2025-09-08T01:58:19,365 Created temporary directory: /tmp/pip-build-tracker-sxbaovq3 2025-09-08T01:58:19,366 Initialized build tracking at /tmp/pip-build-tracker-sxbaovq3 2025-09-08T01:58:19,366 Created build tracker: /tmp/pip-build-tracker-sxbaovq3 2025-09-08T01:58:19,366 Entered build tracker: /tmp/pip-build-tracker-sxbaovq3 2025-09-08T01:58:19,366 Created temporary directory: /tmp/pip-wheel-ezgojau9 2025-09-08T01:58:19,370 Created temporary directory: /tmp/pip-ephem-wheel-cache-5jp9wufa 2025-09-08T01:58:19,427 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T01:58:19,429 2 location(s) to search for versions of mdtraj: 2025-09-08T01:58:19,429 * https://pypi.org/simple/mdtraj/ 2025-09-08T01:58:19,429 * https://www.piwheels.org/simple/mdtraj/ 2025-09-08T01:58:19,429 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2025-09-08T01:58:19,430 Getting page https://pypi.org/simple/mdtraj/ 2025-09-08T01:58:19,431 Found index url 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https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp37-cp37m-linux_armv7l.whl#sha256=cb090c5366b7b76d938daa16ca5a431a4fe751344ec320479b3ba8134a6ff4bd (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,654 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv6l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,654 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv7l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,654 Skipping link: No binaries permitted for mdtraj: 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https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,655 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv6l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,655 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,655 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv6l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,655 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv7l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,656 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv6l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,656 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,656 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv6l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,656 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,656 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,656 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv7l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,657 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv6l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,657 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T01:58:19,657 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2025-09-08T01:58:19,657 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2025-09-08T01:58:19,685 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates 2025-09-08T01:58:19,687 Collecting mdtraj==1.4.1 2025-09-08T01:58:19,688 Created temporary directory: /tmp/pip-unpack-_udf9hn9 2025-09-08T01:58:19,850 Downloading mdtraj-1.4.1.zip (14.8 MB) 2025-09-08T01:58:22,525 Added mdtraj==1.4.1 from https://files.pythonhosted.org/packages/eb/b4/4fd2c5d63e4a1f10047df8a3f83071d41ba9203abf1a86d381f2c16cef94/mdtraj-1.4.1.zip to build tracker '/tmp/pip-build-tracker-sxbaovq3' 2025-09-08T01:58:22,526 Running setup.py (path:/tmp/pip-wheel-ezgojau9/mdtraj_f65622c001274b23870f27ce916056b1/setup.py) egg_info for package mdtraj 2025-09-08T01:58:22,526 Created temporary directory: /tmp/pip-pip-egg-info-w4_17wtv 2025-09-08T01:58:22,526 Preparing metadata (setup.py): started 2025-09-08T01:58:22,527 Running command python setup.py egg_info 2025-09-08T01:58:23,474 Using built-in specs. 2025-09-08T01:58:23,474 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T01:58:23,475 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T01:58:23,475 Target: arm-linux-gnueabihf 2025-09-08T01:58:23,475 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T01:58:23,475 Thread model: posix 2025-09-08T01:58:23,475 Supported LTO compression algorithms: zlib zstd 2025-09-08T01:58:23,475 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T01:58:41,044 performance hint: mdtraj/rmsd/_rmsd.pyx:171:62: Use boundscheck(False) for faster access 2025-09-08T01:58:41,045 performance hint: mdtraj/rmsd/_rmsd.pyx:171:87: Use boundscheck(False) for faster access 2025-09-08T01:58:41,045 performance hint: mdtraj/rmsd/_rmsd.pyx:171:103: Use boundscheck(False) for faster access 2025-09-08T01:58:41,046 performance hint: mdtraj/rmsd/_rmsd.pyx:172:21: Use boundscheck(False) for faster access 2025-09-08T01:58:41,160 C compiler: 2025-09-08T01:58:41,160 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T01:58:41,160 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T01:58:41,160 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T01:58:41,160 Compiling mdtraj/formats/xtc/xtc.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/formats/xtc/trr.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/formats/dcd/dcd.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/formats/binpos/binpos.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/formats/dtr/dtr.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/rmsd/_rmsd.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/rmsd/_lprmsd.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/geometry/src/_geometry.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/geometry/drid.pyx because it changed. 2025-09-08T01:58:41,161 Compiling mdtraj/geometry/neighbors.pyx because it changed. 2025-09-08T01:58:41,161 [ 1/10] Cythonizing mdtraj/formats/binpos/binpos.pyx 2025-09-08T01:58:41,161 [ 2/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2025-09-08T01:58:41,162 [ 3/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2025-09-08T01:58:41,162 [ 4/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2025-09-08T01:58:41,162 [ 5/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2025-09-08T01:58:41,162 [ 6/10] Cythonizing mdtraj/geometry/drid.pyx 2025-09-08T01:58:41,162 [ 7/10] Cythonizing mdtraj/geometry/neighbors.pyx 2025-09-08T01:58:41,162 [ 8/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2025-09-08T01:58:41,162 [ 9/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2025-09-08T01:58:41,162 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2025-09-08T01:58:41,552 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T01:58:41,552 !! 2025-09-08T01:58:41,553 ******************************************************************************** 2025-09-08T01:58:41,553 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T01:58:41,553 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T01:58:41,553 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T01:58:41,553 ******************************************************************************** 2025-09-08T01:58:41,553 !! 2025-09-08T01:58:41,553 self._finalize_license_expression() 2025-09-08T01:58:41,630 running egg_info 2025-09-08T01:58:41,709 creating /tmp/pip-pip-egg-info-w4_17wtv/mdtraj.egg-info 2025-09-08T01:58:41,709 writing /tmp/pip-pip-egg-info-w4_17wtv/mdtraj.egg-info/PKG-INFO 2025-09-08T01:58:41,710 writing dependency_links to /tmp/pip-pip-egg-info-w4_17wtv/mdtraj.egg-info/dependency_links.txt 2025-09-08T01:58:41,711 writing entry points to /tmp/pip-pip-egg-info-w4_17wtv/mdtraj.egg-info/entry_points.txt 2025-09-08T01:58:41,711 writing top-level names to /tmp/pip-pip-egg-info-w4_17wtv/mdtraj.egg-info/top_level.txt 2025-09-08T01:58:41,712 writing manifest file '/tmp/pip-pip-egg-info-w4_17wtv/mdtraj.egg-info/SOURCES.txt' 2025-09-08T01:58:41,987 reading manifest file '/tmp/pip-pip-egg-info-w4_17wtv/mdtraj.egg-info/SOURCES.txt' 2025-09-08T01:58:41,988 reading manifest template 'MANIFEST.in' 2025-09-08T01:58:42,017 writing manifest file '/tmp/pip-pip-egg-info-w4_17wtv/mdtraj.egg-info/SOURCES.txt' 2025-09-08T01:58:43,296 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T01:58:43,301 Source in /tmp/pip-wheel-ezgojau9/mdtraj_f65622c001274b23870f27ce916056b1 has version 1.4.1, which satisfies requirement mdtraj==1.4.1 from https://files.pythonhosted.org/packages/eb/b4/4fd2c5d63e4a1f10047df8a3f83071d41ba9203abf1a86d381f2c16cef94/mdtraj-1.4.1.zip 2025-09-08T01:58:43,301 Removed mdtraj==1.4.1 from https://files.pythonhosted.org/packages/eb/b4/4fd2c5d63e4a1f10047df8a3f83071d41ba9203abf1a86d381f2c16cef94/mdtraj-1.4.1.zip from build tracker '/tmp/pip-build-tracker-sxbaovq3' 2025-09-08T01:58:43,304 Created temporary directory: /tmp/pip-unpack-abu0liet 2025-09-08T01:58:43,305 Created temporary directory: /tmp/pip-unpack-brpe0glz 2025-09-08T01:58:43,305 Building wheels for collected packages: mdtraj 2025-09-08T01:58:43,306 Created temporary directory: /tmp/pip-wheel-4j5s1q0z 2025-09-08T01:58:43,307 DEPRECATION: Building 'mdtraj' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'mdtraj'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T01:58:43,308 Building wheel for mdtraj (setup.py): started 2025-09-08T01:58:43,308 Destination directory: /tmp/pip-wheel-4j5s1q0z 2025-09-08T01:58:43,309 Running command python setup.py bdist_wheel 2025-09-08T01:58:44,261 C compiler: 2025-09-08T01:58:44,265 Using built-in specs. 