2023-07-22T16:36:02,049 Created temporary directory: /tmp/pip-build-tracker-l9pb_0if 2023-07-22T16:36:02,050 Initialized build tracking at /tmp/pip-build-tracker-l9pb_0if 2023-07-22T16:36:02,050 Created build tracker: /tmp/pip-build-tracker-l9pb_0if 2023-07-22T16:36:02,050 Entered build tracker: /tmp/pip-build-tracker-l9pb_0if 2023-07-22T16:36:02,051 Created temporary directory: /tmp/pip-wheel-7dpk83ov 2023-07-22T16:36:02,054 Created temporary directory: /tmp/pip-ephem-wheel-cache-qlvw2l2r 2023-07-22T16:36:02,079 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-07-22T16:36:02,083 2 location(s) to search for versions of mdtraj: 2023-07-22T16:36:02,083 * https://pypi.org/simple/mdtraj/ 2023-07-22T16:36:02,083 * https://www.piwheels.org/simple/mdtraj/ 2023-07-22T16:36:02,083 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2023-07-22T16:36:02,084 Getting page https://pypi.org/simple/mdtraj/ 2023-07-22T16:36:02,085 Found index url 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https://pypi.org/simple/mdtraj/) 2023-07-22T16:36:02,173 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 2023-07-22T16:36:02,173 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2023-07-22T16:36:02,174 Getting page https://www.piwheels.org/simple/mdtraj/ 2023-07-22T16:36:02,175 Found index url https://www.piwheels.org/simple/ 2023-07-22T16:36:02,457 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2023-07-22T16:36:02,460 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/) 2023-07-22T16:36:02,460 Skipping link: No binaries permitted for mdtraj: 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https://www.piwheels.org/simple/mdtraj/) 2023-07-22T16:36:02,461 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/) 2023-07-22T16:36:02,461 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2023-07-22T16:36:02,461 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2023-07-22T16:36:02,487 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2023-07-22T16:36:02,504 Collecting mdtraj==1.9.9 2023-07-22T16:36:02,506 Created temporary directory: /tmp/pip-unpack-uiwfoyic 2023-07-22T16:36:02,556 Downloading mdtraj-1.9.9.tar.gz (2.2 MB) 2023-07-22T16:36:03,847 Added mdtraj==1.9.9 from https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz to build tracker '/tmp/pip-build-tracker-l9pb_0if' 2023-07-22T16:36:03,852 Created temporary directory: /tmp/pip-build-env-_vmb_5d0 2023-07-22T16:36:03,862 Installing build dependencies: started 2023-07-22T16:36:03,863 Running command pip subprocess to install build dependencies 2023-07-22T16:36:05,060 Using pip 23.1.2 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2023-07-22T16:36:05,421 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-07-22T16:36:07,421 Collecting setuptools 2023-07-22T16:36:07,485 Using cached https://www.piwheels.org/simple/setuptools/setuptools-68.0.0-py3-none-any.whl (804 kB) 2023-07-22T16:36:07,741 Collecting wheel 2023-07-22T16:36:07,759 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.0-py3-none-any.whl (64 kB) 2023-07-22T16:36:07,878 Collecting oldest-supported-numpy 2023-07-22T16:36:07,895 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2022.11.19-py3-none-any.whl (4.9 kB) 2023-07-22T16:36:09,435 Collecting Cython~=0.29.36 2023-07-22T16:36:09,811 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.36-cp39-cp39-linux_armv7l.whl (4.9 MB) 2023-07-22T16:36:11,550 Collecting numpy==1.19.3 (from oldest-supported-numpy) 2023-07-22T16:36:12,306 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB) 2023-07-22T16:36:14,381 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2023-07-22T16:36:14,614 Creating /tmp/pip-build-env-_vmb_5d0/overlay/bin 2023-07-22T16:36:14,617 changing mode of /tmp/pip-build-env-_vmb_5d0/overlay/bin/wheel to 755 2023-07-22T16:36:23,125 changing mode of /tmp/pip-build-env-_vmb_5d0/overlay/bin/f2py to 755 2023-07-22T16:36:23,128 changing mode of /tmp/pip-build-env-_vmb_5d0/overlay/bin/f2py3 to 755 2023-07-22T16:36:23,130 changing mode of /tmp/pip-build-env-_vmb_5d0/overlay/bin/f2py3.9 to 755 2023-07-22T16:36:25,833 changing mode of /tmp/pip-build-env-_vmb_5d0/overlay/bin/cygdb to 755 2023-07-22T16:36:25,836 changing mode of /tmp/pip-build-env-_vmb_5d0/overlay/bin/cython to 755 2023-07-22T16:36:25,838 changing mode of /tmp/pip-build-env-_vmb_5d0/overlay/bin/cythonize to 755 2023-07-22T16:36:25,881 Successfully installed Cython-0.29.36 numpy-1.19.3 oldest-supported-numpy-2022.11.19 setuptools-68.0.0 wheel-0.41.0 2023-07-22T16:36:25,894 [notice] A new release of pip is available: 23.1.2 -> 23.2 2023-07-22T16:36:25,894 [notice] To update, run: python3 -m pip install --upgrade pip 2023-07-22T16:36:26,270 Installing build dependencies: finished with status 'done' 2023-07-22T16:36:26,281 Getting requirements to build wheel: started 2023-07-22T16:36:26,282 Running command Getting requirements to build wheel 2023-07-22T16:36:26,962 Using built-in specs. 