2024-05-29T14:28:55,975 Created temporary directory: /tmp/pip-build-tracker-ug8y858_ 2024-05-29T14:28:55,976 Initialized build tracking at /tmp/pip-build-tracker-ug8y858_ 2024-05-29T14:28:55,977 Created build tracker: /tmp/pip-build-tracker-ug8y858_ 2024-05-29T14:28:55,977 Entered build tracker: /tmp/pip-build-tracker-ug8y858_ 2024-05-29T14:28:55,978 Created temporary directory: /tmp/pip-wheel-e9h4t3na 2024-05-29T14:28:55,981 Created temporary directory: /tmp/pip-ephem-wheel-cache-disgi1of 2024-05-29T14:28:56,003 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-29T14:28:56,007 2 location(s) to search for versions of mdtraj: 2024-05-29T14:28:56,007 * https://pypi.org/simple/mdtraj/ 2024-05-29T14:28:56,007 * https://www.piwheels.org/simple/mdtraj/ 2024-05-29T14:28:56,008 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2024-05-29T14:28:56,008 Getting page https://pypi.org/simple/mdtraj/ 2024-05-29T14:28:56,010 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/) 2024-05-29T14:28:56,293 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/) 2024-05-29T14:28:56,293 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 2024-05-29T14:28:56,294 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/) 2024-05-29T14:28:56,294 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/) 2024-05-29T14:28:56,295 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/) 2024-05-29T14:28:56,295 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/) 2024-05-29T14:28:56,296 Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz (from 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https://pypi.org/simple/mdtraj/) 2024-05-29T14:28:56,299 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 2024-05-29T14:28:56,300 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 2024-05-29T14:28:56,301 Found link https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.10.0rc2 2024-05-29T14:28:56,301 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2024-05-29T14:28:56,302 Getting page https://www.piwheels.org/simple/mdtraj/ 2024-05-29T14:28:56,303 Found index url https://www.piwheels.org/simple/ 2024-05-29T14:28:56,508 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2024-05-29T14:28:56,513 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp37-cp37m-linux_armv6l.whl#sha256=355ab9108c6d079032d3b97eaa3ad76e261893dcd45a07b62c5e8a493600e06d (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T14:28:56,514 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp37-cp37m-linux_armv7l.whl#sha256=355ab9108c6d079032d3b97eaa3ad76e261893dcd45a07b62c5e8a493600e06d (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T14:28:56,514 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv6l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T14:28:56,515 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T14:28:56,515 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv6l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T14:28:56,516 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T14:28:56,516 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/) 2024-05-29T14:28:56,517 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/) 2024-05-29T14:28:56,517 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/) 2024-05-29T14:28:56,518 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/) 2024-05-29T14:28:56,519 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/) 2024-05-29T14:28:56,519 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/) 2024-05-29T14:28:56,520 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/) 2024-05-29T14:28:56,520 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/) 2024-05-29T14:28:56,521 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/) 2024-05-29T14:28:56,521 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/) 2024-05-29T14:28:56,522 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2024-05-29T14:28:56,522 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2024-05-29T14:28:56,549 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2024-05-29T14:28:56,569 Collecting mdtraj==1.10.0rc2 2024-05-29T14:28:56,571 Created temporary directory: /tmp/pip-unpack-tqa_8qwe 2024-05-29T14:28:56,871 Downloading mdtraj-1.10.0rc2.tar.gz (1.8 MB) 2024-05-29T14:28:58,075 Added mdtraj==1.10.0rc2 from https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz to build tracker '/tmp/pip-build-tracker-ug8y858_' 2024-05-29T14:28:58,082 Created temporary directory: /tmp/pip-build-env-4f1s3ke4 2024-05-29T14:28:58,087 Installing build dependencies: started 2024-05-29T14:28:58,088 Running command pip subprocess to install build dependencies 2024-05-29T14:28:59,332 Using pip 24.0 from /home/piwheels/.local/lib/python3.11/site-packages/pip (python 3.11) 2024-05-29T14:28:59,928 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-29T14:29:01,486 Collecting setuptools 2024-05-29T14:29:01,567 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.0.0-py3-none-any.whl (863 kB) 2024-05-29T14:29:01,795 Collecting wheel 2024-05-29T14:29:01,812 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-05-29T14:29:02,460 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) 2024-05-29T14:29:02,463 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) 2024-05-29T14:29:02,466 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) 2024-05-29T14:29:02,469 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) 2024-05-29T14:29:02,473 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) 2024-05-29T14:29:02,789 Collecting numpy<2 2024-05-29T14:29:02,821 Using cached https://www.piwheels.org/simple/numpy/numpy-1.26.4-cp311-cp311-linux_armv7l.whl (5.6 MB) 2024-05-29T14:29:03,135 Collecting oldest-supported-numpy 2024-05-29T14:29:03,154 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2023.12.21-py3-none-any.whl (4.9 kB) 2024-05-29T14:29:04,486 Collecting Cython~=0.29.36 2024-05-29T14:29:04,523 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.37-cp311-cp311-linux_armv7l.whl (5.0 MB) 2024-05-29T14:29:05,174 Collecting numpy<2 2024-05-29T14:29:08,400 Using cached https://www.piwheels.org/simple/numpy/numpy-1.23.2-cp311-cp311-linux_armv7l.whl (12.4 MB) 2024-05-29T14:29:12,567 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2024-05-29T14:29:12,800 Creating /tmp/pip-build-env-4f1s3ke4/overlay/local/bin 2024-05-29T14:29:12,802 changing mode of /tmp/pip-build-env-4f1s3ke4/overlay/local/bin/wheel to 755 2024-05-29T14:29:24,368 changing mode of /tmp/pip-build-env-4f1s3ke4/overlay/local/bin/f2py to 755 2024-05-29T14:29:24,370 changing mode of /tmp/pip-build-env-4f1s3ke4/overlay/local/bin/f2py3 to 755 2024-05-29T14:29:24,373 changing mode of /tmp/pip-build-env-4f1s3ke4/overlay/local/bin/f2py3.11 to 755 2024-05-29T14:29:27,460 changing mode of /tmp/pip-build-env-4f1s3ke4/overlay/local/bin/cygdb to 755 2024-05-29T14:29:27,462 changing mode of /tmp/pip-build-env-4f1s3ke4/overlay/local/bin/cython to 755 2024-05-29T14:29:27,464 changing mode of /tmp/pip-build-env-4f1s3ke4/overlay/local/bin/cythonize to 755 2024-05-29T14:29:27,529 Successfully installed Cython-0.29.37 numpy-1.23.2 oldest-supported-numpy-2023.12.21 setuptools-70.0.0 wheel-0.43.0 2024-05-29T14:29:28,242 Installing build dependencies: finished with status 'done' 2024-05-29T14:29:28,255 Getting requirements to build wheel: started 2024-05-29T14:29:28,257 Running command Getting requirements to build wheel 2024-05-29T14:29:28,992 Using built-in specs. 2024-05-29T14:29:28,993 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-29T14:29:28,993 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-29T14:29:28,994 Target: arm-linux-gnueabihf 2024-05-29T14:29:28,994 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 2024-05-29T14:29:28,995 Thread model: posix 2024-05-29T14:29:28,995 Supported LTO compression algorithms: zlib zstd 2024-05-29T14:29:28,996 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-29T14:29:33,975 C compiler: 2024-05-29T14:29:33,976 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-29T14:29:33,977 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-29T14:29:33,977 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-29T14:29:33,978 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-29T14:29:33,978 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-29T14:29:33,979 running egg_info 2024-05-29T14:29:33,982 writing mdtraj.egg-info/PKG-INFO 2024-05-29T14:29:33,985 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-29T14:29:33,987 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-29T14:29:33,988 writing requirements to mdtraj.egg-info/requires.txt 2024-05-29T14:29:33,990 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-29T14:29:34,590 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-29T14:29:34,638 reading manifest template 'MANIFEST.in' 2024-05-29T14:29:35,647 no previously-included directories found matching '__pycache__' 2024-05-29T14:29:35,648 no previously-included directories found matching '*.pyc' 2024-05-29T14:29:35,649 adding license file 'LICENSE' 2024-05-29T14:29:35,661 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-29T14:29:35,760 Getting requirements to build wheel: finished with status 'done' 2024-05-29T14:29:35,771 Created temporary directory: /tmp/pip-modern-metadata-cric0fbh 2024-05-29T14:29:35,774 Preparing metadata (pyproject.toml): started 2024-05-29T14:29:35,775 Running command Preparing metadata (pyproject.toml) 2024-05-29T14:29:36,448 Using built-in specs. 