2025-09-08T01:58:44,266 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T01:58:44,266 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T01:58:44,267 Target: arm-linux-gnueabihf 2025-09-08T01:58:44,267 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T01:58:44,267 Thread model: posix 2025-09-08T01:58:44,267 Supported LTO compression algorithms: zlib zstd 2025-09-08T01:58:44,267 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T01:58:45,592 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T01:58:46,212 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T01:58:46,835 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T01:58:47,958 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T01:58:47,958 !! 2025-09-08T01:58:47,959 ******************************************************************************** 2025-09-08T01:58:47,959 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T01:58:47,959 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T01:58:47,959 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T01:58:47,959 ******************************************************************************** 2025-09-08T01:58:47,959 !! 2025-09-08T01:58:47,960 self._finalize_license_expression() 2025-09-08T01:58:47,960 running bdist_wheel 2025-09-08T01:58:48,256 running build 2025-09-08T01:58:48,256 running build_py 2025-09-08T01:58:48,333 creating build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T01:58:48,334 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T01:58:48,335 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T01:58:48,335 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T01:58:48,336 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T01:58:48,337 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T01:58:48,337 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T01:58:48,338 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T01:58:48,339 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T01:58:48,339 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T01:58:48,340 creating build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T01:58:48,340 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T01:58:48,341 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T01:58:48,341 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T01:58:48,342 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T01:58:48,342 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T01:58:48,343 creating build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,344 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,344 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,345 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,345 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,346 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,346 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,347 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,348 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,348 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,349 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,349 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,350 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,350 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,351 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T01:58:48,352 creating build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,352 copying mdtraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,353 copying mdtraj/geometry/tests/test_drid.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,353 copying mdtraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,354 copying mdtraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,354 copying mdtraj/geometry/tests/test_dssp.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,355 copying mdtraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,355 copying mdtraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,356 copying mdtraj/geometry/tests/test_angles.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,356 copying mdtraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,357 copying mdtraj/geometry/tests/test_order.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,357 copying mdtraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,358 copying mdtraj/geometry/tests/test_thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,358 copying mdtraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,359 copying mdtraj/geometry/tests/test_rdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,359 copying mdtraj/geometry/tests/test_neighbors.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T01:58:48,360 creating build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T01:58:48,360 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T01:58:48,361 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T01:58:48,362 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T01:58:48,362 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T01:58:48,363 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T01:58:48,363 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T01:58:48,364 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T01:58:48,364 copying mdtraj/testing/nosetester.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T01:58:48,365 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T01:58:48,365 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T01:58:48,366 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T01:58:48,367 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T01:58:48,368 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,368 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,368 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,369 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,370 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,370 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,371 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,371 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,372 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,372 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,373 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,373 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,374 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,374 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,375 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,376 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,376 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T01:58:48,377 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T01:58:48,377 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T01:58:48,378 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T01:58:48,379 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T01:58:48,379 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T01:58:48,380 copying mdtraj/formats/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T01:58:48,380 copying mdtraj/formats/pdb/tests/test_element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T01:58:48,381 copying mdtraj/formats/pdb/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T01:58:48,382 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,382 copying mdtraj/utils/test.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,382 copying mdtraj/utils/ffi.