2023-07-22T16:36:26,963 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-07-22T16:36:26,963 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2023-07-22T16:36:26,963 Target: arm-linux-gnueabihf 2023-07-22T16:36:26,963 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-07-22T16:36:26,964 Thread model: posix 2023-07-22T16:36:26,964 Supported LTO compression algorithms: zlib zstd 2023-07-22T16:36:26,964 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2023-07-22T16:36:30,760 C compiler: 2023-07-22T16:36:30,760 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-07-22T16:36:30,760 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-07-22T16:36:30,760 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-07-22T16:36:30,760 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-07-22T16:36:30,760 Attempting to autodetect NEON support... Did not detect NEON support 2023-07-22T16:36:30,761 running egg_info 2023-07-22T16:36:30,766 writing mdtraj.egg-info/PKG-INFO 2023-07-22T16:36:30,768 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2023-07-22T16:36:30,770 writing entry points to mdtraj.egg-info/entry_points.txt 2023-07-22T16:36:30,771 writing requirements to mdtraj.egg-info/requires.txt 2023-07-22T16:36:30,772 writing top-level names to mdtraj.egg-info/top_level.txt 2023-07-22T16:36:30,811 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-07-22T16:36:30,841 reading manifest template 'MANIFEST.in' 2023-07-22T16:36:31,657 no previously-included directories found matching '__pycache__' 2023-07-22T16:36:31,659 no previously-included directories found matching '*.pyc' 2023-07-22T16:36:31,659 adding license file 'LICENSE' 2023-07-22T16:36:31,682 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-07-22T16:36:31,759 Getting requirements to build wheel: finished with status 'done' 2023-07-22T16:36:31,768 Created temporary directory: /tmp/pip-modern-metadata-do32lxls 2023-07-22T16:36:31,770 Preparing metadata (pyproject.toml): started 2023-07-22T16:36:31,771 Running command Preparing metadata (pyproject.toml) 2023-07-22T16:36:32,407 Using built-in specs. 2023-07-22T16:36:32,408 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-07-22T16:36:32,408 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2023-07-22T16:36:32,408 Target: arm-linux-gnueabihf 2023-07-22T16:36:32,408 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-07-22T16:36:32,409 Thread model: posix 2023-07-22T16:36:32,409 Supported LTO compression algorithms: zlib zstd 2023-07-22T16:36:32,409 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2023-07-22T16:36:36,071 ./basesetup.py:451: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-do32lxls --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2023-07-22T16:36:36,071 warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 2023-07-22T16:36:37,992 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. 2023-07-22T16:36:37,993 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. 2023-07-22T16:36:37,993 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. 2023-07-22T16:37:04,461 C compiler: 2023-07-22T16:37:04,462 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-07-22T16:37:04,462 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-07-22T16:37:04,462 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-07-22T16:37:04,462 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-07-22T16:37:04,463 Attempting to autodetect NEON support... Did not detect NEON support 2023-07-22T16:37:04,463 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx 2023-07-22T16:37:04,463 [ 2/12] Cythonizing mdtraj/geometry/drid.pyx 2023-07-22T16:37:04,463 [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx 2023-07-22T16:37:04,463 [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx 2023-07-22T16:37:04,464 [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx 2023-07-22T16:37:04,464 [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2023-07-22T16:37:04,464 [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx 2023-07-22T16:37:04,464 [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx 2023-07-22T16:37:04,464 [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx 2023-07-22T16:37:04,464 [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx 2023-07-22T16:37:04,465 [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx 2023-07-22T16:37:04,465 [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx 2023-07-22T16:37:04,519 running dist_info 2023-07-22T16:37:04,539 creating /tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info 2023-07-22T16:37:04,546 writing /tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info/PKG-INFO 2023-07-22T16:37:04,548 writing dependency_links to /tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info/dependency_links.txt 2023-07-22T16:37:04,550 writing entry points to /tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info/entry_points.txt 2023-07-22T16:37:04,551 writing requirements to /tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info/requires.txt 2023-07-22T16:37:04,552 writing top-level names to /tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info/top_level.txt 2023-07-22T16:37:04,553 writing manifest file '/tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info/SOURCES.txt' 2023-07-22T16:37:04,615 reading manifest file '/tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info/SOURCES.txt' 2023-07-22T16:37:04,617 reading manifest template 'MANIFEST.in' 