~~ 2025-10-16T05:37:11,854 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-lw424sd7/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 2025-10-16T05:37:12,523 mdtraj/formats/dcd/src/dcdplugin.c: In function ‘open_dcd_read’: 2025-10-16T05:37:12,524 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=] 2025-10-16T05:37:12,525 903 | printf("dcdplugin) Warning: DCD header claims %d frames, but \n" 2025-10-16T05:37:12,525 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:12,526 ...... 2025-10-16T05:37:12,526 906 | dcd->nsets, trjsize, newnsets, framesize); 2025-10-16T05:37:12,526 | ~~~~~~~ 2025-10-16T05:37:12,527 | | 2025-10-16T05:37:12,527 | fio_size_t {aka long long int} 2025-10-16T05:37:12,528 mdtraj/formats/dcd/src/dcdplugin.c:904:39: note: format string is defined here 2025-10-16T05:37:12,528 904 | "dcdplugin) file size (%ld) indicates there are actually \n" 2025-10-16T05:37:12,529 | ~~^ 2025-10-16T05:37:12,529 | | 2025-10-16T05:37:12,530 | long int 2025-10-16T05:37:12,530 | %lld 2025-10-16T05:37:12,531 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=] 2025-10-16T05:37:12,531 903 | printf("dcdplugin) Warning: DCD header claims %d frames, but \n" 2025-10-16T05:37:12,532 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:12,533 ...... 2025-10-16T05:37:12,533 906 | dcd->nsets, trjsize, newnsets, framesize); 2025-10-16T05:37:12,534 | ~~~~~~~~~ 2025-10-16T05:37:12,535 | | 2025-10-16T05:37:12,537 | fio_size_t {aka long long int} 2025-10-16T05:37:12,538 mdtraj/formats/dcd/src/dcdplugin.c:905:36: note: format string is defined here 2025-10-16T05:37:12,538 905 | "%d frames of size (%ld)\n", 2025-10-16T05:37:12,539 | ~~^ 2025-10-16T05:37:12,540 | | 2025-10-16T05:37:12,540 | long int 2025-10-16T05:37:12,541 | %lld 2025-10-16T05:37:13,907 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 2025-10-16T05:37:14,042 building 'mdtraj.formats.dtr' extension 2025-10-16T05:37:14,043 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr 2025-10-16T05:37:14,044 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src 2025-10-16T05:37:14,045 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-lw424sd7/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 2025-10-16T05:37:31,938 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-lw424sd7/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 2025-10-16T05:37:34,300 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2025-10-16T05:37:34,301 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=] 2025-10-16T05:37:34,302 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2025-10-16T05:37:34,302 | ~~^ ~ 2025-10-16T05:37:34,303 | | | 2025-10-16T05:37:34,303 | | size_t {aka unsigned int} 2025-10-16T05:37:34,304 | long int 2025-10-16T05:37:34,304 | %d 2025-10-16T05:37:34,305 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=] 2025-10-16T05:37:34,306 487 | printf("size %d framesize %d\n\n", 2025-10-16T05:37:34,306 | ~^ 2025-10-16T05:37:34,307 | | 2025-10-16T05:37:34,307 | int 2025-10-16T05:37:34,308 | %lld 2025-10-16T05:37:34,309 488 | keys[i].size(), m_framesize); 2025-10-16T05:37:34,310 | ~~~~~~~~~~~~~~ 2025-10-16T05:37:34,310 | | 2025-10-16T05:37:34,311 | uint64_t {aka long long unsigned int} 2025-10-16T05:37:34,312 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=] 2025-10-16T05:37:34,313 487 | printf("size %d framesize %d\n\n", 2025-10-16T05:37:34,314 | ~^ 2025-10-16T05:37:34,314 | | 2025-10-16T05:37:34,315 | int 2025-10-16T05:37:34,316 | %lld 2025-10-16T05:37:34,316 488 | keys[i].size(), m_framesize); 2025-10-16T05:37:34,317 | ~~~~~~~~~~~ 2025-10-16T05:37:34,318 | | 2025-10-16T05:37:34,318 | uint64_t {aka long long unsigned int} 2025-10-16T05:37:34,319 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=] 2025-10-16T05:37:34,320 494 | "non-constant time interval at frame %ld\n", i); 2025-10-16T05:37:34,320 | ~~^ ~ 2025-10-16T05:37:34,321 | | | 2025-10-16T05:37:34,322 | | size_t {aka unsigned int} 2025-10-16T05:37:34,322 | long int 2025-10-16T05:37:34,323 | %d 2025-10-16T05:37:34,324 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=] 2025-10-16T05:37:34,325 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2025-10-16T05:37:34,325 | ~~^ ~ 2025-10-16T05:37:34,326 | | | 2025-10-16T05:37:34,326 | | size_t {aka unsigned int} 2025-10-16T05:37:34,327 | long int 2025-10-16T05:37:34,328 | %d 2025-10-16T05:37:34,467 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2025-10-16T05:37:34,468 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=] 2025-10-16T05:37:34,469 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2025-10-16T05:37:34,469 | ~~^ 2025-10-16T05:37:34,470 | | 2025-10-16T05:37:34,470 | long int 2025-10-16T05:37:34,471 | %lld 2025-10-16T05:37:34,472 1302 | 3*natoms, pos.count); 2025-10-16T05:37:34,472 | ~~~~~~~~~ 2025-10-16T05:37:34,473 | | 2025-10-16T05:37:34,474 | uint64_t {aka long long unsigned int} 2025-10-16T05:37:34,475 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=] 2025-10-16T05:37:34,475 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2025-10-16T05:37:34,476 | ~~^ 2025-10-16T05:37:34,477 | | 2025-10-16T05:37:34,477 | long int 2025-10-16T05:37:34,478 | %lld 2025-10-16T05:37:34,479 1311 | 3*natoms, vel.count); 2025-10-16T05:37:34,480 | ~~~~~~~~~ 2025-10-16T05:37:34,480 | | 2025-10-16T05:37:34,481 | uint64_t {aka long long unsigned int} 2025-10-16T05:37:34,501 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2025-10-16T05:37:34,502 