2024-05-17T11:35:33,336 Created temporary directory: /tmp/pip-build-tracker-9u67k3tg 2024-05-17T11:35:33,338 Initialized build tracking at /tmp/pip-build-tracker-9u67k3tg 2024-05-17T11:35:33,338 Created build tracker: /tmp/pip-build-tracker-9u67k3tg 2024-05-17T11:35:33,339 Entered build tracker: /tmp/pip-build-tracker-9u67k3tg 2024-05-17T11:35:33,339 Created temporary directory: /tmp/pip-wheel-hu2hj0f5 2024-05-17T11:35:33,343 Created temporary directory: /tmp/pip-ephem-wheel-cache-getms8hi 2024-05-17T11:35:33,366 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-17T11:35:33,369 2 location(s) to search for versions of mdtraj: 2024-05-17T11:35:33,369 * https://pypi.org/simple/mdtraj/ 2024-05-17T11:35:33,369 * https://www.piwheels.org/simple/mdtraj/ 2024-05-17T11:35:33,370 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2024-05-17T11:35:33,370 Getting page https://pypi.org/simple/mdtraj/ 2024-05-17T11:35:33,372 Found index url 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https://files.pythonhosted.org/packages/3b/fd/4ffba665d0b0346072f61d0e8ef7ab281202db445d99136c717c89169a97/mdtraj-1.9.5-cp38-cp38-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T11:35:33,650 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/68/53/2f666107565f4735abd859b6af6867353eb08d0e9728d90fb0abc12d578e/mdtraj-1.9.5-cp39-cp39-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T11:35:33,650 Found link https://files.pythonhosted.org/packages/d8/cb/5dcc31c7e2c4485bd2aea66233def28954f2dc530607f5c43fefab71a963/mdtraj-1.9.5.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.5 2024-05-17T11:35:33,651 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/fe/a7/2a1392fe56ddd22a9cf5dcff7d684bdd7ce146d5c32839080dd8de7122dd/mdtraj-1.9.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T11:35:33,651 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/ce/ee/2015ff88cacb7c75b5e1cf6a57e8a089549b0e76bcd9474a08845f7ef12f/mdtraj-1.9.6-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T11:35:33,652 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/c0/61/2fb002b9b2ab90567eb1a837ed510152ddadd5b8358ac800b591e37675e0/mdtraj-1.9.6-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T11:35:33,652 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/09/49/85dc22a3c28108dfd0bce8a4268ae3937167b18fac531a0d801505cad7d9/mdtraj-1.9.6-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T11:35:33,653 Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.6 2024-05-17T11:35:33,654 Found link https://files.pythonhosted.org/packages/2f/03/c174bfb6471f796472ce1d8695f6c0d1a20ad6516cb789b70052df45b7a6/mdtraj-1.9.7.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.7 2024-05-17T11:35:33,654 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/5d/1c/75a4c0ec4fb42e5daafaf13a49c03194f76b7deb0134d894a5004d833446/mdtraj-1.9.8-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T11:35:33,655 Found link https://files.pythonhosted.org/packages/53/02/a30f67a8bd3dba6d6e4ecc02bee290f425bf30c504a8a959a04e2be321ac/mdtraj-1.9.8.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.8 2024-05-17T11:35:33,655 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/88/12/ecbe28c87bc3df8c4880cc742923a6f40633ca076c8f44b03533dfce0b66/mdtraj-1.9.9-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T11:35:33,656 Found link https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.9 2024-05-17T11:35:33,657 Found link https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.10.0rc1 2024-05-17T11:35:33,658 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2024-05-17T11:35:33,658 Getting page https://www.piwheels.org/simple/mdtraj/ 2024-05-17T11:35:33,660 Found index url https://www.piwheels.org/simple/ 2024-05-17T11:35:33,877 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2024-05-17T11:35:33,881 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv6l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,882 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv7l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,883 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv6l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,883 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,883 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv6l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,884 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,884 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,885 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv7l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,885 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv6l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,886 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T11:35:33,887 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2024-05-17T11:35:33,887 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2024-05-17T11:35:33,913 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2024-05-17T11:35:33,931 Collecting mdtraj==1.10.0rc1 2024-05-17T11:35:33,934 Created temporary directory: /tmp/pip-unpack-yd9nm40w 2024-05-17T11:35:34,162 Downloading mdtraj-1.10.0rc1.tar.gz (1.8 MB) 2024-05-17T11:35:35,292 Added mdtraj==1.10.0rc1 from https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz to build tracker '/tmp/pip-build-tracker-9u67k3tg' 2024-05-17T11:35:35,299 Created temporary directory: /tmp/pip-build-env-8tpeg6je 2024-05-17T11:35:35,303 Installing build dependencies: started 2024-05-17T11:35:35,305 Running command pip subprocess to install build dependencies 2024-05-17T11:35:36,438 Using pip 24.0 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-05-17T11:35:36,937 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-17T11:35:38,487 Collecting setuptools 2024-05-17T11:35:38,551 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.5.1-py3-none-any.whl (894 kB) 2024-05-17T11:35:38,794 Collecting wheel 2024-05-17T11:35:38,835 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-05-17T11:35:38,998 Collecting oldest-supported-numpy 2024-05-17T11:35:39,022 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2023.12.21-py3-none-any.whl (4.9 kB) 2024-05-17T11:35:40,273 Collecting Cython~=0.29.36 2024-05-17T11:35:40,296 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.37-cp311-cp311-linux_armv7l.whl (5.0 MB) 2024-05-17T11:35:41,541 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-17T11:35:41,544 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-17T11:35:41,548 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-17T11:35:41,551 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-17T11:35:41,554 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-17T11:35:41,884 Collecting numpy==1.23.2 (from oldest-supported-numpy) 2024-05-17T11:35:41,901 Using cached https://www.piwheels.org/simple/numpy/numpy-1.23.2-cp311-cp311-linux_armv7l.whl (12.4 MB) 2024-05-17T11:35:45,136 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2024-05-17T11:35:45,360 Creating /tmp/pip-build-env-8tpeg6je/overlay/local/bin 2024-05-17T11:35:45,362 changing mode of /tmp/pip-build-env-8tpeg6je/overlay/local/bin/wheel to 755 2024-05-17T11:35:56,383 changing mode of /tmp/pip-build-env-8tpeg6je/overlay/local/bin/f2py to 755 2024-05-17T11:35:56,385 changing mode of /tmp/pip-build-env-8tpeg6je/overlay/local/bin/f2py3 to 755 2024-05-17T11:35:56,387 changing mode of /tmp/pip-build-env-8tpeg6je/overlay/local/bin/f2py3.11 to 755 2024-05-17T11:35:59,255 changing mode of /tmp/pip-build-env-8tpeg6je/overlay/local/bin/cygdb to 755 2024-05-17T11:35:59,257 changing mode of /tmp/pip-build-env-8tpeg6je/overlay/local/bin/cython to 755 2024-05-17T11:35:59,260 changing mode of /tmp/pip-build-env-8tpeg6je/overlay/local/bin/cythonize to 755 2024-05-17T11:35:59,314 Successfully installed Cython-0.29.37 numpy-1.23.2 oldest-supported-numpy-2023.12.21 setuptools-69.5.1 wheel-0.43.0 2024-05-17T11:36:00,059 Installing build dependencies: finished with status 'done' 2024-05-17T11:36:00,073 Getting requirements to build wheel: started 2024-05-17T11:36:00,075 Running command Getting requirements to build wheel 2024-05-17T11:36:00,777 Using built-in specs. 