2023-07-22T16:37:05,551 no previously-included directories found matching '__pycache__' 2023-07-22T16:37:05,552 no previously-included directories found matching '*.pyc' 2023-07-22T16:37:05,553 adding license file 'LICENSE' 2023-07-22T16:37:05,572 writing manifest file '/tmp/pip-modern-metadata-do32lxls/mdtraj.egg-info/SOURCES.txt' 2023-07-22T16:37:05,574 creating '/tmp/pip-modern-metadata-do32lxls/mdtraj-1.9.9.dist-info' 2023-07-22T16:37:06,391 Preparing metadata (pyproject.toml): finished with status 'done' 2023-07-22T16:37:06,398 Source in /tmp/pip-wheel-7dpk83ov/mdtraj_e903f56f4a76475db3d85d7b47655f46 has version 1.9.9, which satisfies requirement mdtraj==1.9.9 from https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz 2023-07-22T16:37:06,399 Removed mdtraj==1.9.9 from https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz from build tracker '/tmp/pip-build-tracker-l9pb_0if' 2023-07-22T16:37:06,403 Created temporary directory: /tmp/pip-unpack-5yl9i_li 2023-07-22T16:37:06,403 Building wheels for collected packages: mdtraj 2023-07-22T16:37:06,408 Created temporary directory: /tmp/pip-wheel-5x0w5wg8 2023-07-22T16:37:06,408 Destination directory: /tmp/pip-wheel-5x0w5wg8 2023-07-22T16:37:06,411 Building wheel for mdtraj (pyproject.toml): started 2023-07-22T16:37:06,412 Running command Building wheel for mdtraj (pyproject.toml) 2023-07-22T16:37:07,094 Using built-in specs. 2023-07-22T16:37:07,095 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-07-22T16:37:07,095 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2023-07-22T16:37:07,095 Target: arm-linux-gnueabihf 2023-07-22T16:37:07,095 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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-bootstrap --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 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-07-22T16:37:07,095 Thread model: posix 2023-07-22T16:37:07,096 Supported LTO compression algorithms: zlib zstd 2023-07-22T16:37:07,096 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2023-07-22T16:37:12,521 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. 2023-07-22T16:37:12,522 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. 2023-07-22T16:37:12,522 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. 2023-07-22T16:37:38,731 C compiler: 2023-07-22T16:37:38,731 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-07-22T16:37:38,731 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-07-22T16:37:38,731 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-07-22T16:37:38,731 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-07-22T16:37:38,731 Attempting to autodetect NEON support... Did not detect NEON support 2023-07-22T16:37:38,732 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx 2023-07-22T16:37:38,732 [ 2/12] Cythonizing mdtraj/geometry/drid.pyx 2023-07-22T16:37:38,732 [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx 2023-07-22T16:37:38,732 [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx 2023-07-22T16:37:38,732 [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx 2023-07-22T16:37:38,732 [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2023-07-22T16:37:38,732 [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx 2023-07-22T16:37:38,732 [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx 2023-07-22T16:37:38,733 [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx 2023-07-22T16:37:38,733 [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx 2023-07-22T16:37:38,733 [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx 2023-07-22T16:37:38,733 [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx 2023-07-22T16:37:38,827 running bdist_wheel 2023-07-22T16:37:38,849 running build 2023-07-22T16:37:38,849 running build_py 2023-07-22T16:37:38,859 creating build 2023-07-22T16:37:38,859 creating build/lib.linux-armv7l-cpython-39 2023-07-22T16:37:38,860 creating build/lib.linux-armv7l-cpython-39/mdtraj 2023-07-22T16:37:38,861 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2023-07-22T16:37:38,864 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2023-07-22T16:37:38,865 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2023-07-22T16:37:38,868 creating build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2023-07-22T16:37:38,869 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2023-07-22T16:37:38,871 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2023-07-22T16:37:38,873 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2023-07-22T16:37:38,876 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,877 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,879 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,881 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,883 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,885 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,888 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,890 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,891 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,893 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-22T16:37:38,897 creating build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,898 