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=] 2025-10-16T05:37:34,502 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2025-10-16T05:37:34,503 | ~~^ 2025-10-16T05:37:34,504 | | 2025-10-16T05:37:34,504 | long int 2025-10-16T05:37:34,505 | %lld 2025-10-16T05:37:34,506 1573 | velblob.count, 3*natoms); 2025-10-16T05:37:34,507 | ~~~~~~~~~~~~~ 2025-10-16T05:37:34,507 | | 2025-10-16T05:37:34,508 | uint64_t {aka long long unsigned int} 2025-10-16T05:37:35,809 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2025-10-16T05:37:35,810 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2025-10-16T05:37:35,810 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2025-10-16T05:37:35,811 | ~~~~~~~~^~~~~ 2025-10-16T05:37:38,585 In file included from /usr/include/c++/12/map:60, 2025-10-16T05:37:38,586 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2025-10-16T05:37:38,587 /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> >]’: 2025-10-16T05:37:38,587 /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 2025-10-16T05:37:38,588 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-10-16T05:37:38,588 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:38,656 /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> >]’: 2025-10-16T05:37:38,657 /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 2025-10-16T05:37:38,658 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-10-16T05:37:38,659 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:38,717 In file included from /usr/include/c++/12/map:61: 2025-10-16T05:37:38,718 /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> >]’: 2025-10-16T05:37:38,719 /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 2025-10-16T05:37:38,719 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-10-16T05:37:38,720 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:38,721 531 | std::forward_as_tuple(std::move(__k)), 2025-10-16T05:37:38,721 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:38,722 532 | std::tuple<>()); 2025-10-16T05:37:38,722 | ~~~~~~~~~~~~~~~ 2025-10-16T05:37:38,811 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> >]’, 2025-10-16T05:37:38,811 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28: 2025-10-16T05:37:38,812 /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 2025-10-16T05:37:38,813 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-10-16T05:37:38,813 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:38,814 531 | std::forward_as_tuple(std::move(__k)), 2025-10-16T05:37:38,815 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:38,816 532 | std::tuple<>()); 2025-10-16T05:37:38,817 | ~~~~~~~~~~~~~~~ 2025-10-16T05:37:39,658 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2025-10-16T05:37:39,659 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=] 2025-10-16T05:37:39,659 706 | sprintf(sub, "%03x/", i); 2025-10-16T05:37:39,660 | ^~~~ 2025-10-16T05:37:39,661 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2025-10-16T05:37:39,661 706 | sprintf(sub, "%03x/", i); 2025-10-16T05:37:39,662 | ^~~~~~~ 2025-10-16T05:37:39,663 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2025-10-16T05:37:39,663 706 | sprintf(sub, "%03x/", i); 2025-10-16T05:37:39,664 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2025-10-16T05:37:39,665 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=] 2025-10-16T05:37:39,666 714 | sprintf(subsub, "%03x", j); 2025-10-16T05:37:39,666 | ^~~~ 2025-10-16T05:37:39,667 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2025-10-16T05:37:39,668 714 | sprintf(subsub, "%03x", j); 2025-10-16T05:37:39,669 | ^~~~~~ 2025-10-16T05:37:39,669 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2025-10-16T05:37:39,670 714 | sprintf(subsub, "%03x", j); 2025-10-16T05:37:39,671 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:40,063 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2025-10-16T05:37:40,064 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-10-16T05:37:40,065 667 | sprintf(answer, "%03x/", d1); 2025-10-16T05:37:40,065 | ^ 2025-10-16T05:37:40,066 In function ‘std::string DDreldir(const std::string&, int, int)’, 2025-10-16T05:37:40,066 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2025-10-16T05:37:40,067 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2025-10-16T05:37:40,067 667 | sprintf(answer, "%03x/", d1); 2025-10-16T05:37:40,068 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:40,068 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2025-10-16T05:37:40,069 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=] 2025-10-16T05:37:40,070 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2025-10-16T05:37:40,070 | ^~~~ 2025-10-16T05:37:40,071 In function ‘std::string DDreldir(const std::string&, int, int)’, 2025-10-16T05:37:40,072 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2025-10-16T05:37:40,073 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2025-10-16T05:37:40,073 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2025-10-16T05:37:40,074 | ^~~~~~~~~~~~ 2025-10-16T05:37:40,075 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2025-10-16T05:37:40,076 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2025-10-16T05:37:40,076 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:43,223 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> >]’, 2025-10-16T05:37:43,224 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: 2025-10-16T05:37:43,224 /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 2025-10-16T05:37:43,225 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-10-16T05:37:43,226 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:43,227 531 | std::forward_as_tuple(std::move(__k)), 2025-10-16T05:37:43,227 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-10-16T05:37:43,228 532 | std::tuple<>()); 2025-10-16T05:37:43,228 | ~~~~~~~~~~~~~~~ 2025-10-16T05:37:48,201 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 2025-10-16T05:37:48,572 building 'mdtraj._rmsd' extension 2025-10-16T05:37:48,572 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd 2025-10-16T05:37:48,574 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src 2025-10-16T05:37:48,575 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-lw424sd7/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 2025-10-16T05:38:36,027 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-lw424sd7/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 2025-10-16T05:38:36,463 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-lw424sd7/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 2025-10-16T05:38:36,722 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-lw424sd7/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 2025-10-16T05:38:37,508 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 2025-10-16T05:38:37,825 building 'mdtraj._lprmsd' extension 2025-10-16T05:38:37,827 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-lw424sd7/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 2025-10-16T05:39:05,423 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-lw424sd7/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 2025-10-16T05:39:08,243 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-lw424sd7/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 2025-10-16T05:39:08,444 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-lw424sd7/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 2025-10-16T05:39:09,696 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-lw424sd7/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 2025-10-16T05:39:10,001 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-lw424sd7/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 2025-10-16T05:39:10,262 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-lw424sd7/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 2025-10-16T05:39:11,044 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 2025-10-16T05:39:11,347 building 'mdtraj.core.lib.libtheobald' extension 2025-10-16T05:39:11,347 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-lw424sd7/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 2025-10-16T05:39:12,092 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-lw424sd7/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 2025-10-16T05:39:12,294 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 2025-10-16T05:39:12,319 building 'mdtraj.geometry._geometry' extension 2025-10-16T05:39:12,321 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src 2025-10-16T05:39:12,323 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-lw424sd7/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 2025-10-16T05:39:52,055 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-lw424sd7/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 2025-10-16T05:40:06,318 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-lw424sd7/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 2025-10-16T05:40:10,639 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-lw424sd7/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 2025-10-16T05:40:11,798 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 2025-10-16T05:40:12,175 building 'mdtraj.geometry.drid' extension 2025-10-16T05:40:12,176 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-lw424sd7/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 2025-10-16T05:40:45,083 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-lw424sd7/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 2025-10-16T05:40:45,723 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-lw424sd7/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 2025-10-16T05:40:45,832 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 2025-10-16T05:40:46,140 building 'mdtraj.geometry.neighbors' extension 2025-10-16T05:40:46,140 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-lw424sd7/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 2025-10-16T05:41:16,879 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-lw424sd7/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 2025-10-16T05:41:18,178 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 2025-10-16T05:41:18,475 building 'mdtraj.geometry.neighborlist' extension 2025-10-16T05:41:18,476 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-lw424sd7/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 2025-10-16T05:41:46,119 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-lw424sd7/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 2025-10-16T05:41:50,528 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2025-10-16T05:41:50,529 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2025-10-16T05:41:50,529 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:41:50,530 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2025-10-16T05:41:50,530 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2025-10-16T05:41:50,531 