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,383 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,383 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,384 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,384 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,385 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,385 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,386 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T01:58:48,387 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,387 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,388 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,388 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,389 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,389 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,390 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,390 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,391 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,391 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,392 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,393 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,393 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,394 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T01:58:48,394 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T01:58:48,395 copying mdtraj/utils/external/pyparsing.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T01:58:48,396 copying mdtraj/utils/external/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T01:58:48,397 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T01:58:48,397 copying mdtraj/utils/external/astor/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T01:58:48,398 copying mdtraj/utils/external/astor/misc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T01:58:48,398 copying mdtraj/utils/external/astor/codegen.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T01:58:48,399 copying mdtraj/utils/external/astor/treewalk.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T01:58:48,400 creating build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T01:58:48,400 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T01:58:48,400 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T01:58:48,401 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T01:58:48,402 creating build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T01:58:48,402 copying mdtraj/html/imagebutton_widget.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T01:58:48,402 copying mdtraj/html/trajectory_widget.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T01:58:48,403 copying mdtraj/html/linked_heatmap.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T01:58:48,403 copying mdtraj/html/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T01:58:48,404 copying mdtraj/html/install.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T01:58:48,405 creating build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,406 copying mdtraj/tests/test_io.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,406 copying mdtraj/tests/test_dtr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,407 copying mdtraj/tests/test_trajectory.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,407 copying mdtraj/tests/test_lammpstrj.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,408 copying mdtraj/tests/test_rmsd_memmap.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,408 copying mdtraj/tests/test_mol2.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,409 copying mdtraj/tests/test_psf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,409 copying mdtraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,410 copying mdtraj/tests/test_arc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,410 copying mdtraj/tests/test_crd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,411 copying mdtraj/tests/test_lh5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,411 copying mdtraj/tests/test_netcdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,412 copying mdtraj/tests/test_nmr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,412 copying mdtraj/tests/test_reporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,413 copying mdtraj/tests/test_xyz.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,413 copying mdtraj/tests/test_xml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,414 copying mdtraj/tests/test_topology.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,414 copying mdtraj/tests/test_xtc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,415 copying mdtraj/tests/test_selection.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,415 copying mdtraj/tests/test_lprmsd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,416 copying mdtraj/tests/test_element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,416 copying mdtraj/tests/test_rmsd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,417 copying mdtraj/tests/test_trr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,417 copying mdtraj/tests/test_quaternion.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,418 copying mdtraj/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,418 copying mdtraj/tests/test_hdf5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,419 copying mdtraj/tests/test_hoomdxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,419 copying mdtraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,420 copying mdtraj/tests/test_dcd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,420 copying mdtraj/tests/test_prmtop.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,421 copying mdtraj/tests/test_binpos.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,421 copying mdtraj/tests/test_restart.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,422 copying mdtraj/tests/test_gro.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,422 copying mdtraj/tests/test_capi.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T01:58:48,436 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,436 copying mdtraj/testing/reference/2lines.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,436 copying mdtraj/testing/reference/native2.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,437 copying mdtraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,440 copying mdtraj/testing/reference/tip3p_300K_1ATM_O-O_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,440 copying mdtraj/testing/reference/inpcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,441 copying mdtraj/testing/reference/test_hoomdxml.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,448 copying mdtraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,449 copying mdtraj/testing/reference/md.mdp -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,449 copying mdtraj/testing/reference/ala_dipeptide.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,450 copying mdtraj/testing/reference/1am7_corrected.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,452 copying mdtraj/testing/reference/ala_ala_ala.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,453 copying mdtraj/testing/reference/tip3p_300K_1ATM.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,454 copying mdtraj/testing/reference/native.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,454 copying mdtraj/testing/reference/ala_ala_ala.xpsf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,455 copying mdtraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,455 copying mdtraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,457 copying mdtraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,457 copying mdtraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,460 copying mdtraj/testing/reference/1line.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,460 copying mdtraj/testing/reference/ala_dipeptide.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,462 copying mdtraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,462 copying mdtraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,463 copying mdtraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,464 copying mdtraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,465 copying mdtraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,466 copying mdtraj/testing/reference/monolayer.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,468 copying mdtraj/testing/reference/ala_ala_ala.psf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,468 copying mdtraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,475 copying mdtraj/testing/reference/ala_ala_ala.mdcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,476 copying mdtraj/testing/reference/ncinpcrd.rst7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,476 copying mdtraj/testing/reference/3nch.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,479 copying mdtraj/testing/reference/alanine-dipeptide-implicit.prmtop -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,480 copying mdtraj/testing/reference/ala3_chamber.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,480 copying mdtraj/testing/reference/1vii.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,481 copying mdtraj/testing/reference/freesolve_v0.3.tar.bz2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,483 copying mdtraj/testing/reference/4OH9.