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,900 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,902 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,904 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,907 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,909 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,911 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,913 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,915 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,918 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,920 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,922 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,924 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,926 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,928 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:37:38,931 creating build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-22T16:37:38,932 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-22T16:37:38,935 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-22T16:37:38,937 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-22T16:37:38,938 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-22T16:37:38,941 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-22T16:37:38,943 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-22T16:37:38,945 creating build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-22T16:37:38,946 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-22T16:37:38,949 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-22T16:37:38,953 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-22T16:37:38,956 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-22T16:37:38,958 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-22T16:37:38,961 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-22T16:37:38,963 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,964 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,967 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,970 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,973 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,975 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,978 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,981 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,983 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,985 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,987 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,990 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,993 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,995 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:38,997 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:39,000 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:39,002 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:39,005 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:39,008 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:39,011 creating build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-22T16:37:39,012 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-22T16:37:39,015 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-22T16:37:39,017 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-22T16:37:39,019 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-22T16:37:39,021 creating build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2023-07-22T16:37:39,022 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2023-07-22T16:37:39,025 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2023-07-22T16:37:39,027 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2023-07-22T16:37:39,030 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,031 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,033 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,035 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,038 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,040 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,043 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,045 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,048 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,051 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,053 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,055 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,057 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,059 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-22T16:37:39,062 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2023-07-22T16:37:39,063 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2023-07-22T16:37:39,066 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2023-07-22T16:37:39,069 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2023-07-22T16:37:39,072 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2023-07-22T16:37:39,073 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2023-07-22T16:37:39,075 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2023-07-22T16:37:39,086 running build_ext 2023-07-22T16:37:39,089 building 'mdtraj.formats.xtc' extension 2023-07-22T16:37:39,090 creating build/temp.linux-armv7l-cpython-39 2023-07-22T16:37:39,090 