2024-05-17T11:36:00,777 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-17T11:36:00,778 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-17T11:36:00,779 Target: arm-linux-gnueabihf 2024-05-17T11:36:00,779 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-17T11:36:00,780 Thread model: posix 2024-05-17T11:36:00,781 Supported LTO compression algorithms: zlib zstd 2024-05-17T11:36:00,781 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-17T11:36:05,080 C compiler: 2024-05-17T11:36:05,081 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-17T11:36:05,081 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-17T11:36:05,082 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-17T11:36:05,082 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-17T11:36:05,083 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-17T11:36:05,084 running egg_info 2024-05-17T11:36:05,089 writing mdtraj.egg-info/PKG-INFO 2024-05-17T11:36:05,092 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-17T11:36:05,094 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-17T11:36:05,096 writing requirements to mdtraj.egg-info/requires.txt 2024-05-17T11:36:05,097 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-17T11:36:05,135 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-17T11:36:05,157 reading manifest template 'MANIFEST.in' 2024-05-17T11:36:05,744 no previously-included directories found matching '__pycache__' 2024-05-17T11:36:05,746 no previously-included directories found matching '*.pyc' 2024-05-17T11:36:05,746 adding license file 'LICENSE' 2024-05-17T11:36:05,758 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-17T11:36:05,857 Getting requirements to build wheel: finished with status 'done' 2024-05-17T11:36:05,866 Created temporary directory: /tmp/pip-modern-metadata-vcpqk31_ 2024-05-17T11:36:05,868 Preparing metadata (pyproject.toml): started 2024-05-17T11:36:05,869 Running command Preparing metadata (pyproject.toml) 2024-05-17T11:36:06,537 Using built-in specs. 2024-05-17T11:36:06,537 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-17T11:36:06,538 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-17T11:36:06,539 Target: arm-linux-gnueabihf 2024-05-17T11:36:06,539 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-17T11:36:06,540 Thread model: posix 2024-05-17T11:36:06,540 Supported LTO compression algorithms: zlib zstd 2024-05-17T11:36:06,541 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-17T11:36:10,729 /tmp/pip-wheel-hu2hj0f5/mdtraj_0c0e93efb5cb47fb803270bd63c519f9/basesetup.py:503: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-vcpqk31_ --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2024-05-17T11:36:10,729 warnings.warn( 2024-05-17T11:36:12,559 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T11:36:12,560 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T11:36:12,560 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T11:36:33,877 C compiler: 2024-05-17T11:36:33,878 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-17T11:36:33,878 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-17T11:36:33,878 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-17T11:36:33,879 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-17T11:36:33,879 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-17T11:36:33,880 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-17T11:36:33,881 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-17T11:36:33,881 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-17T11:36:33,882 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-17T11:36:33,882 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-17T11:36:33,883 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-17T11:36:33,883 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-17T11:36:33,884 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-17T11:36:33,884 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-17T11:36:33,885 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-17T11:36:33,969 running dist_info 2024-05-17T11:36:33,976 creating /tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info 2024-05-17T11:36:33,983 writing /tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info/PKG-INFO 2024-05-17T11:36:33,987 writing dependency_links to /tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info/dependency_links.txt 2024-05-17T11:36:33,988 writing entry points to /tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info/entry_points.txt 2024-05-17T11:36:33,990 writing requirements to /tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info/requires.txt 2024-05-17T11:36:33,991 writing top-level names to /tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info/top_level.txt 2024-05-17T11:36:33,993 writing manifest file '/tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info/SOURCES.txt' 2024-05-17T11:36:34,042 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,042 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,043 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,043 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,044 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,045 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,045 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,046 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,046 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,047 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,047 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,048 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,048 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,049 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,049 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,050 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,050 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,051 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,051 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,052 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,052 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,053 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,054 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,054 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,055 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,055 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,056 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,057 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,057 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,057 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:36:34,069 reading manifest file '/tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info/SOURCES.txt' 2024-05-17T11:36:34,072 reading manifest template 'MANIFEST.in' 2024-05-17T11:36:34,629 no previously-included directories found matching '__pycache__' 2024-05-17T11:36:34,631 no previously-included directories found matching '*.pyc' 2024-05-17T11:36:34,631 adding license file 'LICENSE' 2024-05-17T11:36:34,641 writing manifest file '/tmp/pip-modern-metadata-vcpqk31_/mdtraj.egg-info/SOURCES.txt' 2024-05-17T11:36:34,643 creating '/tmp/pip-modern-metadata-vcpqk31_/mdtraj-1.10.0rc1.dist-info' 2024-05-17T11:36:35,527 Preparing metadata (pyproject.toml): finished with status 'done' 2024-05-17T11:36:35,531 Source in /tmp/pip-wheel-hu2hj0f5/mdtraj_0c0e93efb5cb47fb803270bd63c519f9 has version 1.10.0rc1, which satisfies requirement mdtraj==1.10.0rc1 from https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz 2024-05-17T11:36:35,532 Removed mdtraj==1.10.0rc1 from https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz from build tracker '/tmp/pip-build-tracker-9u67k3tg' 2024-05-17T11:36:35,536 Created temporary directory: /tmp/pip-unpack-varhi8un 2024-05-17T11:36:35,537 Created temporary directory: /tmp/pip-unpack-a83hru3x 2024-05-17T11:36:35,546 Building wheels for collected packages: mdtraj 2024-05-17T11:36:35,550 Created temporary directory: /tmp/pip-wheel-2krgiatf 2024-05-17T11:36:35,551 Destination directory: /tmp/pip-wheel-2krgiatf 2024-05-17T11:36:35,553 Building wheel for mdtraj (pyproject.toml): started 2024-05-17T11:36:35,554 Running command Building wheel for mdtraj (pyproject.toml) 2024-05-17T11:36:36,238 Using built-in specs. 2024-05-17T11:36:36,238 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-17T11:36:36,239 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-17T11:36:36,240 Target: arm-linux-gnueabihf 2024-05-17T11:36:36,240 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-17T11:36:36,241 Thread model: posix 2024-05-17T11:36:36,242 Supported LTO compression algorithms: zlib zstd 2024-05-17T11:36:36,242 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-17T11:36:41,959 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T11:36:41,960 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T11:36:41,960 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T11:37:03,231 C compiler: 2024-05-17T11:37:03,232 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-17T11:37:03,232 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-17T11:37:03,233 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-17T11:37:03,233 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-17T11:37:03,234 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-17T11:37:03,234 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-17T11:37:03,235 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-17T11:37:03,235 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-17T11:37:03,236 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-17T11:37:03,237 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-17T11:37:03,237 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-17T11:37:03,238 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-17T11:37:03,239 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-17T11:37:03,240 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-17T11:37:03,240 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-17T11:37:03,346 running bdist_wheel 2024-05-17T11:37:03,382 running build 2024-05-17T11:37:03,383 running build_py 