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2025-10-16T05:41:50,531 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2025-10-16T05:41:50,532 341 | float periodicBoxVectors[3][3]; 2025-10-16T05:41:50,533 | ^~~~~~~~~~~~~~~~~~ 2025-10-16T05:41:50,534 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2025-10-16T05:41:50,534 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2025-10-16T05:41:50,535 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:41:50,536 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2025-10-16T05:41:50,536 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2025-10-16T05:41:50,537 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2025-10-16T05:41:50,538 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2025-10-16T05:41:50,538 341 | float periodicBoxVectors[3][3]; 2025-10-16T05:41:50,539 | ^~~~~~~~~~~~~~~~~~ 2025-10-16T05:41:50,540 mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:41:50,540 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); 2025-10-16T05:41:50,541 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2025-10-16T05:41:50,542 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2025-10-16T05:41:50,542 341 | float periodicBoxVectors[3][3]; 2025-10-16T05:41:50,543 | ^~~~~~~~~~~~~~~~~~ 2025-10-16T05:41:50,544 mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2025-10-16T05:41:50,544 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); 2025-10-16T05:41:50,545 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2025-10-16T05:41:50,546 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2025-10-16T05:41:50,546 341 | float periodicBoxVectors[3][3]; 2025-10-16T05:41:50,547 | ^~~~~~~~~~~~~~~~~~ 2025-10-16T05:41:51,374 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 2025-10-16T05:41:51,789 installing to build/bdist.linux-armv7l/wheel 2025-10-16T05:41:51,790 running install 2025-10-16T05:41:51,814 running install_lib 2025-10-16T05:41:51,826 creating build/bdist.linux-armv7l/wheel 2025-10-16T05:41:51,829 creating build/bdist.linux-armv7l/wheel/mdtraj 2025-10-16T05:41:51,831 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2025-10-16T05:41:51,832 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,836 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2025-10-16T05:41:51,837 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2025-10-16T05:41:51,841 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2025-10-16T05:41:51,844 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb 2025-10-16T05:41:51,846 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2025-10-16T05:41:51,848 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb/data 2025-10-16T05:41:51,851 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdb/data 2025-10-16T05:41:51,854 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,856 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,858 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,861 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,864 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,867 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,871 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdbx 2025-10-16T05:41:51,872 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/pdbx.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2025-10-16T05:41:51,875 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/pdbxfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2025-10-16T05:41:51,878 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/PdbxReader.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2025-10-16T05:41:51,881 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2025-10-16T05:41:51,883 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx/PdbxContainers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats/pdbx 2025-10-16T05:41:51,886 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,889 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,892 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,894 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,934 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,937 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,972 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,974 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,976 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:51,978 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:52,011 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:52,014 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:52,017 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:52,037 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/./mdtraj/formats 2025-10-16T05:41:52,041 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2025-10-16T05:41:52,043 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,046 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,081 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,084 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,087 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,089 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,092 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,147 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,149 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,176 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,178 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,180 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/pi_stacking.