creating build/temp.linux-armv7l-cpython-39/mdtraj 2023-07-22T16:37:39,091 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats 2023-07-22T16:37:39,092 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc 2023-07-22T16:37:39,092 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src 2023-07-22T16:37:39,094 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:37:39,222 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:37:39,366 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-07-22T16:37:39,366 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:37:39,366 788 | int smallnum, smaller, larger, i, is_smaller, run; 2023-07-22T16:37:39,367 | ^~~~~~ 2023-07-22T16:37:39,367 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:37:39,367 785 | int smallidx, minidx, maxidx; 2023-07-22T16:37:39,367 | ^~~~~~ 2023-07-22T16:37:39,374 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-07-22T16:37:39,375 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:37:39,375 1016 | int errval=1; 2023-07-22T16:37:39,375 | ^~~~~~ 2023-07-22T16:37:39,380 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2023-07-22T16:37:39,381 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:37:39,381 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2023-07-22T16:37:39,381 | ^~~~~~ 2023-07-22T16:37:39,382 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:37:39,383 1302 | int smallidx, minidx, maxidx; 2023-07-22T16:37:39,383 | ^~~~~~ 2023-07-22T16:37:39,391 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-07-22T16:37:39,393 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:37:39,393 1509 | int errval=1; 2023-07-22T16:37:39,393 | ^~~~~~ 2023-07-22T16:37:41,510 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:37:41,591 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2023-07-22T16:37:41,591 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2023-07-22T16:37:41,591 66 | int i,j,result; 2023-07-22T16:37:41,592 | ^ 2023-07-22T16:37:41,592 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2023-07-22T16:37:41,592 66 | int i,j,result; 2023-07-22T16:37:41,592 | ^ 2023-07-22T16:37:41,593 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2023-07-22T16:37:41,593 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-07-22T16:37:41,593 119 | if (NULL == xd) 2023-07-22T16:37:41,593 | ^~ 2023-07-22T16:37:41,594 mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-07-22T16:37:41,594 122 | do { 2023-07-22T16:37:41,594 | ^~ 2023-07-22T16:37:41,736 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:37:42,072 In file included from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-22T16:37:42,073 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-22T16:37:42,073 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-22T16:37:42,073 from mdtraj/formats/xtc/xtc.c:781: 2023-07-22T16:37:42,073 /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-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] 2023-07-22T16:37:42,073 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-22T16:37:42,073 | ^~~~~~~ 2023-07-22T16:37:48,587 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2023-07-22T16:37:48,587 mdtraj/formats/xtc/xtc.c:693:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:48,588 693 | #define PyInt_FromLong PyLong_FromLong 2023-07-22T16:37:48,588 | ^~~~~~~~~~~~~~~ 2023-07-22T16:37:48,593 mdtraj/formats/xtc/xtc.c:9554:7: note: ‘__pyx_v_status’ was declared here 2023-07-22T16:37:48,593 9554 | int __pyx_v_status; 2023-07-22T16:37:48,593 | ^~~~~~~~~~~~~~ 2023-07-22T16:37:58,030 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2023-07-22T16:37:58,035 mdtraj/formats/xtc/xtc.c:8073:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,035 8073 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2023-07-22T16:37:58,035 | ^ 2023-07-22T16:37:58,040 mdtraj/formats/xtc/xtc.c:8069:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,040 8069 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2023-07-22T16:37:58,040 | ^ 2023-07-22T16:37:58,045 mdtraj/formats/xtc/xtc.c:8065:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,045 8065 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-22T16:37:58,045 | ^ 2023-07-22T16:37:58,050 mdtraj/formats/xtc/xtc.c:8025:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,050 8025 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-22T16:37:58,050 | ^ 2023-07-22T16:37:58,054 mdtraj/formats/xtc/xtc.c:8007:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,055 8007 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-22T16:37:58,055 | ^ 2023-07-22T16:37:58,058 mdtraj/formats/xtc/xtc.c:8083:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,059 8083 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-22T16:37:58,059 | ^ 2023-07-22T16:37:58,063 mdtraj/formats/xtc/xtc.c:8045:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,063 8045 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2023-07-22T16:37:58,063 | ^ 2023-07-22T16:37:58,068 mdtraj/formats/xtc/xtc.c:8041:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,068 8041 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2023-07-22T16:37:58,068 | ^ 2023-07-22T16:37:58,073 mdtraj/formats/xtc/xtc.c:8037:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,073 8037 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-22T16:37:58,073 | ^ 2023-07-22T16:37:58,077 mdtraj/formats/xtc/xtc.c:7660:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,077 7660 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2023-07-22T16:37:58,078 | ^ 2023-07-22T16:37:58,082 mdtraj/formats/xtc/xtc.c:7656:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:37:58,082 7656 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-22T16:37:58,082 | ^ 2023-07-22T16:38:02,656 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/xtc.