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,484 copying mdtraj/testing/reference/nitrogen.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,487 copying mdtraj/testing/reference/README.md -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,488 copying mdtraj/testing/reference/alanine-dipeptide-explicit.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,489 copying mdtraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,490 copying mdtraj/testing/reference/1vii.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,491 copying mdtraj/testing/reference/alanine-dipeptide-explicit.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,491 copying mdtraj/testing/reference/1am7_protein.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,493 copying mdtraj/testing/reference/well-mixed.hoomdxml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,495 copying mdtraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,496 copying mdtraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,496 copying mdtraj/testing/reference/status-bits.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,497 copying mdtraj/testing/reference/imatinib.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,498 copying mdtraj/testing/reference/tip3p_300K_1ATM_O-H_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,498 copying mdtraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,499 copying mdtraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,500 copying mdtraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,500 copying mdtraj/testing/reference/custom.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,501 copying mdtraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,502 copying mdtraj/testing/reference/frame0.lammpstrj -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,503 copying mdtraj/testing/reference/frame0.xyz.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,504 copying mdtraj/testing/reference/monolayer.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,510 copying mdtraj/testing/reference/alanine.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,510 copying mdtraj/testing/reference/tip3p_300K_1ATM.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,515 copying mdtraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,516 copying mdtraj/testing/reference/1am7_uncorrected.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,518 copying mdtraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,521 copying mdtraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,524 copying mdtraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,525 copying mdtraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,527 copying mdtraj/testing/reference/3lines.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,527 copying mdtraj/testing/reference/3pqr_memb.psf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,628 copying mdtraj/testing/reference/1ncw.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,630 copying mdtraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,633 copying mdtraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,633 copying mdtraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,634 copying mdtraj/testing/reference/alanine-dipeptide-explicit.prmtop -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,636 copying mdtraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,637 copying mdtraj/testing/reference/overflow.crd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,643 copying mdtraj/testing/reference/custom.lammpstrj -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,644 copying mdtraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,645 copying mdtraj/testing/reference/tip3p_300K_1ATM_all-all_rdf.xvg -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,645 copying mdtraj/testing/reference/imatinib.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,646 copying mdtraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,646 copying mdtraj/testing/reference/frame0.gro -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,649 copying mdtraj/testing/reference/lysozyme-ligand-tripos.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,649 copying mdtraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,650 copying mdtraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,651 copying mdtraj/testing/reference/water_hex.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,657 copying mdtraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,658 copying mdtraj/testing/reference/frame0.xyz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,661 copying mdtraj/testing/reference/nitrogen.arc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,664 copying mdtraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,665 copying mdtraj/testing/reference/tz2.truncoct.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T01:58:48,669 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T01:58:48,670 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000000 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T01:58:48,670 copying mdtraj/testing/reference/ala_dipeptide_trj/metadata -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T01:58:48,671 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000002 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T01:58:48,671 copying mdtraj/testing/reference/ala_dipeptide_trj/clickme.dtr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T01:58:48,672 copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000001 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T01:58:48,673 copying mdtraj/testing/reference/ala_dipeptide_trj/timekeys -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T01:58:48,673 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T01:58:48,673 copying mdtraj/testing/reference/frame0.dtr/frame000000000 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T01:58:48,678 copying mdtraj/testing/reference/frame0.dtr/metadata -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T01:58:48,678 copying mdtraj/testing/reference/frame0.dtr/clickme.dtr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T01:58:48,679 copying mdtraj/testing/reference/frame0.dtr/frame000000001 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T01:58:48,683 copying mdtraj/testing/reference/frame0.dtr/timekeys -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T01:58:48,683 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T01:58:48,684 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T01:58:48,684 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T01:58:48,685 creating build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T01:58:48,685 copying mdtraj/html/static/context.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T01:58:48,686 copying mdtraj/html/static/filesaver.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T01:58:48,686 copying mdtraj/html/static/widget_imagebutton.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T01:58:48,687 copying mdtraj/html/static/iview.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T01:58:48,688 copying mdtraj/html/static/widget_trajectory.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T01:58:48,688 copying mdtraj/html/static/surface.min.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T01:58:48,689 copying mdtraj/html/static/objexporter.