2024-05-29T14:29:36,448 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-29T14:29:36,449 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-29T14:29:36,449 Target: arm-linux-gnueabihf 2024-05-29T14:29:36,450 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 2024-05-29T14:29:36,450 Thread model: posix 2024-05-29T14:29:36,451 Supported LTO compression algorithms: zlib zstd 2024-05-29T14:29:36,451 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-29T14:29:40,636 /tmp/pip-wheel-e9h4t3na/mdtraj_deeee3f7d65b48b090dba709cb2215c1/basesetup.py:518: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-cric0fbh --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2024-05-29T14:29:40,636 warnings.warn( 2024-05-29T14:29:42,670 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. 2024-05-29T14:29:42,670 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. 2024-05-29T14:29:42,671 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. 2024-05-29T14:30:03,835 C compiler: 2024-05-29T14:30:03,837 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-29T14:30:03,837 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-29T14:30:03,838 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-29T14:30:03,839 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-29T14:30:03,839 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-29T14:30:03,840 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-29T14:30:03,841 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-29T14:30:03,841 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-29T14:30:03,842 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-29T14:30:03,843 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-29T14:30:03,843 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-29T14:30:03,844 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-29T14:30:03,845 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-29T14:30:03,846 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-29T14:30:03,847 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-29T14:30:03,931 running dist_info 2024-05-29T14:30:03,938 creating /tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info 2024-05-29T14:30:03,945 writing /tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info/PKG-INFO 2024-05-29T14:30:03,949 writing dependency_links to /tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info/dependency_links.txt 2024-05-29T14:30:03,951 writing entry points to /tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info/entry_points.txt 2024-05-29T14:30:03,952 writing requirements to /tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info/requires.txt 2024-05-29T14:30:03,953 writing top-level names to /tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info/top_level.txt 2024-05-29T14:30:03,955 writing manifest file '/tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info/SOURCES.txt' 2024-05-29T14:30:04,002 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,003 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,004 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,004 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,005 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,005 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,006 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,006 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,007 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,007 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,008 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,009 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,009 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,010 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,010 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,011 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,011 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,012 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,013 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,013 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,013 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,014 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,014 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,014 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,015 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,015 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,016 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,016 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,017 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,017 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:04,024 reading manifest file '/tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info/SOURCES.txt' 2024-05-29T14:30:04,026 reading manifest template 'MANIFEST.in' 2024-05-29T14:30:04,676 no previously-included directories found matching '__pycache__' 2024-05-29T14:30:04,678 no previously-included directories found matching '*.pyc' 2024-05-29T14:30:04,678 adding license file 'LICENSE' 2024-05-29T14:30:04,692 writing manifest file '/tmp/pip-modern-metadata-cric0fbh/mdtraj.egg-info/SOURCES.txt' 2024-05-29T14:30:04,693 creating '/tmp/pip-modern-metadata-cric0fbh/mdtraj-1.10.0rc2.dist-info' 2024-05-29T14:30:05,602 Preparing metadata (pyproject.toml): finished with status 'done' 2024-05-29T14:30:05,607 Source in /tmp/pip-wheel-e9h4t3na/mdtraj_deeee3f7d65b48b090dba709cb2215c1 has version 1.10.0rc2, which satisfies requirement mdtraj==1.10.0rc2 from https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz 2024-05-29T14:30:05,608 Removed mdtraj==1.10.0rc2 from https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz from build tracker '/tmp/pip-build-tracker-ug8y858_' 2024-05-29T14:30:05,612 Created temporary directory: /tmp/pip-unpack-hm1dmqzo 2024-05-29T14:30:05,613 Created temporary directory: /tmp/pip-unpack-bnc7d420 2024-05-29T14:30:05,622 Building wheels for collected packages: mdtraj 2024-05-29T14:30:05,627 Created temporary directory: /tmp/pip-wheel-n38wapug 2024-05-29T14:30:05,627 Destination directory: /tmp/pip-wheel-n38wapug 2024-05-29T14:30:05,629 Building wheel for mdtraj (pyproject.toml): started 2024-05-29T14:30:05,631 Running command Building wheel for mdtraj (pyproject.toml) 2024-05-29T14:30:06,350 Using built-in specs. 2024-05-29T14:30:06,351 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-29T14:30:06,351 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-29T14:30:06,352 Target: arm-linux-gnueabihf 2024-05-29T14:30:06,352 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 2024-05-29T14:30:06,353 Thread model: posix 2024-05-29T14:30:06,353 Supported LTO compression algorithms: zlib zstd 2024-05-29T14:30:06,354 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-29T14:30:12,136 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. 2024-05-29T14:30:12,137 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. 2024-05-29T14:30:12,138 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. 2024-05-29T14:30:33,274 C compiler: 2024-05-29T14:30:33,275 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-29T14:30:33,275 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-29T14:30:33,276 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-29T14:30:33,277 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-29T14:30:33,277 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-29T14:30:33,278 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-29T14:30:33,279 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-29T14:30:33,279 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-29T14:30:33,280 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-29T14:30:33,281 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-29T14:30:33,281 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-29T14:30:33,282 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-29T14:30:33,283 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-29T14:30:33,283 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-29T14:30:33,284 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-29T14:30:33,395 running bdist_wheel 2024-05-29T14:30:33,432 running build 2024-05-29T14:30:33,433 running build_py 2024-05-29T14:30:33,443 creating build 2024-05-29T14:30:33,444 creating build/lib.linux-armv7l-cpython-311 2024-05-29T14:30:33,445 creating build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-29T14:30:33,447 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-29T14:30:33,449 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-29T14:30:33,451 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-29T14:30:33,454 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,456 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,458 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,461 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,463 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,465 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,468 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,470 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,473 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-29T14:30:33,476 creating build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,478 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,480 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,483 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,486 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,488 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,491 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,493 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,496 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,498 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,501 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,503 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,506 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,508 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,510 