2024-05-17T11:37:03,392 creating build 2024-05-17T11:37:03,393 creating build/lib.linux-armv7l-cpython-311 2024-05-17T11:37:03,393 creating build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-17T11:37:03,395 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-17T11:37:03,397 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-17T11:37:03,399 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-17T11:37:03,403 creating build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,404 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,406 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,409 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,411 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,413 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,415 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,418 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,420 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,422 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,425 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,427 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,429 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,431 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,434 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,436 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:37:03,439 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,440 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,442 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,444 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,446 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,448 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,451 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,453 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,456 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,458 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,461 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,463 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,465 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,467 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,470 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,473 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,475 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,478 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,480 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,484 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,485 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,487 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,488 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,490 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,492 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,495 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,497 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,499 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-17T11:37:03,502 creating build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-17T11:37:03,503 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-17T11:37:03,505 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-17T11:37:03,507 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-17T11:37:03,510 creating build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-17T11:37:03,511 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-17T11:37:03,514 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-17T11:37:03,515 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-17T11:37:03,518 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-17T11:37:03,521 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-17T11:37:03,524 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-17T11:37:03,527 creating build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-17T11:37:03,528 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-17T11:37:03,530 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-17T11:37:03,532 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-17T11:37:03,534 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-17T11:37:03,536 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-17T11:37:03,538 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-17T11:37:03,541 creating build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-17T11:37:03,542 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-17T11:37:03,544 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-17T11:37:03,546 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-17T11:37:03,549 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-17T11:37:03,551 creating build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-17T11:37:03,552 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-17T11:37:03,554 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-17T11:37:03,556 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-17T11:37:03,559 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-17T11:37:03,560 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-17T11:37:03,562 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-17T11:37:03,565 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-17T11:37:03,568 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,570 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,572 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,575 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,577 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,579 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,582 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,585 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,587 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,589 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,591 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,594 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,596 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,598 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-17T11:37:03,605 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-17T11:37:03,606 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-17T11:37:03,609 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-17T11:37:03,617 running build_ext 2024-05-17T11:37:03,620 building 'mdtraj.formats.xtc' extension 2024-05-17T11:37:03,621 creating build/temp.linux-armv7l-cpython-311 2024-05-17T11:37:03,622 creating build/temp.linux-armv7l-cpython-311/mdtraj 2024-05-17T11:37:03,623 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats 2024-05-17T11:37:03,624 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc 2024-05-17T11:37:03,625 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src 2024-05-17T11:37:03,626 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:37:03,744 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:37:03,901 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-17T11:37:03,902 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:03,902 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-17T11:37:03,903 | ^~~~~~ 2024-05-17T11:37:03,904 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:03,904 785 | int smallidx, minidx, maxidx; 2024-05-17T11:37:03,905 | ^~~~~~ 2024-05-17T11:37:03,913 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-17T11:37:03,914 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:03,915 1016 | int errval=1; 2024-05-17T11:37:03,915 | ^~~~~~ 2024-05-17T11:37:03,921 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-17T11:37:03,922 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:03,923 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-17T11:37:03,923 | ^~~~~~ 2024-05-17T11:37:03,924 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:03,925 1302 | int smallidx, minidx, maxidx; 2024-05-17T11:37:03,926 | ^~~~~~ 2024-05-17T11:37:03,936 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-17T11:37:03,937 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:03,938 1509 | int errval=1; 2024-05-17T11:37:03,938 | ^~~~~~ 2024-05-17T11:37:06,563 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:37:06,645 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2024-05-17T11:37:06,646 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 2024-05-17T11:37:06,647 66 | int i,j,result; 2024-05-17T11:37:06,647 | ^ 2024-05-17T11:37:06,648 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 2024-05-17T11:37:06,649 66 | int i,j,result; 2024-05-17T11:37:06,649 | ^ 2024-05-17T11:37:06,650 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2024-05-17T11:37:06,651 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2024-05-17T11:37:06,651 119 | if (NULL == xd) 2024-05-17T11:37:06,652 | ^~ 2024-05-17T11:37:06,652 mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2024-05-17T11:37:06,653 122 | do { 2024-05-17T11:37:06,654 | ^~ 2024-05-17T11:37:06,789 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:37:07,241 In file included from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-17T11:37:07,241 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T11:37:07,242 