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T01:58:48,695 running build_ext 2025-09-08T01:58:48,696 building 'mdtraj.formats.xtc' extension 2025-09-08T01:58:48,697 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src 2025-09-08T01:58:48,698 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src/xdrfile.o 2025-09-08T01:58:48,840 mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2025-09-08T01:58:48,840 mdtraj/formats/xtc/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:58:48,841 495 | while (size >= num && num_of_bits < 32) 2025-09-08T01:58:48,841 | ^~ 2025-09-08T01:58:48,841 mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2025-09-08T01:58:48,841 mdtraj/formats/xtc/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:58:48,841 541 | while (bytes[num_of_bytes] >= num) 2025-09-08T01:58:48,841 | ^~ 2025-09-08T01:58:48,843 mdtraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2025-09-08T01:58:48,843 mdtraj/formats/xtc/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:58:48,843 650 | if (num_of_bits >= num_of_bytes * 8) 2025-09-08T01:58:48,843 | ^~ 2025-09-08T01:58:48,843 mdtraj/formats/xtc/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:58:48,843 652 | for (i = 0; i < num_of_bytes; i++) 2025-09-08T01:58:48,844 | ^ 2025-09-08T01:58:48,844 mdtraj/formats/xtc/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:58:48,844 660 | for (i = 0; i < num_of_bytes-1; i++) 2025-09-08T01:58:48,844 | ^ 2025-09-08T01:58:48,845 mdtraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2025-09-08T01:58:48,845 mdtraj/formats/xtc/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:58:48,845 700 | if (lastbits < num_of_bits) 2025-09-08T01:58:48,845 | ^ 2025-09-08T01:58:48,847 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2025-09-08T01:58:48,848 mdtraj/formats/xtc/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:58:48,848 815 | if(size3>xfp->buf1size) 2025-09-08T01:58:48,848 | ^ 2025-09-08T01:58:48,850 mdtraj/formats/xtc/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:58:48,850 869 | maxidx = (LASTIDX size3) 2025-09-08T01:58:48,852 | ^ 2025-09-08T01:58:48,854 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-09-08T01:58:48,854 788 | int smallnum, smaller, larger, i, is_smaller, run; 2025-09-08T01:58:48,854 | ^~~~~~ 2025-09-08T01:58:48,854 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-09-08T01:58:48,854 785 | int smallidx, minidx, maxidx; 2025-09-08T01:58:48,854 | ^~~~~~ 2025-09-08T01:58:48,855 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2025-09-08T01:58:48,856 mdtraj/formats/xtc/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:58:48,856 1027 | if(size3>xfp->buf1size) 2025-09-08T01:58:48,856 | ^ 2025-09-08T01:58:48,861 mdtraj/formats/xtc/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:58:48,861 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2025-09-08T01:58:48,861 | ^ 2025-09-08T01:58:48,862 mdtraj/formats/xtc/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:58:48,862 1156 | maxidx = (LASTIDXxfp->buf1size) 2025-09-08T01:58:48,869 | ^ 2025-09-08T01:58:48,872 mdtraj/formats/xtc/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:58:48,872 1383 | maxidx = (LASTIDXxfp->buf1size) { 2025-09-08T01:58:48,879 | ^ 2025-09-08T01:58:48,886 mdtraj/formats/xtc/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:58:48,886 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2025-09-08T01:58:48,886 | ^ 2025-09-08T01:58:48,887 mdtraj/formats/xtc/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:58:48,887 1639 | maxidx = (LASTIDXn_frames == -1L); 2025-09-08T01:58:52,737 | ^~ 2025-09-08T01:59:01,774 In function ‘__Pyx_PyLong_From_int’, 2025-09-08T01:59:01,774 inlined from ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’ at mdtraj/formats/xtc/xtc.c:12165:16, 2025-09-08T01:59:01,774 inlined from ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’ at mdtraj/formats/xtc/xtc.c:11847:13: 2025-09-08T01:59:01,799 mdtraj/formats/xtc/xtc.c:21983:20: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-08T01:59:01,799 21983 | return PyLong_FromLong((long) value); 2025-09-08T01:59:01,799 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T01:59:01,800 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pw_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_17_write’: 2025-09-08T01:59:01,813 mdtraj/formats/xtc/xtc.c:11869:7: note: ‘__pyx_v_status’ was declared here 2025-09-08T01:59:01,813 11869 | int __pyx_v_status; 2025-09-08T01:59:01,813 | ^~~~~~~~~~~~~~ 2025-09-08T01:59:18,464 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/xtc.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/mdtraj/formats/xtc.cpython-313-arm-linux-gnueabihf.so 2025-09-08T01:59:18,614 building 'mdtraj.formats.trr' extension 2025-09-08T01:59:18,616 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/formats/xtc -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src/xdrfile.o 2025-09-08T01:59:18,759 mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2025-09-08T01:59:18,759 mdtraj/formats/xtc/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:59:18,759 495 | while (size >= num && num_of_bits < 32) 2025-09-08T01:59:18,759 | ^~ 2025-09-08T01:59:18,760 mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2025-09-08T01:59:18,760 mdtraj/formats/xtc/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:59:18,760 541 | while (bytes[num_of_bytes] >= num) 2025-09-08T01:59:18,760 | ^~ 2025-09-08T01:59:18,761 mdtraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2025-09-08T01:59:18,761 mdtraj/formats/xtc/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:59:18,761 650 | if (num_of_bits >= num_of_bytes * 8) 2025-09-08T01:59:18,762 | ^~ 2025-09-08T01:59:18,762 mdtraj/formats/xtc/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:59:18,762 652 | for (i = 0; i < num_of_bytes; i++) 2025-09-08T01:59:18,762 | ^ 2025-09-08T01:59:18,762 mdtraj/formats/xtc/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:59:18,762 660 | for (i = 0; i < num_of_bytes-1; i++) 2025-09-08T01:59:18,762 | ^ 2025-09-08T01:59:18,763 mdtraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2025-09-08T01:59:18,763 mdtraj/formats/xtc/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:59:18,764 700 | if (lastbits < num_of_bits) 2025-09-08T01:59:18,764 | ^ 2025-09-08T01:59:18,765 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2025-09-08T01:59:18,766 mdtraj/formats/xtc/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:59:18,766 815 | if(size3>xfp->buf1size) 2025-09-08T01:59:18,766 | ^ 2025-09-08T01:59:18,768 mdtraj/formats/xtc/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:59:18,768 869 | maxidx = (LASTIDX size3) 2025-09-08T01:59:18,770 | ^ 2025-09-08T01:59:18,772 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-09-08T01:59:18,772 788 | int smallnum, smaller, larger, i, is_smaller, run; 2025-09-08T01:59:18,772 | ^~~~~~ 2025-09-08T01:59:18,772 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-09-08T01:59:18,772 785 | int smallidx, minidx, maxidx; 2025-09-08T01:59:18,772 | ^~~~~~ 2025-09-08T01:59:18,773 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2025-09-08T01:59:18,773 mdtraj/formats/xtc/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:59:18,774 1027 | if(size3>xfp->buf1size) 2025-09-08T01:59:18,774 | ^ 2025-09-08T01:59:18,778 mdtraj/formats/xtc/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:59:18,778 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2025-09-08T01:59:18,779 | ^ 2025-09-08T01:59:18,779 mdtraj/formats/xtc/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:59:18,779 1156 | maxidx = (LASTIDXxfp->buf1size) 2025-09-08T01:59:18,787 | ^ 2025-09-08T01:59:18,789 mdtraj/formats/xtc/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:59:18,789 1383 | maxidx = (LASTIDXxfp->buf1size) { 2025-09-08T01:59:18,797 | ^ 2025-09-08T01:59:18,803 mdtraj/formats/xtc/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T01:59:18,803 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2025-09-08T01:59:18,803 | ^ 2025-09-08T01:59:18,804 mdtraj/formats/xtc/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T01:59:18,805 1639 | maxidx = (LASTIDXn_frames == -1L); 2025-09-08T01:59:23,289 | ^~ 2025-09-08T01:59:32,054 In function ‘__Pyx_PyLong_From_int’, 2025-09-08T01:59:32,054 inlined from ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_16_write’ at mdtraj/formats/xtc/trr.c:12128:16, 2025-09-08T01:59:32,054 inlined from ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_17_write’ at mdtraj/formats/xtc/trr.c:11794:13: 2025-09-08T01:59:32,080 mdtraj/formats/xtc/trr.c:21923:20: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-08T01:59:32,080 21923 | return PyLong_FromLong((long) value); 2025-09-08T01:59:32,080 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T01:59:32,080 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pw_6mdtraj_7formats_3trr_17TRRTrajectoryFile_17_write’: 2025-09-08T01:59:32,094 mdtraj/formats/xtc/trr.c:11816:7: note: ‘__pyx_v_status’ was declared here 2025-09-08T01:59:32,094 11816 | int __pyx_v_status; 2025-09-08T01:59:32,094 | ^~~~~~~~~~~~~~ 2025-09-08T01:59:49,161 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-313/mdtraj/formats/xtc/trr.