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,513 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:30:33,517 creating build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-29T14:30:33,518 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-29T14:30:33,522 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-29T14:30:33,525 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-29T14:30:33,528 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-29T14:30:33,529 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-29T14:30:33,534 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-29T14:30:33,537 creating build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-29T14:30:33,538 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-29T14:30:33,540 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-29T14:30:33,542 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-29T14:30:33,546 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,547 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,550 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,553 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,555 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,558 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,561 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,564 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,567 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,570 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,573 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,575 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,578 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,581 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,584 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,588 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,590 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,594 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,597 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,600 creating build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-29T14:30:33,602 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-29T14:30:33,605 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-29T14:30:33,608 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-29T14:30:33,611 creating build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-29T14:30:33,612 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-29T14:30:33,615 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-29T14:30:33,618 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-29T14:30:33,621 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-29T14:30:33,624 creating build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-29T14:30:33,626 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-29T14:30:33,628 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-29T14:30:33,631 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-29T14:30:33,634 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-29T14:30:33,636 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-29T14:30:33,638 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-29T14:30:33,642 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,643 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,646 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,649 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,651 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,654 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,657 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,659 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,661 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,663 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,666 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,668 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,670 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,673 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-29T14:30:33,675 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-29T14:30:33,676 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-29T14:30:33,678 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-29T14:30:33,681 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-29T14:30:33,689 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-29T14:30:33,690 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-29T14:30:33,693 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-29T14:30:33,701 running build_ext 2024-05-29T14:30:33,704 building 'mdtraj.formats.xtc' extension 2024-05-29T14:30:33,705 creating build/temp.linux-armv7l-cpython-311 2024-05-29T14:30:33,705 creating build/temp.linux-armv7l-cpython-311/mdtraj 2024-05-29T14:30:33,706 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats 2024-05-29T14:30:33,707 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc 2024-05-29T14:30:33,708 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src 2024-05-29T14:30:33,709 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-4f1s3ke4/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 2024-05-29T14:30:33,835 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-4f1s3ke4/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 2024-05-29T14:30:33,990 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-29T14:30:33,991 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:30:33,991 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-29T14:30:33,992 | ^~~~~~ 2024-05-29T14:30:33,992 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:30:33,993 785 | int smallidx, minidx, maxidx; 2024-05-29T14:30:33,994 | ^~~~~~ 2024-05-29T14:30:33,999 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-29T14:30:34,002 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:30:34,004 1016 | int errval=1; 2024-05-29T14:30:34,006 | ^~~~~~ 2024-05-29T14:30:34,008 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-29T14:30:34,010 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:30:34,012 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-29T14:30:34,013 | ^~~~~~ 2024-05-29T14:30:34,015 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:30:34,017 1302 | int smallidx, minidx, maxidx; 2024-05-29T14:30:34,019 | ^~~~~~ 2024-05-29T14:30:34,026 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-29T14:30:34,028 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:30:34,030 1509 | int errval=1; 2024-05-29T14:30:34,032 | ^~~~~~ 2024-05-29T14:30:36,638 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-4f1s3ke4/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 2024-05-29T14:30:36,717 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2024-05-29T14:30:36,718 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 2024-05-29T14:30:36,718 66 | int i,j,result; 2024-05-29T14:30:36,719 | ^ 2024-05-29T14:30:36,720 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 2024-05-29T14:30:36,721 66 | int i,j,result; 2024-05-29T14:30:36,721 | ^ 2024-05-29T14:30:36,722 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2024-05-29T14:30:36,723 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2024-05-29T14:30:36,723 119 | if (NULL == xd) 2024-05-29T14:30:36,724 | ^~ 2024-05-29T14:30:36,725 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’ 2024-05-29T14:30:36,726 122 | do { 2024-05-29T14:30:36,726 | ^~ 2024-05-29T14:30:36,862 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:30:37,288 In file included from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-29T14:30:37,288 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T14:30:37,289 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-29T14:30:37,289 from mdtraj/formats/xtc/xtc.c:784: 2024-05-29T14:30:37,290 /tmp/pip-build-env-4f1s3ke4/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] 2024-05-29T14:30:37,290 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T14:30:37,291 | ^~~~~~~ 2024-05-29T14:30:45,737 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2024-05-29T14:30:45,740 mdtraj/formats/xtc/xtc.c:696:40: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:45,741 696 | #define PyInt_FromLong PyLong_FromLong 2024-05-29T14:30:45,743 | ^~~~~~~~~~~~~~~ 2024-05-29T14:30:45,749 mdtraj/formats/xtc/xtc.c:9563:7: note: ‘__pyx_v_status’ was declared here 2024-05-29T14:30:45,750 9563 | int __pyx_v_status; 2024-05-29T14:30:45,750 | ^~~~~~~~~~~~~~ 2024-05-29T14:30:56,645 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2024-05-29T14:30:56,653 mdtraj/formats/xtc/xtc.c:8082:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,654 8082 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-29T14:30:56,654 | ^ 2024-05-29T14:30:56,661 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 2024-05-29T14:30:56,663 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-29T14:30:56,666 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,669 mdtraj/formats/xtc/xtc.c:8078:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,671 8078 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-29T14:30:56,673 | ^ 2024-05-29T14:30:56,677 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 2024-05-29T14:30:56,678 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-29T14:30:56,678 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,686 mdtraj/formats/xtc/xtc.c:8074:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,686 8074 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T14:30:56,687 | ^ 2024-05-29T14:30:56,693 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 2024-05-29T14:30:56,694 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-29T14:30:56,694 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,702 mdtraj/formats/xtc/xtc.c:8034:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,702 8034 