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-17T11:37:07,242 from mdtraj/formats/xtc/xtc.c:784: 2024-05-17T11:37:07,243 /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-17T11:37:07,243 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T11:37:07,244 | ^~~~~~~ 2024-05-17T11:37:15,703 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2024-05-17T11:37:15,703 mdtraj/formats/xtc/xtc.c:696:40: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:15,704 696 | #define PyInt_FromLong PyLong_FromLong 2024-05-17T11:37:15,705 | ^~~~~~~~~~~~~~~ 2024-05-17T11:37:15,712 mdtraj/formats/xtc/xtc.c:9563:7: note: ‘__pyx_v_status’ was declared here 2024-05-17T11:37:15,714 9563 | int __pyx_v_status; 2024-05-17T11:37:15,714 | ^~~~~~~~~~~~~~ 2024-05-17T11:37:26,642 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2024-05-17T11:37:26,650 mdtraj/formats/xtc/xtc.c:8082:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,651 8082 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-17T11:37:26,651 | ^ 2024-05-17T11:37:26,656 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 2024-05-17T11:37:26,657 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-17T11:37:26,657 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,664 mdtraj/formats/xtc/xtc.c:8078:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,665 8078 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-17T11:37:26,665 | ^ 2024-05-17T11:37:26,670 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 2024-05-17T11:37:26,671 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-17T11:37:26,671 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,678 mdtraj/formats/xtc/xtc.c:8074:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,678 8074 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T11:37:26,679 | ^ 2024-05-17T11:37:26,684 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 2024-05-17T11:37:26,685 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-17T11:37:26,686 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,692 mdtraj/formats/xtc/xtc.c:8034:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,693 8034 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T11:37:26,693 | ^ 2024-05-17T11:37:26,698 mdtraj/formats/xtc/xtc.c:6481:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 2024-05-17T11:37:26,699 6481 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; 2024-05-17T11:37:26,700 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,706 mdtraj/formats/xtc/xtc.c:8016:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,707 8016 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T11:37:26,707 | ^ 2024-05-17T11:37:26,712 mdtraj/formats/xtc/xtc.c:6477:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 2024-05-17T11:37:26,713 6477 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; 2024-05-17T11:37:26,714 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,720 mdtraj/formats/xtc/xtc.c:8092:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,721 8092 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T11:37:26,721 | ^ 2024-05-17T11:37:26,726 mdtraj/formats/xtc/xtc.c:6473:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 2024-05-17T11:37:26,727 6473 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; 2024-05-17T11:37:26,728 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,734 mdtraj/formats/xtc/xtc.c:8054:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,734 8054 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-17T11:37:26,735 | ^ 2024-05-17T11:37:26,740 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 2024-05-17T11:37:26,741 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-17T11:37:26,741 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,748 mdtraj/formats/xtc/xtc.c:8050:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,748 8050 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-17T11:37:26,749 | ^ 2024-05-17T11:37:26,754 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 2024-05-17T11:37:26,755 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-17T11:37:26,755 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,762 mdtraj/formats/xtc/xtc.c:8046:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,762 8046 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T11:37:26,763 | ^ 2024-05-17T11:37:26,768 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 2024-05-17T11:37:26,769 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-17T11:37:26,769 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,775 mdtraj/formats/xtc/xtc.c:7669:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,776 7669 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-17T11:37:26,777 | ^ 2024-05-17T11:37:26,782 mdtraj/formats/xtc/xtc.c:6469:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 2024-05-17T11:37:26,782 6469 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2024-05-17T11:37:26,783 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:26,789 mdtraj/formats/xtc/xtc.c:7665:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:26,789 7665 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T11:37:26,790 | ^ 2024-05-17T11:37:26,795 mdtraj/formats/xtc/xtc.c:6469:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 2024-05-17T11:37:26,796 6469 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2024-05-17T11:37:26,796 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:31,428 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:37:31,576 building 'mdtraj.formats.trr' extension 2024-05-17T11:37:31,577 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:37:31,688 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:37:31,833 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-17T11:37:31,834 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:31,834 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-17T11:37:31,835 | ^~~~~~ 2024-05-17T11:37:31,835 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:31,836 785 | int smallidx, minidx, maxidx; 2024-05-17T11:37:31,837 | ^~~~~~ 2024-05-17T11:37:31,845 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-17T11:37:31,846 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:31,847 1016 | int errval=1; 2024-05-17T11:37:31,848 | ^~~~~~ 2024-05-17T11:37:31,853 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-17T11:37:31,854 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:31,855 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-17T11:37:31,856 | ^~~~~~ 2024-05-17T11:37:31,856 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:31,857 1302 | int smallidx, minidx, maxidx; 2024-05-17T11:37:31,858 | ^~~~~~ 2024-05-17T11:37:31,868 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-17T11:37:31,869 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-17T11:37:31,870 1509 | int errval=1; 2024-05-17T11:37:31,871 | ^~~~~~ 2024-05-17T11:37:34,462 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:37:35,281 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:37:35,665 In file included from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-17T11:37:35,666 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T11:37:35,667 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-17T11:37:35,667 from mdtraj/formats/xtc/trr.c:784: 2024-05-17T11:37:35,668 /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-17T11:37:35,668 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T11:37:35,669 | ^~~~~~~ 2024-05-17T11:37:44,905 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2024-05-17T11:37:44,906 mdtraj/formats/xtc/trr.c:696:40: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:44,906 696 | #define PyInt_FromLong PyLong_FromLong 2024-05-17T11:37:44,906 | ^~~~~~~~~~~~~~~ 2024-05-17T11:37:44,916 mdtraj/formats/xtc/trr.c:11089:7: note: ‘__pyx_v_status’ was declared here 2024-05-17T11:37:44,917 11089 | int __pyx_v_status; 2024-05-17T11:37:44,918 | ^~~~~~~~~~~~~~ 2024-05-17T11:37:56,217 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2024-05-17T11:37:56,225 mdtraj/formats/xtc/trr.c:8442:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,226 8442 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-17T11:37:56,227 | ^ 2024-05-17T11:37:56,232 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2024-05-17T11:37:56,233 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-17T11:37:56,233 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,240 mdtraj/formats/xtc/trr.c:8438:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,241 8438 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T11:37:56,242 | ^ 2024-05-17T11:37:56,254 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2024-05-17T11:37:56,262 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-17T11:37:56,262 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,263 mdtraj/formats/xtc/trr.c:1935:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,263 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-17T11:37:56,264 | ^ 2024-05-17T11:37:56,265 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-05-17T11:37:56,265 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-17T11:37:56,266 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,267 