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/mdtraj/formats/trr.cpython-313-arm-linux-gnueabihf.so 2025-09-08T01:59:49,315 building 'mdtraj.formats.dcd' extension 2025-09-08T01:59:49,316 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/dcd 2025-09-08T01:59:49,316 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/dcd/src 2025-09-08T01:59:49,316 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/dcd/dcd.o 2025-09-08T01:59:51,354 In file included from mdtraj/formats/dcd/include/dcdplugin.h:1, 2025-09-08T01:59:51,354 from mdtraj/formats/dcd/dcd.c:1160: 2025-09-08T01:59:51,355 mdtraj/formats/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2025-09-08T01:59:51,355 473 | static int fio_write_str(fio_fd fd, const char *str) { 2025-09-08T01:59:51,355 | ^~~~~~~~~~~~~ 2025-09-08T01:59:51,355 mdtraj/formats/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2025-09-08T01:59:51,355 469 | static int fio_read_int32(fio_fd fd, int *i) { 2025-09-08T01:59:51,355 | ^~~~~~~~~~~~~~ 2025-09-08T01:59:51,355 mdtraj/formats/dcd/include/fastio.h:465:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 2025-09-08T01:59:51,355 465 | static int fio_write_int32(fio_fd fd, int i) { 2025-09-08T01:59:51,356 | ^~~~~~~~~~~~~~~ 2025-09-08T01:59:51,356 mdtraj/formats/dcd/include/fastio.h:456:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2025-09-08T01:59:51,356 456 | static fio_size_t fio_ftell(fio_fd fd) { 2025-09-08T01:59:51,356 | ^~~~~~~~~ 2025-09-08T01:59:51,356 mdtraj/formats/dcd/include/fastio.h:449:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 2025-09-08T01:59:51,356 449 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { 2025-09-08T01:59:51,356 | ^~~~~~~~~ 2025-09-08T01:59:51,356 mdtraj/formats/dcd/include/fastio.h:414:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 2025-09-08T01:59:51,356 414 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { 2025-09-08T01:59:51,356 | ^~~~~~~~~ 2025-09-08T01:59:51,357 mdtraj/formats/dcd/include/fastio.h:393:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2025-09-08T01:59:51,357 393 | static int fio_fclose(fio_fd fd) { 2025-09-08T01:59:51,357 | ^~~~~~~~~~ 2025-09-08T01:59:51,357 mdtraj/formats/dcd/include/fastio.h:365:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2025-09-08T01:59:51,357 365 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2025-09-08T01:59:51,357 | ^~~~~~~~ 2025-09-08T02:00:03,192 In function ‘__Pyx_PyLong_From_int’, 2025-09-08T02:00:03,192 inlined from ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’ at mdtraj/formats/dcd/dcd.c:10066:17: 2025-09-08T02:00:03,215 mdtraj/formats/dcd/dcd.c:19380:20: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-08T02:00:03,215 19380 | return PyLong_FromLong((long) value); 2025-09-08T02:00:03,215 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:03,215 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2025-09-08T02:00:03,224 mdtraj/formats/dcd/dcd.c:8814:7: note: ‘__pyx_v_i’ was declared here 2025-09-08T02:00:03,224 8814 | int __pyx_v_i; 2025-09-08T02:00:03,225 | ^~~~~~~~~ 2025-09-08T02:00:07,822 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/formats/dcd -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o 2025-09-08T02:00:08,040 mdtraj/formats/dcd/src/dcdplugin.c: In function ‘read_dcdheader’: 2025-09-08T02:00:08,040 mdtraj/formats/dcd/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T02:00:08,040 129 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { 2025-09-08T02:00:08,040 | ^~ 2025-09-08T02:00:08,041 mdtraj/formats/dcd/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T02:00:08,041 146 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { 2025-09-08T02:00:08,041 | ^~ 2025-09-08T02:00:08,041 mdtraj/formats/dcd/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T02:00:08,041 164 | if (input_integer[0] != dcdcordmagic) { 2025-09-08T02:00:08,041 | ^~ 2025-09-08T02:00:08,045 mdtraj/formats/dcd/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T02:00:08,045 341 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { 2025-09-08T02:00:08,045 | ^~ 2025-09-08T02:00:08,046 mdtraj/formats/dcd/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T02:00:08,046 358 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { 2025-09-08T02:00:08,046 | ^~ 2025-09-08T02:00:08,050 mdtraj/formats/dcd/src/dcdplugin.c: In function ‘read_dcdstep’: 2025-09-08T02:00:08,051 mdtraj/formats/dcd/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T02:00:08,051 540 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2025-09-08T02:00:08,051 | ^~ 2025-09-08T02:00:08,051 mdtraj/formats/dcd/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T02:00:08,051 544 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; 2025-09-08T02:00:08,052 | ^~ 2025-09-08T02:00:08,078 In file included from mdtraj/formats/dcd/src/dcdplugin.c:55: 2025-09-08T02:00:08,078 mdtraj/formats/dcd/include/endianswap.h: At top level: 2025-09-08T02:00:08,078 mdtraj/formats/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2025-09-08T02:00:08,078 96 | static void swap2_aligned(void *v, long ndata) { 2025-09-08T02:00:08,078 | ^~~~~~~~~~~~~ 2025-09-08T02:00:08,079 mdtraj/formats/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2025-09-08T02:00:08,079 32 | static void swap2_unaligned(void *v, long ndata) { 2025-09-08T02:00:08,079 | ^~~~~~~~~~~~~~~ 2025-09-08T02:00:08,079 In file included from mdtraj/formats/dcd/src/dcdplugin.c:46: 2025-09-08T02:00:08,079 mdtraj/formats/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2025-09-08T02:00:08,079 473 | static int fio_write_str(fio_fd fd, const char *str) { 2025-09-08T02:00:08,079 | ^~~~~~~~~~~~~ 2025-09-08T02:00:08,079 mdtraj/formats/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2025-09-08T02:00:08,079 469 | static int fio_read_int32(fio_fd fd, int *i) { 2025-09-08T02:00:08,079 | ^~~~~~~~~~~~~~ 2025-09-08T02:00:09,427 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-313/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/mdtraj/formats/dcd.cpython-313-arm-linux-gnueabihf.so 2025-09-08T02:00:09,563 building 'mdtraj.formats.binpos' extension 2025-09-08T02:00:09,563 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/binpos 2025-09-08T02:00:09,563 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/binpos/src 2025-09-08T02:00:09,563 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/formats/binpos -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/binpos/binpos.o 2025-09-08T02:00:22,580 In function ‘__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read’, 2025-09-08T02:00:22,580 inlined from ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’ at mdtraj/formats/binpos/binpos.c:7934:13: 2025-09-08T02:00:22,589 mdtraj/formats/binpos/binpos.c:8533:6: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-08T02:00:22,589 8533 | if (__pyx_t_1) { 2025-09-08T02:00:22,589 | ^ 2025-09-08T02:00:22,590 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2025-09-08T02:00:22,598 mdtraj/formats/binpos/binpos.c:7949:7: note: ‘__pyx_v_status’ was declared here 2025-09-08T02:00:22,598 7949 | int __pyx_v_status; 2025-09-08T02:00:22,598 | ^~~~~~~~~~~~~~ 2025-09-08T02:00:22,600 In function ‘__Pyx_PyLong_From_int’, 2025-09-08T02:00:22,600 inlined from ‘__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read’ at mdtraj/formats/binpos/binpos.c:8543:18, 2025-09-08T02:00:22,600 inlined from ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’ at mdtraj/formats/binpos/binpos.c:7934:13: 2025-09-08T02:00:22,620 mdtraj/formats/binpos/binpos.c:18699:20: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-08T02:00:22,620 18699 | return PyLong_FromLong((long) value); 2025-09-08T02:00:22,620 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:22,621 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2025-09-08T02:00:22,629 mdtraj/formats/binpos/binpos.c:7946:7: note: ‘__pyx_v_i’ was declared here 2025-09-08T02:00:22,629 7946 | int __pyx_v_i; 2025-09-08T02:00:22,629 | ^~~~~~~~~ 2025-09-08T02:00:27,092 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/formats/binpos -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/binpos/src/binposplugin.o 2025-09-08T02:00:27,208 mdtraj/formats/binpos/src/binposplugin.c: In function ‘tell_timestep’: 2025-09-08T02:00:27,208 mdtraj/formats/binpos/src/binposplugin.c:128:9: warning: unused variable ‘i’ [-Wunused-variable] 2025-09-08T02:00:27,208 128 | int i, numatoms, frame; 2025-09-08T02:00:27,209 | ^ 2025-09-08T02:00:27,427 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/mdtraj/formats/binpos/binpos.o build/temp.linux-armv7l-cpython-313/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/mdtraj/formats/binpos.cpython-313-arm-linux-gnueabihf.so 2025-09-08T02:00:27,561 building 'mdtraj.formats.dtr' extension 2025-09-08T02:00:27,562 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/dtr 2025-09-08T02:00:27,562 creating build/temp.linux-armv7l-cpython-313/mdtraj/formats/dtr/src 2025-09-08T02:00:27,563 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/dtr/dtr.o 2025-09-08T02:00:29,878 mdtraj/formats/dtr/dtr.