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T14:30:56,703 | ^ 2024-05-29T14:30:56,709 mdtraj/formats/xtc/xtc.c:6481:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 2024-05-29T14:30:56,709 6481 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; 2024-05-29T14:30:56,710 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,717 mdtraj/formats/xtc/xtc.c:8016:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,718 8016 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T14:30:56,718 | ^ 2024-05-29T14:30:56,725 mdtraj/formats/xtc/xtc.c:6477:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 2024-05-29T14:30:56,725 6477 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; 2024-05-29T14:30:56,726 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,733 mdtraj/formats/xtc/xtc.c:8092:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,734 8092 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T14:30:56,734 | ^ 2024-05-29T14:30:56,741 mdtraj/formats/xtc/xtc.c:6473:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 2024-05-29T14:30:56,741 6473 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; 2024-05-29T14:30:56,742 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,749 mdtraj/formats/xtc/xtc.c:8054:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,750 8054 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-29T14:30:56,750 | ^ 2024-05-29T14:30:56,756 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 2024-05-29T14:30:56,757 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-29T14:30:56,758 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,765 mdtraj/formats/xtc/xtc.c:8050:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,765 8050 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-29T14:30:56,766 | ^ 2024-05-29T14:30:56,772 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 2024-05-29T14:30:56,773 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-29T14:30:56,773 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,781 mdtraj/formats/xtc/xtc.c:8046:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,781 8046 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T14:30:56,782 | ^ 2024-05-29T14:30:56,788 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 2024-05-29T14:30:56,788 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-29T14:30:56,789 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,796 mdtraj/formats/xtc/xtc.c:7669:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,796 7669 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-29T14:30:56,797 | ^ 2024-05-29T14:30:56,803 mdtraj/formats/xtc/xtc.c:6469:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 2024-05-29T14:30:56,804 6469 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2024-05-29T14:30:56,804 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:30:56,811 mdtraj/formats/xtc/xtc.c:7665:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:30:56,812 7665 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T14:30:56,813 | ^ 2024-05-29T14:30:56,819 mdtraj/formats/xtc/xtc.c:6469:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 2024-05-29T14:30:56,819 6469 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2024-05-29T14:30:56,820 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:01,568 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 2024-05-29T14:31:01,725 building 'mdtraj.formats.trr' extension 2024-05-29T14:31:01,727 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-4f1s3ke4/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 2024-05-29T14:31:01,841 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-4f1s3ke4/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 2024-05-29T14:31:01,992 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-29T14:31:01,993 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:31:01,993 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-29T14:31:01,994 | ^~~~~~ 2024-05-29T14:31:01,994 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:31:01,995 785 | int smallidx, minidx, maxidx; 2024-05-29T14:31:01,996 | ^~~~~~ 2024-05-29T14:31:02,002 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-29T14:31:02,002 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:31:02,003 1016 | int errval=1; 2024-05-29T14:31:02,003 | ^~~~~~ 2024-05-29T14:31:02,008 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-29T14:31:02,009 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:31:02,009 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-29T14:31:02,010 | ^~~~~~ 2024-05-29T14:31:02,010 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:31:02,011 1302 | int smallidx, minidx, maxidx; 2024-05-29T14:31:02,011 | ^~~~~~ 2024-05-29T14:31:02,020 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-29T14:31:02,021 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-29T14:31:02,022 1509 | int errval=1; 2024-05-29T14:31:02,022 | ^~~~~~ 2024-05-29T14:31:04,601 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-4f1s3ke4/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 2024-05-29T14:31:05,407 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-4f1s3ke4/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 2024-05-29T14:31:05,811 In file included from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-29T14:31:05,811 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T14:31:05,812 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-29T14:31:05,813 from mdtraj/formats/xtc/trr.c:784: 2024-05-29T14:31:05,813 /tmp/pip-build-env-4f1s3ke4/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] 2024-05-29T14:31:05,814 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T14:31:05,814 | ^~~~~~~ 2024-05-29T14:31:15,033 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2024-05-29T14:31:15,034 mdtraj/formats/xtc/trr.c:696:40: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:15,035 696 | #define PyInt_FromLong PyLong_FromLong 2024-05-29T14:31:15,035 | ^~~~~~~~~~~~~~~ 2024-05-29T14:31:15,045 mdtraj/formats/xtc/trr.c:11089:7: note: ‘__pyx_v_status’ was declared here 2024-05-29T14:31:15,046 11089 | int __pyx_v_status; 2024-05-29T14:31:15,047 | ^~~~~~~~~~~~~~ 2024-05-29T14:31:26,288 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2024-05-29T14:31:26,296 mdtraj/formats/xtc/trr.c:8442:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,297 8442 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-29T14:31:26,298 | ^ 2024-05-29T14:31:26,303 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2024-05-29T14:31:26,303 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-29T14:31:26,304 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,311 mdtraj/formats/xtc/trr.c:8438:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,312 8438 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T14:31:26,312 | ^ 2024-05-29T14:31:26,318 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2024-05-29T14:31:26,318 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-29T14:31:26,319 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,320 mdtraj/formats/xtc/trr.c:1935:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,320 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-29T14:31:26,320 | ^ 2024-05-29T14:31:26,326 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-05-29T14:31:26,327 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-29T14:31:26,327 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,334 mdtraj/formats/xtc/trr.c:8432:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,335 8432 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-05-29T14:31:26,335 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-29T14:31:26,341 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2024-05-29T14:31:26,342 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-29T14:31:26,342 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,349 mdtraj/formats/xtc/trr.c:8385:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,350 8385 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-29T14:31:26,350 | ^ 2024-05-29T14:31:26,356 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2024-05-29T14:31:26,357 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-29T14:31:26,357 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,364 mdtraj/formats/xtc/trr.c:8381:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,364 8381 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T14:31:26,365 | ^ 2024-05-29T14:31:26,371 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2024-05-29T14:31:26,371 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-29T14:31:26,372 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,372 mdtraj/formats/xtc/trr.c:1935:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,373 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-29T14:31:26,374 | ^ 2024-05-29T14:31:26,379 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-05-29T14:31:26,380 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-29T14:31:26,380 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,387 mdtraj/formats/xtc/trr.c:8375:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,388 8375 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-05-29T14:31:26,388 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-29T14:31:26,394 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2024-05-29T14:31:26,395 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-29T14:31:26,395 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,402 mdtraj/formats/xtc/trr.c:8775:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,403 8775 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T14:31:26,403 | ^ 2024-05-29T14:31:26,409 mdtraj/formats/xtc/trr.c:7001:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2024-05-29T14:31:26,410 