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,183 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,185 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,214 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,215 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,218 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,220 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,222 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,224 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/./mdtraj/geometry 2025-10-16T05:41:52,227 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2025-10-16T05:41:52,228 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2025-10-16T05:41:52,230 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2025-10-16T05:41:52,232 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2025-10-16T05:41:52,234 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2025-10-16T05:41:52,236 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2025-10-16T05:41:52,238 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/./mdtraj/reporters 2025-10-16T05:41:52,241 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2025-10-16T05:41:52,242 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2025-10-16T05:41:52,244 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2025-10-16T05:41:52,246 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2025-10-16T05:41:52,249 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/./mdtraj/testing 2025-10-16T05:41:52,251 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2025-10-16T05:41:52,252 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2025-10-16T05:41:52,255 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2025-10-16T05:41:52,257 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/./mdtraj/nmr 2025-10-16T05:41:52,259 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2025-10-16T05:41:52,260 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2025-10-16T05:41:52,263 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2025-10-16T05:41:52,264 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,267 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,269 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,271 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,273 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,275 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,278 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,279 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,281 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,284 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,286 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,289 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,291 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils/unit 2025-10-16T05:41:52,293 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2025-10-16T05:41:52,295 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2025-10-16T05:41:52,297 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2025-10-16T05:41:52,299 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2025-10-16T05:41:52,301 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2025-10-16T05:41:52,303 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2025-10-16T05:41:52,305 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/./mdtraj/utils 2025-10-16T05:41:52,307 copying build/lib.linux-armv7l-cpython-311/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2025-10-16T05:41:52,309 copying build/lib.linux-armv7l-cpython-311/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2025-10-16T05:41:52,312 copying build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj 2025-10-16T05:41:52,347 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2025-10-16T05:41:52,348 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2025-10-16T05:41:52,350 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2025-10-16T05:41:52,352 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/scripts 2025-10-16T05:41:52,355 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2025-10-16T05:41:52,356 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2025-10-16T05:41:52,358 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2025-10-16T05:41:52,362 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2025-10-16T05:41:52,364 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2025-10-16T05:41:52,366 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2025-10-16T05:41:52,370 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2025-10-16T05:41:52,371 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2025-10-16T05:41:52,373 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2025-10-16T05:41:52,375 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/./mdtraj/core/lib 2025-10-16T05:41:52,378 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/./mdtraj/core 2025-10-16T05:41:52,379 copying build/lib.linux-armv7l-cpython-311/mdtraj/_version.