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7formats_3dtr_17DTRTrajectoryFile_6get_times(__pyx_obj_6mdtraj_7formats_3dtr_DTRTrajectoryFile*)’: 2025-09-08T02:00:29,878 mdtraj/formats/dtr/dtr.cpp:7434:31: warning: comparison of integer expressions of different signedness: ‘molfile_ssize_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-08T02:00:29,878 7434 | __pyx_t_10 = (__pyx_v_count != __pyx_v_self->n_frames); 2025-09-08T02:00:29,878 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:48,303 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o 2025-09-08T02:00:50,531 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2025-09-08T02:00:50,531 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=] 2025-09-08T02:00:50,531 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2025-09-08T02:00:50,531 | ~~^ ~ 2025-09-08T02:00:50,531 | | | 2025-09-08T02:00:50,531 | | size_t {aka unsigned int} 2025-09-08T02:00:50,531 | long int 2025-09-08T02:00:50,531 | %d 2025-09-08T02:00:50,532 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=] 2025-09-08T02:00:50,532 487 | printf("size %d framesize %d\n\n", 2025-09-08T02:00:50,532 | ~^ 2025-09-08T02:00:50,532 | | 2025-09-08T02:00:50,532 | int 2025-09-08T02:00:50,532 | %lld 2025-09-08T02:00:50,532 488 | keys[i].size(), m_framesize); 2025-09-08T02:00:50,532 | ~~~~~~~~~~~~~~ 2025-09-08T02:00:50,532 | | 2025-09-08T02:00:50,533 | uint64_t {aka long long unsigned int} 2025-09-08T02:00:50,533 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=] 2025-09-08T02:00:50,533 487 | printf("size %d framesize %d\n\n", 2025-09-08T02:00:50,533 | ~^ 2025-09-08T02:00:50,533 | | 2025-09-08T02:00:50,533 | int 2025-09-08T02:00:50,533 | %lld 2025-09-08T02:00:50,533 488 | keys[i].size(), m_framesize); 2025-09-08T02:00:50,533 | ~~~~~~~~~~~ 2025-09-08T02:00:50,533 | | 2025-09-08T02:00:50,533 | uint64_t {aka long long unsigned int} 2025-09-08T02:00:50,534 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=] 2025-09-08T02:00:50,534 494 | "non-constant time interval at frame %ld\n", i); 2025-09-08T02:00:50,534 | ~~^ ~ 2025-09-08T02:00:50,534 | | | 2025-09-08T02:00:50,534 | | size_t {aka unsigned int} 2025-09-08T02:00:50,534 | long int 2025-09-08T02:00:50,534 | %d 2025-09-08T02:00:50,534 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=] 2025-09-08T02:00:50,534 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2025-09-08T02:00:50,535 | ~~^ ~ 2025-09-08T02:00:50,535 | | | 2025-09-08T02:00:50,535 | | size_t {aka unsigned int} 2025-09-08T02:00:50,535 | long int 2025-09-08T02:00:50,535 | %d 2025-09-08T02:00:50,609 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void* read_file(int, off_t, size_t&)’: 2025-09-08T02:00:50,609 mdtraj/formats/dtr/src/dtrplugin.cxx:902:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-08T02:00:50,609 902 | if (rc==-1) { 2025-09-08T02:00:50,609 | ~~^~~~ 2025-09-08T02:00:50,654 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2025-09-08T02:00:50,654 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=] 2025-09-08T02:00:50,654 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2025-09-08T02:00:50,654 | ~~^ 2025-09-08T02:00:50,654 | | 2025-09-08T02:00:50,654 | long int 2025-09-08T02:00:50,654 | %lld 2025-09-08T02:00:50,654 1302 | 3*natoms, pos.count); 2025-09-08T02:00:50,654 | ~~~~~~~~~ 2025-09-08T02:00:50,655 | | 2025-09-08T02:00:50,655 | uint64_t {aka long long unsigned int} 2025-09-08T02:00:50,655 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=] 2025-09-08T02:00:50,656 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2025-09-08T02:00:50,656 | ~~^ 2025-09-08T02:00:50,656 | | 2025-09-08T02:00:50,656 | long int 2025-09-08T02:00:50,656 | %lld 2025-09-08T02:00:50,656 1311 | 3*natoms, vel.count); 2025-09-08T02:00:50,656 | ~~~~~~~~~ 2025-09-08T02:00:50,656 | | 2025-09-08T02:00:50,656 | uint64_t {aka long long unsigned int} 2025-09-08T02:00:50,679 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2025-09-08T02:00:50,679 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=] 2025-09-08T02:00:50,679 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2025-09-08T02:00:50,679 | ~~^ 2025-09-08T02:00:50,679 | | 2025-09-08T02:00:50,679 | long int 2025-09-08T02:00:50,679 | %lld 2025-09-08T02:00:50,679 1573 | velblob.count, 3*natoms); 2025-09-08T02:00:50,680 | ~~~~~~~~~~~~~ 2025-09-08T02:00:50,680 | | 2025-09-08T02:00:50,680 | uint64_t {aka long long unsigned int} 2025-09-08T02:00:51,604 In file included from mdtraj/formats/dtr/src/dtrplugin.cxx:66: 2025-09-08T02:00:51,605 mdtraj/formats/dtr/include/endianswap.h: At global scope: 2025-09-08T02:00:51,605 mdtraj/formats/dtr/include/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] 2025-09-08T02:00:51,605 124 | static void swap8_aligned(void *v, long ndata) { 2025-09-08T02:00:51,605 | ^~~~~~~~~~~~~ 2025-09-08T02:00:51,605 mdtraj/formats/dtr/include/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] 2025-09-08T02:00:51,605 110 | static void swap4_aligned(void *v, long ndata) { 2025-09-08T02:00:51,605 | ^~~~~~~~~~~~~ 2025-09-08T02:00:51,606 mdtraj/formats/dtr/include/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] 2025-09-08T02:00:51,606 96 | static void swap2_aligned(void *v, long ndata) { 2025-09-08T02:00:51,606 | ^~~~~~~~~~~~~ 2025-09-08T02:00:51,606 mdtraj/formats/dtr/include/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] 2025-09-08T02:00:51,606 32 | static void swap2_unaligned(void *v, long ndata) { 2025-09-08T02:00:51,606 | ^~~~~~~~~~~~~~~ 2025-09-08T02:00:51,606 In file included from mdtraj/formats/dtr/src/dtrplugin.cxx:65: 2025-09-08T02:00:51,606 mdtraj/formats/dtr/include/vmddir.h:132:12: warning: ‘int vmd_file_is_executable(const char*)’ defined but not used [-Wunused-function] 2025-09-08T02:00:51,607 132 | static int vmd_file_is_executable(const char * filename) { 2025-09-08T02:00:51,607 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:51,777 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2025-09-08T02:00:51,777 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2025-09-08T02:00:51,777 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2025-09-08T02:00:51,777 | ~~~~~~~~^~~~~ 2025-09-08T02:00:54,721 In file included from /usr/include/c++/14/map:62, 2025-09-08T02:00:54,721 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2025-09-08T02:00:54,721 /usr/include/c++/14/bits/stl_tree.h: In 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> >]’: 2025-09-08T02:00:54,721 /usr/include/c++/14/bits/stl_tree.h:2208:5: 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 2025-09-08T02:00:54,721 2208 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-08T02:00:54,721 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:54,785 /usr/include/c++/14/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> >]’: 2025-09-08T02:00:54,785 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-08T02:00:54,785 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-08T02:00:54,785 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:54,840 In file included from /usr/include/c++/14/map:63: 2025-09-08T02:00:54,840 /usr/include/c++/14/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> >]’: 2025-09-08T02:00:54,840 /usr/include/c++/14/bits/stl_map.h:532:44: 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 2025-09-08T02:00:54,841 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-08T02:00:54,841 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:54,841 533 | std::forward_as_tuple(std::move(__k)), 2025-09-08T02:00:54,841 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:54,841 534 | std::tuple<>()); 2025-09-08T02:00:54,841 | ~~~~~~~~~~~~~~~ 2025-09-08T02:00:55,170 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2025-09-08T02:00:55,171 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=] 2025-09-08T02:00:55,171 706 | sprintf(sub, "%03x/", i); 2025-09-08T02:00:55,171 | ^~~~ 2025-09-08T02:00:55,171 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2025-09-08T02:00:55,171 706 | sprintf(sub, "%03x/", i); 2025-09-08T02:00:55,171 | ^~~~~~~ 2025-09-08T02:00:55,171 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2025-09-08T02:00:55,171 706 | sprintf(sub, "%03x/", i); 2025-09-08T02:00:55,171 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-08T02:00:55,171 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=] 2025-09-08T02:00:55,172 714 | sprintf(subsub, "%03x", j); 2025-09-08T02:00:55,172 | ^~~~ 2025-09-08T02:00:55,172 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2025-09-08T02:00:55,172 714 | sprintf(subsub, "%03x", j); 2025-09-08T02:00:55,172 | ^~~~~~ 2025-09-08T02:00:55,172 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2025-09-08T02:00:55,172 714 | sprintf(subsub, "%03x", j); 2025-09-08T02:00:55,172 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:55,906 