7001 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-05-29T14:31:26,410 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,417 mdtraj/formats/xtc/trr.c:8771:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,418 8771 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-29T14:31:26,418 | ^ 2024-05-29T14:31:26,424 mdtraj/formats/xtc/trr.c:7001:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2024-05-29T14:31:26,425 7001 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-05-29T14:31:26,425 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,432 mdtraj/formats/xtc/trr.c:8616:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,433 8616 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T14:31:26,433 | ^ 2024-05-29T14:31:26,439 mdtraj/formats/xtc/trr.c:6997:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2024-05-29T14:31:26,440 6997 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-05-29T14:31:26,440 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,447 mdtraj/formats/xtc/trr.c:8612:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,448 8612 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-29T14:31:26,448 | ^ 2024-05-29T14:31:26,454 mdtraj/formats/xtc/trr.c:6997:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2024-05-29T14:31:26,455 6997 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-05-29T14:31:26,455 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,462 mdtraj/formats/xtc/trr.c:8668:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,463 8668 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T14:31:26,463 | ^ 2024-05-29T14:31:26,469 mdtraj/formats/xtc/trr.c:6981:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2024-05-29T14:31:26,470 6981 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-05-29T14:31:26,470 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:26,477 mdtraj/formats/xtc/trr.c:8664:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:26,478 8664 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-29T14:31:26,478 | ^ 2024-05-29T14:31:26,484 mdtraj/formats/xtc/trr.c:6981:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2024-05-29T14:31:26,485 6981 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-05-29T14:31:26,485 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:31:33,137 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 2024-05-29T14:31:33,300 building 'mdtraj.formats.dcd' extension 2024-05-29T14:31:33,300 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd 2024-05-29T14:31:33,301 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src 2024-05-29T14:31:33,302 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-4f1s3ke4/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 2024-05-29T14:31:33,697 In file included from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-29T14:31:33,697 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T14:31:33,698 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-29T14:31:33,698 from mdtraj/formats/dcd/dcd.c:782: 2024-05-29T14:31:33,699 /tmp/pip-build-env-4f1s3ke4/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] 2024-05-29T14:31:33,699 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T14:31:33,700 | ^~~~~~~ 2024-05-29T14:31:42,799 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2024-05-29T14:31:42,800 mdtraj/formats/dcd/dcd.c:694:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:31:42,800 694 | #define PyInt_FromLong PyLong_FromLong 2024-05-29T14:31:42,801 | ^~~~~~~~~~~~~~~ 2024-05-29T14:31:42,805 mdtraj/formats/dcd/dcd.c:5458:7: note: ‘__pyx_v_i’ was declared here 2024-05-29T14:31:42,805 5458 | int __pyx_v_i; 2024-05-29T14:31:42,806 | ^~~~~~~~~ 2024-05-29T14:31:46,083 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-4f1s3ke4/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 2024-05-29T14:31:47,637 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 2024-05-29T14:31:47,767 building 'mdtraj.formats.dtr' extension 2024-05-29T14:31:47,768 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr 2024-05-29T14:31:47,769 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src 2024-05-29T14:31:47,770 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-4f1s3ke4/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 2024-05-29T14:31:48,148 In file included from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-29T14:31:48,149 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T14:31:48,149 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-29T14:31:48,150 from mdtraj/formats/dtr/dtr.cpp:803: 2024-05-29T14:31:48,150 /tmp/pip-build-env-4f1s3ke4/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] 2024-05-29T14:31:48,151 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T14:31:48,151 | ^~~~~~~ 2024-05-29T14:32:02,563 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-4f1s3ke4/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 2024-05-29T14:32:04,938 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2024-05-29T14:32:04,939 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=] 2024-05-29T14:32:04,940 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2024-05-29T14:32:04,940 | ~~^ ~ 2024-05-29T14:32:04,941 | | | 2024-05-29T14:32:04,942 | | size_t {aka unsigned int} 2024-05-29T14:32:04,942 | long int 2024-05-29T14:32:04,943 | %d 2024-05-29T14:32:04,944 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=] 2024-05-29T14:32:04,944 487 | printf("size %d framesize %d\n\n", 2024-05-29T14:32:04,946 | ~^ 2024-05-29T14:32:04,946 | | 2024-05-29T14:32:04,947 | int 2024-05-29T14:32:04,947 | %lld 2024-05-29T14:32:04,948 488 | keys[i].size(), m_framesize); 2024-05-29T14:32:04,948 | ~~~~~~~~~~~~~~ 2024-05-29T14:32:04,949 | | 2024-05-29T14:32:04,949 | uint64_t {aka long long unsigned int} 2024-05-29T14:32:04,950 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=] 2024-05-29T14:32:04,951 487 | printf("size %d framesize %d\n\n", 2024-05-29T14:32:04,951 | ~^ 2024-05-29T14:32:04,952 | | 2024-05-29T14:32:04,952 | int 2024-05-29T14:32:04,953 | %lld 2024-05-29T14:32:04,954 488 | keys[i].size(), m_framesize); 2024-05-29T14:32:04,954 | ~~~~~~~~~~~ 2024-05-29T14:32:04,955 | | 2024-05-29T14:32:04,956 | uint64_t {aka long long unsigned int} 2024-05-29T14:32:04,956 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=] 2024-05-29T14:32:04,957 494 | "non-constant time interval at frame %ld\n", i); 2024-05-29T14:32:04,957 | ~~^ ~ 2024-05-29T14:32:04,958 | | | 2024-05-29T14:32:04,959 | | size_t {aka unsigned int} 2024-05-29T14:32:04,959 | long int 2024-05-29T14:32:04,960 | %d 2024-05-29T14:32:04,961 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=] 2024-05-29T14:32:04,961 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2024-05-29T14:32:04,962 | ~~^ ~ 2024-05-29T14:32:04,963 | | | 2024-05-29T14:32:04,963 | | size_t {aka unsigned int} 2024-05-29T14:32:04,964 | long int 2024-05-29T14:32:04,965 | %d 2024-05-29T14:32:05,105 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-29T14:32:05,106 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=] 2024-05-29T14:32:05,107 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2024-05-29T14:32:05,108 | ~~^ 2024-05-29T14:32:05,108 | | 2024-05-29T14:32:05,109 | long int 2024-05-29T14:32:05,110 | %lld 2024-05-29T14:32:05,111 1302 | 3*natoms, pos.count); 2024-05-29T14:32:05,111 | ~~~~~~~~~ 2024-05-29T14:32:05,112 | | 2024-05-29T14:32:05,112 | uint64_t {aka long long unsigned int} 2024-05-29T14:32:05,113 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=] 2024-05-29T14:32:05,113 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2024-05-29T14:32:05,114 | ~~^ 2024-05-29T14:32:05,114 | | 2024-05-29T14:32:05,115 | long int 2024-05-29T14:32:05,115 | %lld 2024-05-29T14:32:05,116 1311 | 3*natoms, vel.count); 2024-05-29T14:32:05,117 | ~~~~~~~~~ 2024-05-29T14:32:05,117 | | 2024-05-29T14:32:05,118 | uint64_t {aka long long unsigned int} 2024-05-29T14:32:05,139 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-29T14:32:05,139 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=] 2024-05-29T14:32:05,140 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2024-05-29T14:32:05,141 | ~~^ 2024-05-29T14:32:05,141 | | 2024-05-29T14:32:05,142 | long int 2024-05-29T14:32:05,143 | %lld 2024-05-29T14:32:05,144 1573 | velblob.count, 3*natoms); 2024-05-29T14:32:05,144 | ~~~~~~~~~~~~~ 2024-05-29T14:32:05,145 | | 2024-05-29T14:32:05,146 | uint64_t {aka long long unsigned int} 2024-05-29T14:32:06,450 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2024-05-29T14:32:06,451 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2024-05-29T14:32:06,452 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2024-05-29T14:32:06,453 | ~~~~~~~~^~~~~ 2024-05-29T14:32:09,237 In file included from /usr/include/c++/12/map:60, 2024-05-29T14:32:09,237 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-29T14:32:09,238 /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> >]’: 2024-05-29T14:32:09,239 /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 2024-05-29T14:32:09,239 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-29T14:32:09,240 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:09,308 /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> >]’: 2024-05-29T14:32:09,309 /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 2024-05-29T14:32:09,309 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-29T14:32:09,310 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:09,369 In file included from /usr/include/c++/12/map:61: 2024-05-29T14:32:09,370 /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> >]’: 2024-05-29T14:32:09,370 /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 2024-05-29T14:32:09,371 