mdtraj/formats/xtc/trr.c:8432:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,268 8432 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-05-17T11:37:56,268 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-17T11:37:56,271 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2024-05-17T11:37:56,272 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-17T11:37:56,272 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,279 mdtraj/formats/xtc/trr.c:8385:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,280 8385 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-17T11:37:56,280 | ^ 2024-05-17T11:37:56,286 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2024-05-17T11:37:56,287 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-17T11:37:56,287 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,295 mdtraj/formats/xtc/trr.c:8381:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,296 8381 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T11:37:56,297 | ^ 2024-05-17T11:37:56,302 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2024-05-17T11:37:56,302 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-17T11:37:56,303 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,303 mdtraj/formats/xtc/trr.c:1935:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,304 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-17T11:37:56,305 | ^ 2024-05-17T11:37:56,310 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-05-17T11:37:56,311 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-17T11:37:56,312 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,319 mdtraj/formats/xtc/trr.c:8375:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,319 8375 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-05-17T11:37:56,320 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-17T11:37:56,326 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2024-05-17T11:37:56,326 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-17T11:37:56,327 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,334 mdtraj/formats/xtc/trr.c:8775:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,335 8775 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T11:37:56,335 | ^ 2024-05-17T11:37:56,341 mdtraj/formats/xtc/trr.c:7001:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2024-05-17T11:37:56,342 7001 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-05-17T11:37:56,343 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,350 mdtraj/formats/xtc/trr.c:8771:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,350 8771 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-17T11:37:56,351 | ^ 2024-05-17T11:37:56,357 mdtraj/formats/xtc/trr.c:7001:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2024-05-17T11:37:56,358 7001 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-05-17T11:37:56,358 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,365 mdtraj/formats/xtc/trr.c:8616:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,366 8616 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T11:37:56,366 | ^ 2024-05-17T11:37:56,372 mdtraj/formats/xtc/trr.c:6997:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2024-05-17T11:37:56,373 6997 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-05-17T11:37:56,373 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,381 mdtraj/formats/xtc/trr.c:8612:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,381 8612 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-17T11:37:56,382 | ^ 2024-05-17T11:37:56,388 mdtraj/formats/xtc/trr.c:6997:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2024-05-17T11:37:56,388 6997 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-05-17T11:37:56,389 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,396 mdtraj/formats/xtc/trr.c:8668:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,397 8668 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T11:37:56,398 | ^ 2024-05-17T11:37:56,403 mdtraj/formats/xtc/trr.c:6981:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2024-05-17T11:37:56,404 6981 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-05-17T11:37:56,405 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:37:56,412 mdtraj/formats/xtc/trr.c:8664:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:37:56,412 8664 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-17T11:37:56,413 | ^ 2024-05-17T11:37:56,419 mdtraj/formats/xtc/trr.c:6981:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2024-05-17T11:37:56,420 6981 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-05-17T11:37:56,421 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:03,176 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:38:03,324 building 'mdtraj.formats.dcd' extension 2024-05-17T11:38:03,325 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd 2024-05-17T11:38:03,326 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src 2024-05-17T11:38:03,327 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:38:03,731 In file included from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-17T11:38:03,732 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T11:38:03,733 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-17T11:38:03,733 from mdtraj/formats/dcd/dcd.c:782: 2024-05-17T11:38:03,734 /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-17T11:38:03,734 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T11:38:03,735 | ^~~~~~~ 2024-05-17T11:38:12,836 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2024-05-17T11:38:12,837 mdtraj/formats/dcd/dcd.c:694:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:38:12,837 694 | #define PyInt_FromLong PyLong_FromLong 2024-05-17T11:38:12,838 | ^~~~~~~~~~~~~~~ 2024-05-17T11:38:12,842 mdtraj/formats/dcd/dcd.c:5458:7: note: ‘__pyx_v_i’ was declared here 2024-05-17T11:38:12,842 5458 | int __pyx_v_i; 2024-05-17T11:38:12,843 | ^~~~~~~~~ 2024-05-17T11:38:16,010 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:38:17,567 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:38:17,702 building 'mdtraj.formats.dtr' extension 2024-05-17T11:38:17,702 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr 2024-05-17T11:38:17,703 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src 2024-05-17T11:38:17,704 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:38:18,028 In file included from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-17T11:38:18,029 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T11:38:18,030 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-17T11:38:18,030 from mdtraj/formats/dtr/dtr.cpp:803: 2024-05-17T11:38:18,031 /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-17T11:38:18,031 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T11:38:18,032 | ^~~~~~~ 2024-05-17T11:38:32,437 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:38:34,842 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2024-05-17T11:38:34,842 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=] 2024-05-17T11:38:34,843 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2024-05-17T11:38:34,843 | ~~^ ~ 2024-05-17T11:38:34,844 | | | 2024-05-17T11:38:34,845 | | size_t {aka unsigned int} 2024-05-17T11:38:34,845 | long int 2024-05-17T11:38:34,846 | %d 2024-05-17T11:38:34,847 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=] 2024-05-17T11:38:34,848 487 | printf("size %d framesize %d\n\n", 2024-05-17T11:38:34,849 | ~^ 2024-05-17T11:38:34,849 | | 2024-05-17T11:38:34,850 | int 2024-05-17T11:38:34,851 | %lld 2024-05-17T11:38:34,852 488 | keys[i].size(), m_framesize); 2024-05-17T11:38:34,852 | ~~~~~~~~~~~~~~ 2024-05-17T11:38:34,853 | | 2024-05-17T11:38:34,854 | uint64_t {aka long long unsigned int} 2024-05-17T11:38:34,855 mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-17T11:38:34,855 487 | printf("size %d framesize %d\n\n", 2024-05-17T11:38:34,856 | ~^ 2024-05-17T11:38:34,857 | | 2024-05-17T11:38:34,858 | int 2024-05-17T11:38:34,858 | %lld 2024-05-17T11:38:34,859 488 | keys[i].size(), m_framesize); 2024-05-17T11:38:34,859 | ~~~~~~~~~~~ 2024-05-17T11:38:34,860 | | 2024-05-17T11:38:34,861 | uint64_t {aka long long unsigned int} 2024-05-17T11:38:34,861 mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-17T11:38:34,862 494 | "non-constant time interval at frame %ld\n", i); 2024-05-17T11:38:34,863 | ~~^ ~ 2024-05-17T11:38:34,863 | | | 2024-05-17T11:38:34,864 | | size_t {aka unsigned int} 2024-05-17T11:38:34,865 | long int 2024-05-17T11:38:34,865 | %d 2024-05-17T11:38:34,866 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=] 2024-05-17T11:38:34,867 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2024-05-17T11:38:34,867 | ~~^ ~ 2024-05-17T11:38:34,868 | | | 2024-05-17T11:38:34,868 | | size_t {aka unsigned int} 2024-05-17T11:38:34,869 | long int 2024-05-17T11:38:34,869 | %d 2024-05-17T11:38:35,008 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-17T11:38:35,009 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=] 2024-05-17T11:38:35,009 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2024-05-17T11:38:35,010 | ~~^ 2024-05-17T11:38:35,011 | | 2024-05-17T11:38:35,012 | long int 2024-05-17T11:38:35,012 | %lld 2024-05-17T11:38:35,013 1302 | 3*natoms, pos.count); 2024-05-17T11:38:35,014 | ~~~~~~~~~ 2024-05-17T11:38:35,015 | | 2024-05-17T11:38:35,015 | uint64_t {aka long long unsigned int} 2024-05-17T11:38:35,016 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=] 2024-05-17T11:38:35,017 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2024-05-17T11:38:35,018 | ~~^ 2024-05-17T11:38:35,018 | | 2024-05-17T11:38:35,019 | long int 2024-05-17T11:38:35,019 | %lld 2024-05-17T11:38:35,020 1311 | 3*natoms, vel.count); 2024-05-17T11:38:35,021 | ~~~~~~~~~ 2024-05-17T11:38:35,021 | | 2024-05-17T11:38:35,022 | uint64_t {aka long long unsigned int} 2024-05-17T11:38:35,042 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-17T11:38:35,043 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=] 2024-05-17T11:38:35,043 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2024-05-17T11:38:35,044 | ~~^ 2024-05-17T11:38:35,045 | | 2024-05-17T11:38:35,046 | long int 2024-05-17T11:38:35,046 | %lld 2024-05-17T11:38:35,047 1573 | velblob.count, 3*natoms); 2024-05-17T11:38:35,047 | ~~~~~~~~~~~~~ 2024-05-17T11:38:35,048 | | 2024-05-17T11:38:35,048 | uint64_t {aka long long unsigned int} 2024-05-17T11:38:36,350 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2024-05-17T11:38:36,375 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2024-05-17T11:38:36,376 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2024-05-17T11:38:36,377 | ~~~~~~~~^~~~~ 2024-05-17T11:38:39,146 In file included from /usr/include/c++/12/map:60, 2024-05-17T11:38:39,147 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-17T11:38:39,147 /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-17T11:38:39,148 /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-17T11:38:39,148 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-17T11:38:39,149 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:39,217 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-17T11:38:39,218 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-17T11:38:39,219 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-17T11:38:39,219 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:39,278 In file included from /usr/include/c++/12/map:61: 2024-05-17T11:38:39,279 /usr/include/c++/12/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-17T11:38:39,279 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-17T11:38:39,280 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-17T11:38:39,280 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:39,281 531 | std::forward_as_tuple(std::move(__k)), 2024-05-17T11:38:39,281 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:39,282 532 | std::tuple<>()); 2024-05-17T11:38:39,283 | ~~~~~~~~~~~~~~~ 2024-05-17T11:38:39,371 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> >]’, 2024-05-17T11:38:39,372 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28: 2024-05-17T11:38:39,373 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-17T11:38:39,373 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-17T11:38:39,374 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:39,375 531 | std::forward_as_tuple(std::move(__k)), 2024-05-17T11:38:39,375 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:39,376 532 | std::tuple<>()); 2024-05-17T11:38:39,377 | ~~~~~~~~~~~~~~~ 2024-05-17T11:38:40,221 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2024-05-17T11:38:40,222 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=] 2024-05-17T11:38:40,223 706 | sprintf(sub, "%03x/", i); 2024-05-17T11:38:40,224 | ^~~~ 2024-05-17T11:38:40,224 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2024-05-17T11:38:40,225 706 | sprintf(sub, "%03x/", i); 2024-05-17T11:38:40,226 | ^~~~~~~ 2024-05-17T11:38:40,227 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2024-05-17T11:38:40,228 706 | sprintf(sub, "%03x/", i); 2024-05-17T11:38:40,228 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2024-05-17T11:38:40,229 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=] 2024-05-17T11:38:40,230 714 | sprintf(subsub, "%03x", j); 2024-05-17T11:38:40,230 | ^~~~ 2024-05-17T11:38:40,231 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2024-05-17T11:38:40,231 714 | sprintf(subsub, "%03x", j); 2024-05-17T11:38:40,232 | ^~~~~~ 2024-05-17T11:38:40,233 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2024-05-17T11:38:40,233 714 | sprintf(subsub, "%03x", j); 2024-05-17T11:38:40,234 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:40,628 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2024-05-17T11:38:40,629 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-17T11:38:40,629 667 | sprintf(answer, "%03x/", d1); 2024-05-17T11:38:40,630 | ^ 2024-05-17T11:38:40,630 In function ‘std::string DDreldir(const std::string&, int, int)’, 2024-05-17T11:38:40,631 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2024-05-17T11:38:40,631 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2024-05-17T11:38:40,632 667 | sprintf(answer, "%03x/", d1); 2024-05-17T11:38:40,633 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:40,634 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2024-05-17T11:38:40,634 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=] 2024-05-17T11:38:40,635 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-17T11:38:40,636 | ^~~~ 2024-05-17T11:38:40,637 In function ‘std::string DDreldir(const std::string&, int, int)’, 2024-05-17T11:38:40,638 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2024-05-17T11:38:40,638 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2024-05-17T11:38:40,639 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-17T11:38:40,640 | ^~~~~~~~~~~~ 2024-05-17T11:38:40,641 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2024-05-17T11:38:40,641 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-17T11:38:40,642 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:43,811 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’, 2024-05-17T11:38:43,812 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: 2024-05-17T11:38:43,813 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-17T11:38:43,814 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-17T11:38:43,815 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:43,815 531 | std::forward_as_tuple(std::move(__k)), 2024-05-17T11:38:43,816 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T11:38:43,817 532 | std::tuple<>()); 2024-05-17T11:38:43,817 | ~~~~~~~~~~~~~~~ 2024-05-17T11:38:48,835 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:38:49,174 building 'mdtraj._rmsd' extension 2024-05-17T11:38:49,175 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd 2024-05-17T11:38:49,176 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src 2024-05-17T11:38:49,177 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:39:29,802 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:39:30,007 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:39:30,267 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:39:31,047 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:39:31,353 building 'mdtraj._lprmsd' extension 2024-05-17T11:39:31,355 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:39:31,621 In file included from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-17T11:39:31,622 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T11:39:31,623 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-17T11:39:31,623 from mdtraj/rmsd/_lprmsd.cpp:812: 2024-05-17T11:39:31,623 /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-17T11:39:31,624 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T11:39:31,624 | ^~~~~~~ 2024-05-17T11:39:55,875 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:39:58,761 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:39:58,977 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:40:00,267 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:40:00,570 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:40:00,829 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:40:01,581 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:40:01,874 building 'mdtraj.core.lib.libtheobald' extension 2024-05-17T11:40:01,874 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2024-05-17T11:40:02,626 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2024-05-17T11:40:02,832 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o 2024-05-17T11:40:02,859 building 'mdtraj.geometry._geometry' extension 2024-05-17T11:40:02,860 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-17T11:40:02,861 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src 2024-05-17T11:40:02,862 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:40:03,140 In file included from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-17T11:40:03,141 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T11:40:03,142 from /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-17T11:40:03,142 from mdtraj/geometry/src/_geometry.cpp:814: 2024-05-17T11:40:03,143 /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-17T11:40:03,143 