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2025-09-08T02:00:55,906 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-08T02:00:55,906 667 | sprintf(answer, "%03x/", d1); 2025-09-08T02:00:55,906 | ^ 2025-09-08T02:00:55,906 In function ‘std::string DDreldir(const std::string&, int, int)’, 2025-09-08T02:00:55,907 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2025-09-08T02:00:55,907 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2025-09-08T02:00:55,907 667 | sprintf(answer, "%03x/", d1); 2025-09-08T02:00:55,907 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:55,907 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2025-09-08T02:00:55,907 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=] 2025-09-08T02:00:55,907 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2025-09-08T02:00:55,907 | ^~~~ 2025-09-08T02:00:55,908 In function ‘std::string DDreldir(const std::string&, int, int)’, 2025-09-08T02:00:55,908 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2025-09-08T02:00:55,908 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2025-09-08T02:00:55,908 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2025-09-08T02:00:55,908 | ^~~~~~~~~~~~ 2025-09-08T02:00:55,908 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2025-09-08T02:00:55,908 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2025-09-08T02:00:55,908 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:59,694 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> >]’, 2025-09-08T02:00:59,694 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: 2025-09-08T02:00:59,694 /usr/include/c++/14/bits/stl_map.h:532:44: 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 2025-09-08T02:00:59,694 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-08T02:00:59,694 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:59,694 533 | std::forward_as_tuple(std::move(__k)), 2025-09-08T02:00:59,695 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:59,695 534 | std::tuple<>()); 2025-09-08T02:00:59,695 | ~~~~~~~~~~~~~~~ 2025-09-08T02:00:59,696 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> >]’, 2025-09-08T02:00:59,696 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28, 2025-09-08T02:00:59,696 inlined from ‘int desres::molfile::DtrReader::frame_from_bytes(const void*, uint64_t, molfile_timestep_t*) const’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1737:29: 2025-09-08T02:00:59,696 /usr/include/c++/14/bits/stl_map.h:532:44: 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 2025-09-08T02:00:59,696 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-08T02:00:59,697 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:59,697 533 | std::forward_as_tuple(std::move(__k)), 2025-09-08T02:00:59,697 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:00:59,697 534 | std::tuple<>()); 2025-09-08T02:00:59,697 | ~~~~~~~~~~~~~~~ 2025-09-08T02:01:04,292 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-313/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/mdtraj/formats/dtr.cpython-313-arm-linux-gnueabihf.so 2025-09-08T02:01:04,640 building 'mdtraj._rmsd' extension 2025-09-08T02:01:04,640 creating build/temp.linux-armv7l-cpython-313/mdtraj/rmsd 2025-09-08T02:01:04,641 creating build/temp.linux-armv7l-cpython-313/mdtraj/rmsd/src 2025-09-08T02:01:04,641 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c mdtraj/rmsd/_rmsd.c -o build/temp.linux-armv7l-cpython-313/mdtraj/rmsd/_rmsd.o -msse2 -O3 -funroll-loops 2025-09-08T02:01:04,650 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’ 2025-09-08T02:01:04,657 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T02:01:04,831 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T02:01:04,844 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T02:01:04,844 exec(compile('"'"''"'"''"'"' 2025-09-08T02:01:04,844 # This is -- a caller that pip uses to run setup.py 2025-09-08T02:01:04,844 # 2025-09-08T02:01:04,844 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T02:01:04,844 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T02:01:04,844 # - It provides a clear error message when setuptools is not installed. 2025-09-08T02:01:04,844 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T02:01:04,844 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T02:01:04,844 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T02:01:04,844 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T02:01:04,844 import os, sys, tokenize, traceback 2025-09-08T02:01:04,844 2025-09-08T02:01:04,844 try: 2025-09-08T02:01:04,844 import setuptools 2025-09-08T02:01:04,844 except ImportError: 2025-09-08T02:01:04,844 print( 2025-09-08T02:01:04,844 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T02:01:04,844 "the build environment with exception:", 2025-09-08T02:01:04,844 file=sys.stderr, 2025-09-08T02:01:04,844 ) 2025-09-08T02:01:04,844 traceback.print_exc() 2025-09-08T02:01:04,844 sys.exit(1) 2025-09-08T02:01:04,844 2025-09-08T02:01:04,844 __file__ = %r 2025-09-08T02:01:04,844 sys.argv[0] = __file__ 2025-09-08T02:01:04,844 2025-09-08T02:01:04,844 if os.path.exists(__file__): 2025-09-08T02:01:04,844 filename = __file__ 2025-09-08T02:01:04,844 with tokenize.open(__file__) as f: 2025-09-08T02:01:04,844 setup_py_code = f.read() 2025-09-08T02:01:04,844 else: 2025-09-08T02:01:04,844 filename = "" 2025-09-08T02:01:04,844 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T02:01:04,844 2025-09-08T02:01:04,844 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T02:01:04,844 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-ezgojau9/mdtraj_f65622c001274b23870f27ce916056b1/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-4j5s1q0z[/] 2025-09-08T02:01:04,844 [bold magenta]cwd[/]: /tmp/pip-wheel-ezgojau9/mdtraj_f65622c001274b23870f27ce916056b1/ 2025-09-08T02:01:04,845 Building wheel for mdtraj (setup.py): finished with status 'error' 2025-09-08T02:01:04,845 ERROR: Failed building wheel for mdtraj 2025-09-08T02:01:04,846 Running setup.py clean for mdtraj 2025-09-08T02:01:04,847 Running command python setup.py clean 2025-09-08T02:01:05,850 C compiler: 2025-09-08T02:01:05,854 Using built-in specs. 2025-09-08T02:01:05,855 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T02:01:05,855 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T02:01:05,855 Target: arm-linux-gnueabihf 2025-09-08T02:01:05,856 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T02:01:05,856 Thread model: posix 2025-09-08T02:01:05,856 Supported LTO compression algorithms: zlib zstd 2025-09-08T02:01:05,856 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T02:01:07,159 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T02:01:07,775 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T02:01:08,407 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T02:01:09,608 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T02:01:09,609 !! 2025-09-08T02:01:09,609 ******************************************************************************** 2025-09-08T02:01:09,609 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T02:01:09,609 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T02:01:09,609 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T02:01:09,609 ******************************************************************************** 2025-09-08T02:01:09,610 !! 2025-09-08T02:01:09,610 self._finalize_license_expression() 2025-09-08T02:01:09,684 running clean 2025-09-08T02:01:09,830 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T02:01:09,833 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T02:01:09,862 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T02:01:09,862 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T02:01:09,862 removing 'build' 2025-09-08T02:01:10,034 Failed to build mdtraj 2025-09-08T02:01:10,035 ERROR: Failed to build one or more wheels 2025-09-08T02:01:10,036 Exception information: 2025-09-08T02:01:10,036 Traceback (most recent call last): 2025-09-08T02:01:10,036 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T02:01:10,036 status = _inner_run() 2025-09-08T02:01:10,036 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T02:01:10,036 return self.run(options, args) 2025-09-08T02:01:10,036 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T02:01:10,036 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T02:01:10,036 return func(self, options, args) 2025-09-08T02:01:10,036 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T02:01:10,036 raise CommandError("Failed to build one or more wheels") 2025-09-08T02:01:10,036 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T02:01:10,041 Removed build tracker: '/tmp/pip-build-tracker-sxbaovq3'