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-29T14:32:09,372 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:09,372 531 | std::forward_as_tuple(std::move(__k)), 2024-05-29T14:32:09,373 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:09,373 532 | std::tuple<>()); 2024-05-29T14:32:09,374 | ~~~~~~~~~~~~~~~ 2024-05-29T14:32:09,463 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> >]’, 2024-05-29T14:32:09,464 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28: 2024-05-29T14:32:09,465 /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 2024-05-29T14:32:09,465 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-29T14:32:09,466 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:09,466 531 | std::forward_as_tuple(std::move(__k)), 2024-05-29T14:32:09,467 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:09,467 532 | std::tuple<>()); 2024-05-29T14:32:09,468 | ~~~~~~~~~~~~~~~ 2024-05-29T14:32:10,314 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2024-05-29T14:32:10,315 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=] 2024-05-29T14:32:10,316 706 | sprintf(sub, "%03x/", i); 2024-05-29T14:32:10,316 | ^~~~ 2024-05-29T14:32:10,317 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2024-05-29T14:32:10,317 706 | sprintf(sub, "%03x/", i); 2024-05-29T14:32:10,318 | ^~~~~~~ 2024-05-29T14:32:10,318 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2024-05-29T14:32:10,319 706 | sprintf(sub, "%03x/", i); 2024-05-29T14:32:10,320 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2024-05-29T14:32:10,321 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=] 2024-05-29T14:32:10,321 714 | sprintf(subsub, "%03x", j); 2024-05-29T14:32:10,322 | ^~~~ 2024-05-29T14:32:10,323 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2024-05-29T14:32:10,324 714 | sprintf(subsub, "%03x", j); 2024-05-29T14:32:10,324 | ^~~~~~ 2024-05-29T14:32:10,325 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2024-05-29T14:32:10,326 714 | sprintf(subsub, "%03x", j); 2024-05-29T14:32:10,327 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:10,723 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2024-05-29T14:32:10,723 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-29T14:32:10,724 667 | sprintf(answer, "%03x/", d1); 2024-05-29T14:32:10,725 | ^ 2024-05-29T14:32:10,725 In function ‘std::string DDreldir(const std::string&, int, int)’, 2024-05-29T14:32:10,726 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2024-05-29T14:32:10,727 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2024-05-29T14:32:10,728 667 | sprintf(answer, "%03x/", d1); 2024-05-29T14:32:10,728 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:10,729 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2024-05-29T14:32:10,730 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=] 2024-05-29T14:32:10,731 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-29T14:32:10,731 | ^~~~ 2024-05-29T14:32:10,732 In function ‘std::string DDreldir(const std::string&, int, int)’, 2024-05-29T14:32:10,732 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2024-05-29T14:32:10,733 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2024-05-29T14:32:10,733 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-29T14:32:10,734 | ^~~~~~~~~~~~ 2024-05-29T14:32:10,734 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2024-05-29T14:32:10,735 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-29T14:32:10,735 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:13,892 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> >]’, 2024-05-29T14:32:13,893 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: 2024-05-29T14:32:13,893 /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 2024-05-29T14:32:13,894 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-29T14:32:13,895 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:13,895 531 | std::forward_as_tuple(std::move(__k)), 2024-05-29T14:32:13,896 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T14:32:13,896 532 | std::tuple<>()); 2024-05-29T14:32:13,897 | ~~~~~~~~~~~~~~~ 2024-05-29T14:32:18,944 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 2024-05-29T14:32:19,311 building 'mdtraj._rmsd' extension 2024-05-29T14:32:19,312 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd 2024-05-29T14:32:19,313 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src 2024-05-29T14:32:19,314 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-4f1s3ke4/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 2024-05-29T14:32:59,960 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-4f1s3ke4/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 2024-05-29T14:33:00,167 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-4f1s3ke4/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 2024-05-29T14:33:00,429 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-4f1s3ke4/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 2024-05-29T14:33:01,217 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 2024-05-29T14:33:01,754 building 'mdtraj._lprmsd' extension 2024-05-29T14:33:01,755 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-4f1s3ke4/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 2024-05-29T14:33:02,026 In file included from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-29T14:33:02,027 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T14:33:02,028 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-29T14:33:02,028 from mdtraj/rmsd/_lprmsd.cpp:812: 2024-05-29T14:33:02,029 /tmp/pip-build-env-4f1s3ke4/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] 2024-05-29T14:33:02,029 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T14:33:02,030 | ^~~~~~~ 2024-05-29T14:33:26,166 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-4f1s3ke4/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 2024-05-29T14:33:29,003 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-4f1s3ke4/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 2024-05-29T14:33:29,207 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-4f1s3ke4/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 2024-05-29T14:33:30,478 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-4f1s3ke4/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 2024-05-29T14:33:30,783 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-4f1s3ke4/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 2024-05-29T14:33:31,043 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-4f1s3ke4/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 2024-05-29T14:33:31,826 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 2024-05-29T14:33:32,122 building 'mdtraj.core.lib.libtheobald' extension 2024-05-29T14:33:32,123 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-4f1s3ke4/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 2024-05-29T14:33:32,877 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-4f1s3ke4/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 2024-05-29T14:33:33,081 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 2024-05-29T14:33:33,111 building 'mdtraj.geometry._geometry' extension 2024-05-29T14:33:33,112 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-29T14:33:33,113 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src 2024-05-29T14:33:33,114 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-4f1s3ke4/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 2024-05-29T14:33:33,394 In file included from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-29T14:33:33,394 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T14:33:33,395 from /tmp/pip-build-env-4f1s3ke4/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-29T14:33:33,395 from mdtraj/geometry/src/_geometry.cpp:814: 2024-05-29T14:33:33,396 /tmp/pip-build-env-4f1s3ke4/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] 2024-05-29T14:33:33,397 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T14:33:33,397 | ^~~~~~~ 2024-05-29T14:34:07,649 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-4f1s3ke4/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 2024-05-29T14:34:21,944 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-4f1s3ke4/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 2024-05-29T14:34:25,961 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-4f1s3ke4/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 2024-05-29T14:34:27,107 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 2024-05-29T14:34:27,470 building 'mdtraj.geometry.drid' extension 2024-05-29T14:34:27,471 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-4f1s3ke4/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 2024-05-29T14:34:56,917 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-4f1s3ke4/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 2024-05-29T14:34:57,563 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:34:57,672 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 2024-05-29T14:34:57,973 building 'mdtraj.geometry.neighbors' extension 2024-05-29T14:34:57,974 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-4f1s3ke4/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 2024-05-29T14:35:25,470 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-4f1s3ke4/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 2024-05-29T14:35:26,775 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 2024-05-29T14:35:27,074 building 'mdtraj.geometry.neighborlist' extension 2024-05-29T14:35:27,075 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-4f1s3ke4/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 2024-05-29T14:35:51,916 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-4f1s3ke4/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 2024-05-29T14:35:56,385 