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T11:40:03,144 | ^~~~~~~ 2024-05-17T11:40:37,538 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:40:51,761 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:40:55,795 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:40:56,915 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:40:57,269 building 'mdtraj.geometry.drid' extension 2024-05-17T11:40:57,269 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:41:26,842 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:41:27,486 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:41:27,593 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:41:27,884 building 'mdtraj.geometry.neighbors' extension 2024-05-17T11:41:27,885 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:41:55,273 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:41:56,577 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:41:56,855 building 'mdtraj.geometry.neighborlist' extension 2024-05-17T11:41:56,856 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:42:21,770 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-17T11:42:26,229 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2024-05-17T11:42:26,230 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2024-05-17T11:42:26,231 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:42:26,231 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2024-05-17T11:42:26,232 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-17T11:42:26,233 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-17T11:42:26,233 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-17T11:42:26,234 341 | float periodicBoxVectors[3][3]; 2024-05-17T11:42:26,235 | ^~~~~~~~~~~~~~~~~~ 2024-05-17T11:42:26,236 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2024-05-17T11:42:26,236 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2024-05-17T11:42:26,236 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:42:26,237 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2024-05-17T11:42:26,237 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-17T11:42:26,238 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-17T11:42:26,239 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-17T11:42:26,239 341 | float periodicBoxVectors[3][3]; 2024-05-17T11:42:26,240 | ^~~~~~~~~~~~~~~~~~ 2024-05-17T11:42:26,240 mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:42:26,241 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); 2024-05-17T11:42:26,241 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-17T11:42:26,242 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-17T11:42:26,242 341 | float periodicBoxVectors[3][3]; 2024-05-17T11:42:26,243 | ^~~~~~~~~~~~~~~~~~ 2024-05-17T11:42:26,244 mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-17T11:42:26,245 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); 2024-05-17T11:42:26,246 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-17T11:42:26,247 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-17T11:42:26,248 341 | float periodicBoxVectors[3][3]; 2024-05-17T11:42:26,248 | ^~~~~~~~~~~~~~~~~~ 2024-05-17T11:42:27,089 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so 2024-05-17T11:42:27,437 installing to build/bdist.linux-armv7l/wheel 2024-05-17T11:42:27,437 running install 2024-05-17T11:42:27,464 running install_lib 2024-05-17T11:42:27,472 creating build/bdist.linux-armv7l 2024-05-17T11:42:27,473 creating build/bdist.linux-armv7l/wheel 2024-05-17T11:42:27,475 creating build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T11:42:27,477 copying build/lib.linux-armv7l-cpython-311/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T11:42:27,479 copying build/lib.linux-armv7l-cpython-311/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T11:42:27,482 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,483 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,488 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,491 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,511 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,514 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,515 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,518 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,520 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,558 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,561 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,563 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,566 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,569 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,571 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,602 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,604 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,606 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,629 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,632 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T11:42:27,635 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,636 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,638 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,641 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,643 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,645 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,648 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,650 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,653 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,686 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,688 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,710 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,713 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,715 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,718 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,731 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,752 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-17T11:42:27,753 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-17T11:42:27,755 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-17T11:42:27,756 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-17T11:42:27,758 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-17T11:42:27,761 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-17T11:42:27,763 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-17T11:42:27,766 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,769 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,772 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,775 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,777 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,780 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,782 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T11:42:27,785 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,786 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,788 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,791 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,792 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,794 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,796 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,799 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,801 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,804 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,810 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,812 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,815 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,816 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,818 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,820 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,822 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T11:42:27,824 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,826 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,828 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,830 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,832 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,834 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T11:42:27,836 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-17T11:42:27,837 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-17T11:42:27,839 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-17T11:42:27,841 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-17T11:42:27,843 copying build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T11:42:27,864 copying build/lib.linux-armv7l-cpython-311/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T11:42:27,867 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T11:42:27,868 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T11:42:27,871 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T11:42:27,872 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T11:42:27,875 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T11:42:27,879 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-17T11:42:27,880 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-17T11:42:27,882 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-17T11:42:27,884 