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2025-10-16T05:41:52,381 copying build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./mdtraj 2025-10-16T05:41:52,411 copying build/lib.linux-armv7l-cpython-311/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/./mdtraj 2025-10-16T05:41:52,412 running install_egg_info 2025-10-16T05:41:52,429 running egg_info 2025-10-16T05:41:52,438 writing mdtraj.egg-info/PKG-INFO 2025-10-16T05:41:52,445 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2025-10-16T05:41:52,447 writing entry points to mdtraj.egg-info/entry_points.txt 2025-10-16T05:41:52,450 writing requirements to mdtraj.egg-info/requires.txt 2025-10-16T05:41:52,451 writing top-level names to mdtraj.egg-info/top_level.txt 2025-10-16T05:41:52,485 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,486 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,486 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,487 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,487 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,488 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,488 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,489 dependency /tmp/pip-build-env-lw424sd7/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h 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won't be automatically included in the manifest: the path must be relative 2025-10-16T05:41:52,494 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,495 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,496 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,496 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,497 dependency 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won't be automatically included in the manifest: the path must be relative 2025-10-16T05:41:52,499 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,500 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,501 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,502 dependency /tmp/pip-build-env-lw424sd7/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 2025-10-16T05:41:52,502 dependency 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won't be automatically included in the manifest: the path must be relative 2025-10-16T05:41:52,516 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2025-10-16T05:41:52,540 reading manifest template 'MANIFEST.in' 2025-10-16T05:41:53,129 no previously-included directories found matching '__pycache__' 2025-10-16T05:41:53,130 no previously-included directories found matching '*.pyc' 2025-10-16T05:41:53,131 adding license file 'LICENSE' 2025-10-16T05:41:53,145 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2025-10-16T05:41:53,152 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/./mdtraj-1.11.0-py3.11.egg-info 2025-10-16T05:41:53,166 running install_scripts 2025-10-16T05:41:53,222 creating build/bdist.linux-armv7l/wheel/mdtraj-1.11.0.dist-info/WHEEL 2025-10-16T05:41:53,226 creating '/tmp/pip-wheel-_bx5fxrn/.tmp-6ef4pud6/mdtraj-1.11.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-10-16T05:41:53,228 adding 'mdtraj/__init__.py' 2025-10-16T05:41:53,485 adding 'mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so' 2025-10-16T05:41:53,902 adding 'mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so' 2025-10-16T05:41:53,916 adding 'mdtraj/_version.py' 2025-10-16T05:41:53,919 adding 'mdtraj/io.py' 2025-10-16T05:41:53,920 adding 'mdtraj/version.py' 2025-10-16T05:41:53,922 adding 'mdtraj/core/__init__.py' 2025-10-16T05:41:53,924 adding 'mdtraj/core/element.py' 2025-10-16T05:41:53,927 adding 'mdtraj/core/residue_names.py' 2025-10-16T05:41:53,930 adding 'mdtraj/core/selection.py' 2025-10-16T05:41:53,938 adding 'mdtraj/core/topology.py' 2025-10-16T05:41:53,948 adding 'mdtraj/core/trajectory.py' 2025-10-16T05:41:53,950 adding 'mdtraj/core/lib/center.h' 2025-10-16T05:41:53,958 adding 'mdtraj/core/lib/libtheobald.a' 2025-10-16T05:41:53,959 adding 'mdtraj/core/lib/theobald_rmsd.h' 2025-10-16T05:41:53,961 adding 'mdtraj/formats/__init__.py' 2025-10-16T05:41:53,964 adding 'mdtraj/formats/amberrst.py' 2025-10-16T05:41:53,967 adding 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2025-10-16T05:41:56,798 adding 'mdtraj/geometry/rg.py' 2025-10-16T05:41:56,800 adding 'mdtraj/geometry/sasa.py' 2025-10-16T05:41:56,802 adding 'mdtraj/geometry/shape.py' 2025-10-16T05:41:56,805 adding 'mdtraj/geometry/thermodynamic_properties.py' 2025-10-16T05:41:56,807 adding 'mdtraj/nmr/__init__.py' 2025-10-16T05:41:56,809 adding 'mdtraj/nmr/scalar_couplings.py' 2025-10-16T05:41:56,811 adding 'mdtraj/nmr/shift_wrappers.py' 2025-10-16T05:41:56,814 adding 'mdtraj/reporters/__init__.py' 2025-10-16T05:41:56,817 adding 'mdtraj/reporters/basereporter.py' 2025-10-16T05:41:56,819 adding 'mdtraj/reporters/dcdreporter.py' 2025-10-16T05:41:56,822 adding 'mdtraj/reporters/hdf5reporter.py' 2025-10-16T05:41:56,824 adding 'mdtraj/reporters/netcdfreporter.py' 2025-10-16T05:41:57,044 adding 'mdtraj/reporters/xtcreporter.py' 2025-10-16T05:41:57,046 adding 'mdtraj/scripts/__init__.py' 2025-10-16T05:41:57,049 adding 'mdtraj/scripts/mdconvert.py' 2025-10-16T05:41:57,051 adding 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'mdtraj-1.11.0.dist-info/RECORD' 2025-10-16T05:41:57,217 removing build/bdist.linux-armv7l/wheel 2025-10-16T05:41:58,745 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2025-10-16T05:41:58,931 Created wheel for mdtraj: filename=mdtraj-1.11.0-cp311-cp311-linux_armv7l.whl size=7113507 sha256=f5543eba3ebb02839509a2709a78b34c8daf869d2cb82448f27c270cf00293fc 2025-10-16T05:41:58,933 Stored in directory: /tmp/pip-ephem-wheel-cache-ep_05icm/wheels/33/c5/62/606c5b59dcaf780ea68c5b9a5766ccfe94e7c27a5c1e533d71 2025-10-16T05:41:58,955 Successfully built mdtraj 2025-10-16T05:41:59,301 Removed build tracker: '/tmp/pip-build-tracker-4iuttqoe'