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2024-05-29T14:35:56,386 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2024-05-29T14:35:56,386 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:35:56,387 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2024-05-29T14:35:56,387 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-29T14:35:56,388 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-29T14:35:56,389 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-29T14:35:56,390 341 | float periodicBoxVectors[3][3]; 2024-05-29T14:35:56,390 | ^~~~~~~~~~~~~~~~~~ 2024-05-29T14:35:56,391 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2024-05-29T14:35:56,391 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2024-05-29T14:35:56,392 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:35:56,393 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2024-05-29T14:35:56,394 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-29T14:35:56,394 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-29T14:35:56,395 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-29T14:35:56,396 341 | float periodicBoxVectors[3][3]; 2024-05-29T14:35:56,396 | ^~~~~~~~~~~~~~~~~~ 2024-05-29T14:35:56,397 mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:35:56,398 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); 2024-05-29T14:35:56,398 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-29T14:35:56,399 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-29T14:35:56,400 341 | float periodicBoxVectors[3][3]; 2024-05-29T14:35:56,400 | ^~~~~~~~~~~~~~~~~~ 2024-05-29T14:35:56,401 mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-29T14:35:56,402 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); 2024-05-29T14:35:56,402 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-29T14:35:56,403 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-29T14:35:56,404 341 | float periodicBoxVectors[3][3]; 2024-05-29T14:35:56,405 | ^~~~~~~~~~~~~~~~~~ 2024-05-29T14:35:57,255 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 2024-05-29T14:35:57,572 installing to build/bdist.linux-armv7l/wheel 2024-05-29T14:35:57,572 running install 2024-05-29T14:35:57,597 running install_lib 2024-05-29T14:35:57,606 creating build/bdist.linux-armv7l 2024-05-29T14:35:57,607 creating build/bdist.linux-armv7l/wheel 2024-05-29T14:35:57,608 creating build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T14:35:57,610 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,611 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,613 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,617 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,619 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,621 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,623 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,625 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,628 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,630 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,633 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,635 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,638 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,641 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,643 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,646 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,649 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,651 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,657 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,660 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T14:35:57,662 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,665 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,667 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T14:35:57,669 copying build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T14:35:57,701 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,702 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,759 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,791 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,822 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,825 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,827 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,830 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,833 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,836 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,838 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,841 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,870 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,872 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,874 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,876 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,879 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,881 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,883 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,886 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T14:35:57,889 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T14:35:57,890 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T14:35:57,895 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T14:35:57,897 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T14:35:57,900 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T14:35:57,902 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-29T14:35:57,904 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-29T14:35:57,906 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-29T14:35:57,908 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-29T14:35:57,911 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T14:35:57,916 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T14:35:57,919 copying build/lib.linux-armv7l-cpython-311/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T14:35:57,922 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-29T14:35:57,923 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-29T14:35:57,926 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-29T14:35:57,928 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-29T14:35:57,931 copying build/lib.linux-armv7l-cpython-311/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T14:35:57,934 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:57,935 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:57,939 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:57,972 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:57,974 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:57,977 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:57,979 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,030 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,033 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,036 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,039 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,042 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,045 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,047 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,050 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,053 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,056 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,086 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,089 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-29T14:35:58,091 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-29T14:35:58,091 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-29T14:35:58,094 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-29T14:35:58,097 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-29T14:35:58,098 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-29T14:35:58,101 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-29T14:35:58,104 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,106 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,123 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,125 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,127 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T14:35:58,130 copying build/lib.linux-armv7l-cpython-311/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T14:35:58,133 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-29T14:35:58,134 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-29T14:35:58,137 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-29T14:35:58,139 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-29T14:35:58,142 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T14:35:58,143 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T14:35:58,145 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T14:35:58,147 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T14:35:58,150 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T14:35:58,152 copying build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T14:35:58,217 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T14:35:58,218 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T14:35:58,220 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T14:35:58,223 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T14:35:58,226 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T14:35:58,228 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T14:35:58,230 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T14:35:58,233 running install_egg_info 2024-05-29T14:35:58,245 running egg_info 2024-05-29T14:35:58,251 writing mdtraj.egg-info/PKG-INFO 2024-05-29T14:35:58,254 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-29T14:35:58,256 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-29T14:35:58,257 writing requirements to