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-17T11:42:27,887 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T11:42:27,890 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T11:42:27,893 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T11:42:27,894 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T11:42:27,896 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T11:42:27,898 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T11:42:27,899 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T11:42:27,902 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T11:42:27,904 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T11:42:27,906 copying build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T11:42:27,933 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T11:42:27,934 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T11:42:27,936 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T11:42:27,938 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T11:42:27,941 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T11:42:27,943 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-17T11:42:27,945 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-17T11:42:27,946 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-17T11:42:27,948 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-17T11:42:27,951 running install_egg_info 2024-05-17T11:42:27,965 running egg_info 2024-05-17T11:42:27,970 writing mdtraj.egg-info/PKG-INFO 2024-05-17T11:42:27,973 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-17T11:42:27,974 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-17T11:42:27,975 writing requirements to mdtraj.egg-info/requires.txt 2024-05-17T11:42:27,976 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-17T11:42:28,010 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,011 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,012 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,012 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,013 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,014 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,014 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,015 dependency 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be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,019 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,019 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,020 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,021 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,021 dependency 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be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,025 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,026 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,026 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,027 dependency /tmp/pip-build-env-8tpeg6je/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,028 dependency 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be automatically included in the manifest: the path must be relative 2024-05-17T11:42:28,040 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-17T11:42:28,062 reading manifest template 'MANIFEST.in' 2024-05-17T11:42:28,660 no previously-included directories found matching '__pycache__' 2024-05-17T11:42:28,661 no previously-included directories found matching '*.pyc' 2024-05-17T11:42:28,661 adding license file 'LICENSE' 2024-05-17T11:42:28,673 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-17T11:42:28,675 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.10.0rc1-py3.11.egg-info 2024-05-17T11:42:28,689 running install_scripts 2024-05-17T11:42:28,744 creating build/bdist.linux-armv7l/wheel/mdtraj-1.10.0rc1.dist-info/WHEEL 2024-05-17T11:42:28,747 creating '/tmp/pip-wheel-2krgiatf/.tmp-ymrbcgow/mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-17T11:42:28,750 adding 'mdtraj/__init__.py' 2024-05-17T11:42:28,978 adding 'mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so' 2024-05-17T11:42:29,348 adding 'mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so' 2024-05-17T11:42:29,362 adding 'mdtraj/io.py' 2024-05-17T11:42:29,363 adding 'mdtraj/version.py' 2024-05-17T11:42:29,365 adding 'mdtraj/core/__init__.py' 2024-05-17T11:42:29,367 adding 'mdtraj/core/element.py' 2024-05-17T11:42:29,370 adding 'mdtraj/core/residue_names.py' 2024-05-17T11:42:29,372 adding 'mdtraj/core/selection.py' 2024-05-17T11:42:29,380 adding 'mdtraj/core/topology.py' 2024-05-17T11:42:29,389 adding 'mdtraj/core/trajectory.py' 2024-05-17T11:42:29,391 adding 'mdtraj/core/lib/center.h' 2024-05-17T11:42:29,399 adding 'mdtraj/core/lib/libtheobald.a' 2024-05-17T11:42:29,401 adding 'mdtraj/core/lib/theobald_rmsd.h' 2024-05-17T11:42:29,403 adding 'mdtraj/formats/__init__.py' 2024-05-17T11:42:29,406 adding 'mdtraj/formats/amberrst.py' 2024-05-17T11:42:29,408 adding 'mdtraj/formats/arc.py' 2024-05-17T11:42:29,555 adding 'mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so' 2024-05-17T11:42:29,990 adding 'mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so' 2024-05-17T11:42:30,005 adding 'mdtraj/formats/gro.py' 2024-05-17T11:42:30,007 adding 'mdtraj/formats/gsd.py' 2024-05-17T11:42:30,011 adding 'mdtraj/formats/hdf5.py' 2024-05-17T11:42:30,013 adding 'mdtraj/formats/hoomdxml.py' 2024-05-17T11:42:30,016 adding 'mdtraj/formats/lammpstrj.py' 2024-05-17T11:42:30,019 adding 'mdtraj/formats/lh5.py' 2024-05-17T11:42:30,021 adding 'mdtraj/formats/mdcrd.py' 2024-05-17T11:42:30,023 adding 'mdtraj/formats/mol2.py' 2024-05-17T11:42:30,026 adding 'mdtraj/formats/netcdf.py' 2024-05-17T11:42:30,028 adding 'mdtraj/formats/openmmxml.py' 2024-05-17T11:42:30,030 adding 'mdtraj/formats/pdbx.py' 2024-05-17T11:42:30,032 adding 'mdtraj/formats/prmtop.py' 2024-05-17T11:42:30,034 adding 'mdtraj/formats/psf.py' 2024-05-17T11:42:30,035 adding 'mdtraj/formats/registry.py' 2024-05-17T11:42:30,299 adding 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2024-05-17T11:42:31,968 adding 'mdtraj/reporters/__init__.py' 2024-05-17T11:42:31,970 adding 'mdtraj/reporters/basereporter.py' 2024-05-17T11:42:31,971 adding 'mdtraj/reporters/dcdreporter.py' 2024-05-17T11:42:31,973 adding 'mdtraj/reporters/hdf5reporter.py' 2024-05-17T11:42:31,974 adding 'mdtraj/reporters/netcdfreporter.py' 2024-05-17T11:42:31,976 adding 'mdtraj/reporters/xtcreporter.py' 2024-05-17T11:42:31,978 adding 'mdtraj/scripts/__init__.py' 2024-05-17T11:42:31,980 adding 'mdtraj/scripts/mdconvert.py' 2024-05-17T11:42:31,982 adding 'mdtraj/scripts/mdinspect.py' 2024-05-17T11:42:31,984 adding 'mdtraj/testing/__init__.py' 2024-05-17T11:42:31,986 adding 'mdtraj/testing/docscrape.py' 2024-05-17T11:42:31,988 adding 'mdtraj/testing/docstrings.py' 2024-05-17T11:42:31,990 adding 'mdtraj/testing/testing.py' 2024-05-17T11:42:31,992 adding 'mdtraj/utils/__init__.py' 2024-05-17T11:42:31,993 adding 'mdtraj/utils/contextmanagers.py' 2024-05-17T11:42:31,995 adding 'mdtraj/utils/delay_import.py' 2024-05-17T11:42:31,996 adding 'mdtraj/utils/rotation.py' 2024-05-17T11:42:31,998 adding 'mdtraj/utils/singleton.py' 2024-05-17T11:42:31,999 adding 'mdtraj/utils/unitcell.py' 2024-05-17T11:42:32,001 adding 'mdtraj/utils/validation.py' 2024-05-17T11:42:32,002 adding 'mdtraj/utils/zipped.py' 2024-05-17T11:42:32,005 adding 'mdtraj/utils/unit/__init__.py' 2024-05-17T11:42:32,006 adding 'mdtraj/utils/unit/basedimension.py' 2024-05-17T11:42:32,008 adding 'mdtraj/utils/unit/baseunit.py' 2024-05-17T11:42:32,010 adding 'mdtraj/utils/unit/constants.py' 2024-05-17T11:42:32,013 adding 'mdtraj/utils/unit/doctests.py' 2024-05-17T11:42:32,015 adding 'mdtraj/utils/unit/mymatrix.py' 2024-05-17T11:42:32,017 adding 'mdtraj/utils/unit/prefix.py' 2024-05-17T11:42:32,021 adding 'mdtraj/utils/unit/quantity.py' 2024-05-17T11:42:32,023 adding 'mdtraj/utils/unit/standard_dimensions.py' 2024-05-17T11:42:32,026 adding 'mdtraj/utils/unit/unit.py' 2024-05-17T11:42:32,029 adding 'mdtraj/utils/unit/unit_definitions.py' 2024-05-17T11:42:32,031 adding 'mdtraj/utils/unit/unit_math.py' 2024-05-17T11:42:32,032 adding 'mdtraj/utils/unit/unit_operators.py' 2024-05-17T11:42:32,037 adding 'mdtraj-1.10.0rc1.dist-info/LICENSE' 2024-05-17T11:42:32,039 adding 'mdtraj-1.10.0rc1.dist-info/METADATA' 2024-05-17T11:42:32,040 adding 'mdtraj-1.10.0rc1.dist-info/WHEEL' 2024-05-17T11:42:32,040 adding 'mdtraj-1.10.0rc1.dist-info/entry_points.txt' 2024-05-17T11:42:32,041 adding 'mdtraj-1.10.0rc1.dist-info/top_level.txt' 2024-05-17T11:42:32,043 adding 'mdtraj-1.10.0rc1.dist-info/RECORD' 2024-05-17T11:42:32,122 removing build/bdist.linux-armv7l/wheel 2024-05-17T11:42:32,970 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2024-05-17T11:42:33,107 Created wheel for mdtraj: filename=mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl size=6326304 sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b 2024-05-17T11:42:33,108 Stored in directory: /tmp/pip-ephem-wheel-cache-getms8hi/wheels/85/85/9f/1f23e5cba7cf642da3a68279da7c8301358b5a8ce6c3f9256f 2024-05-17T11:42:33,124 Successfully built mdtraj 2024-05-17T11:42:33,280 Removed build tracker: '/tmp/pip-build-tracker-9u67k3tg'