mdtraj.egg-info/requires.txt 2024-05-29T14:35:58,258 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-29T14:35:58,296 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,297 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,297 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,298 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,298 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,299 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,299 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,300 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,300 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,301 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,301 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,302 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,302 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,303 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,303 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,304 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,305 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,305 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,306 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,306 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,307 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,307 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,307 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,308 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,308 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,309 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,309 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,310 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,310 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,311 dependency /tmp/pip-build-env-4f1s3ke4/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 2024-05-29T14:35:58,326 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-29T14:35:58,348 reading manifest template 'MANIFEST.in' 2024-05-29T14:35:59,073 no previously-included directories found matching '__pycache__' 2024-05-29T14:35:59,074 no previously-included directories found matching '*.pyc' 2024-05-29T14:35:59,075 adding license file 'LICENSE' 2024-05-29T14:35:59,088 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-29T14:35:59,090 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.10.0rc2-py3.11.egg-info 2024-05-29T14:35:59,103 running install_scripts 2024-05-29T14:35:59,159 creating build/bdist.linux-armv7l/wheel/mdtraj-1.10.0rc2.dist-info/WHEEL 2024-05-29T14:35:59,163 creating '/tmp/pip-wheel-n38wapug/.tmp-sxjb38pc/mdtraj-1.10.0rc2-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-29T14:35:59,166 adding 'mdtraj/__init__.py' 2024-05-29T14:35:59,402 adding 'mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:35:59,786 adding 'mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:35:59,800 adding 'mdtraj/io.py' 2024-05-29T14:35:59,801 adding 'mdtraj/version.py' 2024-05-29T14:35:59,803 adding 'mdtraj/core/__init__.py' 2024-05-29T14:35:59,806 adding 'mdtraj/core/element.py' 2024-05-29T14:35:59,809 adding 'mdtraj/core/residue_names.py' 2024-05-29T14:35:59,812 adding 'mdtraj/core/selection.py' 2024-05-29T14:35:59,820 adding 'mdtraj/core/topology.py' 2024-05-29T14:35:59,829 adding 'mdtraj/core/trajectory.py' 2024-05-29T14:35:59,832 adding 'mdtraj/core/lib/center.h' 2024-05-29T14:35:59,840 adding 'mdtraj/core/lib/libtheobald.a' 2024-05-29T14:35:59,842 adding 'mdtraj/core/lib/theobald_rmsd.h' 2024-05-29T14:35:59,844 adding 'mdtraj/formats/__init__.py' 2024-05-29T14:35:59,848 adding 'mdtraj/formats/amberrst.py' 2024-05-29T14:35:59,850 adding 'mdtraj/formats/arc.py' 2024-05-29T14:36:00,002 adding 'mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:36:00,419 adding 'mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:36:00,435 adding 'mdtraj/formats/gro.py' 2024-05-29T14:36:00,438 adding 'mdtraj/formats/gsd.py' 2024-05-29T14:36:00,443 adding 'mdtraj/formats/hdf5.py' 2024-05-29T14:36:00,445 adding 'mdtraj/formats/hoomdxml.py' 2024-05-29T14:36:00,448 adding 'mdtraj/formats/lammpstrj.py' 2024-05-29T14:36:00,451 adding 'mdtraj/formats/lh5.py' 2024-05-29T14:36:00,454 adding 'mdtraj/formats/mdcrd.py' 2024-05-29T14:36:00,456 adding 'mdtraj/formats/mol2.py' 2024-05-29T14:36:00,460 adding 'mdtraj/formats/netcdf.py' 2024-05-29T14:36:00,462 adding 'mdtraj/formats/openmmxml.py' 2024-05-29T14:36:00,464 adding 'mdtraj/formats/pdbx.py' 2024-05-29T14:36:00,466 adding 'mdtraj/formats/prmtop.py' 2024-05-29T14:36:00,469 adding 'mdtraj/formats/psf.py' 2024-05-29T14:36:00,470 adding 'mdtraj/formats/registry.py' 2024-05-29T14:36:00,744 adding 'mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:36:01,014 adding 'mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:36:01,023 adding 'mdtraj/formats/xyzfile.py' 2024-05-29T14:36:01,025 adding 'mdtraj/formats/pdb/__init__.py' 2024-05-29T14:36:01,030 adding 'mdtraj/formats/pdb/pdbfile.py' 2024-05-29T14:36:01,035 adding 'mdtraj/formats/pdb/pdbstructure.py' 2024-05-29T14:36:01,038 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2024-05-29T14:36:01,040 adding 'mdtraj/formats/pdb/data/residues.xml' 2024-05-29T14:36:01,042 adding 'mdtraj/geometry/__init__.py' 2024-05-29T14:36:01,538 adding 'mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:36:01,556 adding 'mdtraj/geometry/alignment.py' 2024-05-29T14:36:01,558 adding 'mdtraj/geometry/angle.py' 2024-05-29T14:36:01,561 adding 'mdtraj/geometry/contact.py' 2024-05-29T14:36:01,563 adding 'mdtraj/geometry/dihedral.py' 2024-05-29T14:36:01,566 adding 'mdtraj/geometry/distance.py' 2024-05-29T14:36:01,853 adding 'mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:36:01,862 adding 'mdtraj/geometry/dssp.py' 2024-05-29T14:36:01,865 adding 'mdtraj/geometry/hbond.py' 2024-05-29T14:36:01,868 adding 'mdtraj/geometry/internal.py' 2024-05-29T14:36:02,164 adding 'mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:36:02,445 adding 'mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so' 2024-05-29T14:36:02,455 adding 'mdtraj/geometry/order.py' 2024-05-29T14:36:02,457 adding 'mdtraj/geometry/rdf.py' 2024-05-29T14:36:02,459 adding 'mdtraj/geometry/rg.py' 2024-05-29T14:36:02,461 adding 'mdtraj/geometry/sasa.py' 2024-05-29T14:36:02,463 adding 'mdtraj/geometry/shape.py' 2024-05-29T14:36:02,465 adding 'mdtraj/geometry/thermodynamic_properties.py' 2024-05-29T14:36:02,467 adding 'mdtraj/nmr/__init__.py' 2024-05-29T14:36:02,468 adding 'mdtraj/nmr/scalar_couplings.py' 2024-05-29T14:36:02,471 adding 'mdtraj/nmr/shift_wrappers.py' 2024-05-29T14:36:02,473 adding 'mdtraj/reporters/__init__.py' 2024-05-29T14:36:02,475 adding 'mdtraj/reporters/basereporter.py' 2024-05-29T14:36:02,477 adding 'mdtraj/reporters/dcdreporter.py' 2024-05-29T14:36:02,479 adding 'mdtraj/reporters/hdf5reporter.py' 2024-05-29T14:36:02,480 adding 'mdtraj/reporters/netcdfreporter.py' 2024-05-29T14:36:02,482 adding 'mdtraj/reporters/xtcreporter.py' 2024-05-29T14:36:02,484 adding 'mdtraj/scripts/__init__.py' 2024-05-29T14:36:02,487 adding 'mdtraj/scripts/mdconvert.py' 2024-05-29T14:36:02,489 adding 'mdtraj/scripts/mdinspect.py' 2024-05-29T14:36:02,491 adding 'mdtraj/testing/__init__.py' 2024-05-29T14:36:02,494 adding 'mdtraj/testing/docscrape.py' 2024-05-29T14:36:02,496 adding 'mdtraj/testing/docstrings.py' 2024-05-29T14:36:02,498 adding 'mdtraj/testing/testing.py' 2024-05-29T14:36:02,501 adding 'mdtraj/utils/__init__.py' 2024-05-29T14:36:02,502 adding 'mdtraj/utils/contextmanagers.py' 2024-05-29T14:36:02,504 adding 'mdtraj/utils/delay_import.py' 2024-05-29T14:36:02,506 adding 'mdtraj/utils/rotation.py' 2024-05-29T14:36:02,507 adding 'mdtraj/utils/singleton.py' 2024-05-29T14:36:02,509 adding 'mdtraj/utils/unitcell.py' 2024-05-29T14:36:02,511 adding 'mdtraj/utils/validation.py' 2024-05-29T14:36:02,513 adding 'mdtraj/utils/zipped.py' 2024-05-29T14:36:02,515 adding 'mdtraj/utils/unit/__init__.py' 2024-05-29T14:36:02,517 adding 'mdtraj/utils/unit/basedimension.py' 2024-05-29T14:36:02,519 adding 'mdtraj/utils/unit/baseunit.py' 2024-05-29T14:36:02,521 adding 'mdtraj/utils/unit/constants.py' 2024-05-29T14:36:02,524 adding 'mdtraj/utils/unit/doctests.py' 2024-05-29T14:36:02,526 adding 'mdtraj/utils/unit/mymatrix.py' 2024-05-29T14:36:02,529 adding 'mdtraj/utils/unit/prefix.py' 2024-05-29T14:36:02,533 adding 'mdtraj/utils/unit/quantity.py' 2024-05-29T14:36:02,535 adding 'mdtraj/utils/unit/standard_dimensions.py' 2024-05-29T14:36:02,539 adding 'mdtraj/utils/unit/unit.py' 2024-05-29T14:36:02,541 adding 'mdtraj/utils/unit/unit_definitions.py' 2024-05-29T14:36:02,543 adding 'mdtraj/utils/unit/unit_math.py' 2024-05-29T14:36:02,545 adding 'mdtraj/utils/unit/unit_operators.py' 2024-05-29T14:36:02,551 adding 'mdtraj-1.10.0rc2.dist-info/LICENSE' 2024-05-29T14:36:02,553 adding 'mdtraj-1.10.0rc2.dist-info/METADATA' 2024-05-29T14:36:02,554 adding 'mdtraj-1.10.0rc2.dist-info/WHEEL' 2024-05-29T14:36:02,555 adding 'mdtraj-1.10.0rc2.dist-info/entry_points.txt' 2024-05-29T14:36:02,556 adding 'mdtraj-1.10.0rc2.dist-info/top_level.txt' 2024-05-29T14:36:02,559 adding 'mdtraj-1.10.0rc2.dist-info/RECORD' 2024-05-29T14:36:02,637 removing build/bdist.linux-armv7l/wheel 2024-05-29T14:36:03,473 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2024-05-29T14:36:03,614 Created wheel for mdtraj: filename=mdtraj-1.10.0rc2-cp311-cp311-linux_armv7l.whl size=6326240 sha256=bb4a20fe32bcfb564d4efcd3c10b2d6c88728eecacf8bd1b53dd402e387c444f 2024-05-29T14:36:03,615 Stored in directory: /tmp/pip-ephem-wheel-cache-disgi1of/wheels/75/13/7d/491dd7be5a5eae34b1e46c8cca5deea185ac91c28d9f785049 2024-05-29T14:36:03,631 Successfully built mdtraj 2024-05-29T14:36:03,801 Removed build tracker: '/tmp/pip-build-tracker-ug8y858_'