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:38:02,824 building 'mdtraj.formats.trr' extension 2023-07-22T16:38:02,825 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:38:02,942 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:38:03,071 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-07-22T16:38:03,071 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:38:03,072 788 | int smallnum, smaller, larger, i, is_smaller, run; 2023-07-22T16:38:03,072 | ^~~~~~ 2023-07-22T16:38:03,072 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:38:03,072 785 | int smallidx, minidx, maxidx; 2023-07-22T16:38:03,072 | ^~~~~~ 2023-07-22T16:38:03,079 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-07-22T16:38:03,079 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:38:03,079 1016 | int errval=1; 2023-07-22T16:38:03,079 | ^~~~~~ 2023-07-22T16:38:03,083 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2023-07-22T16:38:03,084 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:38:03,084 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2023-07-22T16:38:03,084 | ^~~~~~ 2023-07-22T16:38:03,085 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:38:03,085 1302 | int smallidx, minidx, maxidx; 2023-07-22T16:38:03,085 | ^~~~~~ 2023-07-22T16:38:03,093 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-07-22T16:38:03,094 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-07-22T16:38:03,094 1509 | int errval=1; 2023-07-22T16:38:03,094 | ^~~~~~ 2023-07-22T16:38:05,208 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:38:05,860 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:38:06,178 In file included from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-22T16:38:06,179 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-22T16:38:06,179 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-22T16:38:06,179 from mdtraj/formats/xtc/trr.c:781: 2023-07-22T16:38:06,179 /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-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] 2023-07-22T16:38:06,179 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-22T16:38:06,179 | ^~~~~~~ 2023-07-22T16:38:13,021 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2023-07-22T16:38:13,021 mdtraj/formats/xtc/trr.c:693:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:13,021 693 | #define PyInt_FromLong PyLong_FromLong 2023-07-22T16:38:13,021 | ^~~~~~~~~~~~~~~ 2023-07-22T16:38:13,028 mdtraj/formats/xtc/trr.c:11080:7: note: ‘__pyx_v_status’ was declared here 2023-07-22T16:38:13,028 11080 | int __pyx_v_status; 2023-07-22T16:38:13,029 | ^~~~~~~~~~~~~~ 2023-07-22T16:38:22,836 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2023-07-22T16:38:22,841 mdtraj/formats/xtc/trr.c:8433:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,842 8433 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2023-07-22T16:38:22,842 | ^ 2023-07-22T16:38:22,847 mdtraj/formats/xtc/trr.c:8429:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,848 8429 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-22T16:38:22,848 | ^ 2023-07-22T16:38:22,849 mdtraj/formats/xtc/trr.c:1929:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,849 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2023-07-22T16:38:22,849 | ^ 2023-07-22T16:38:22,853 mdtraj/formats/xtc/trr.c:6970:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2023-07-22T16:38:22,853 6970 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2023-07-22T16:38:22,853 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:38:22,858 mdtraj/formats/xtc/trr.c:8423:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,858 8423 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2023-07-22T16:38:22,858 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-07-22T16:38:22,864 mdtraj/formats/xtc/trr.c:8376:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,864 8376 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2023-07-22T16:38:22,864 | ^ 2023-07-22T16:38:22,869 mdtraj/formats/xtc/trr.c:8372:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,870 8372 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-22T16:38:22,870 | ^ 2023-07-22T16:38:22,871 mdtraj/formats/xtc/trr.c:1929:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,871 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2023-07-22T16:38:22,871 | ^ 2023-07-22T16:38:22,875 mdtraj/formats/xtc/trr.c:6986:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2023-07-22T16:38:22,875 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2023-07-22T16:38:22,875 | ^~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:38:22,880 mdtraj/formats/xtc/trr.c:8366:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,880 8366 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2023-07-22T16:38:22,880 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-07-22T16:38:22,885 mdtraj/formats/xtc/trr.c:8766:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,886 8766 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-22T16:38:22,886 | ^ 2023-07-22T16:38:22,891 mdtraj/formats/xtc/trr.c:8762:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,891 8762 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-07-22T16:38:22,892 | ^ 2023-07-22T16:38:22,897 mdtraj/formats/xtc/trr.c:8607:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,897 8607 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-22T16:38:22,897 | ^ 2023-07-22T16:38:22,903 mdtraj/formats/xtc/trr.c:8603:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,903 8603 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-07-22T16:38:22,903 | ^ 2023-07-22T16:38:22,908 mdtraj/formats/xtc/trr.c:8659:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,908 8659 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-22T16:38:22,908 | ^ 2023-07-22T16:38:22,914 mdtraj/formats/xtc/trr.c:8655:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:22,914 8655 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-07-22T16:38:22,914 | ^ 2023-07-22T16:38:29,316 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/trr.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:38:29,492 building 'mdtraj.formats.tng' extension 2023-07-22T16:38:29,494 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng 2023-07-22T16:38:29,494 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src 2023-07-22T16:38:29,495 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression 2023-07-22T16:38:29,497 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib 2023-07-22T16:38:29,498 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwlzh.o 2023-07-22T16:38:30,208 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwt.o 2023-07-22T16:38:30,582 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/coder.o 2023-07-22T16:38:31,277 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/dict.o 2023-07-22T16:38:31,404 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/fixpoint.o 2023-07-22T16:38:31,585 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffman.o 2023-07-22T16:38:32,260 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffmem.o 2023-07-22T16:38:32,699 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/lz77.o 2023-07-22T16:38:33,005 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/merge_sort.o 2023-07-22T16:38:33,183 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/mtf.o 2023-07-22T16:38:33,270 mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: 2023-07-22T16:38:33,270 mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-07-22T16:38:33,270 196 | while (dict[ptr]!=v) 2023-07-22T16:38:33,271 | ^~ 2023-07-22T16:38:33,571 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/rle.o 2023-07-22T16:38:33,620 mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: 2023-07-22T16:38:33,620 mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-07-22T16:38:33,621 56 | if (v==vals[i]) 2023-07-22T16:38:33,621 | ^~ 2023-07-22T16:38:33,749 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/tng_compress.o 2023-07-22T16:38:35,984 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/vals16.o 2023-07-22T16:38:36,117 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/warnmalloc.o 2023-07-22T16:38:36,257 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/widemuldiv.o 2023-07-22T16:38:36,493 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc2.o 2023-07-22T16:38:38,087 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc3.o 2023-07-22T16:38:40,380 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/md5.o 2023-07-22T16:38:40,799 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/tng_io.o 2023-07-22T16:38:40,967 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: 2023-07-22T16:38:40,970 mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-22T16:38:40,970 1064 | tng_data->input_endianness_swap_func_32 = 2023-07-22T16:38:40,970 | ^ 2023-07-22T16:38:40,971 mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-22T16:38:40,971 1073 | tng_data->input_endianness_swap_func_64 = 2023-07-22T16:38:40,971 | ^ 2023-07-22T16:38:40,972 mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-22T16:38:40,972 1089 | tng_data->input_endianness_swap_func_32 = 2023-07-22T16:38:40,972 | ^ 2023-07-22T16:38:40,972 mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-22T16:38:40,973 1098 | tng_data->input_endianness_swap_func_64 = 2023-07-22T16:38:40,973 | ^ 2023-07-22T16:38:41,057 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: 2023-07-22T16:38:41,062 mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 2023-07-22T16:38:41,062 9565 | if(tng_data->output_endianness_swap_func_32 == 2023-07-22T16:38:41,062 | ^~ 2023-07-22T16:38:41,066 mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 2023-07-22T16:38:41,067 9570 | else if(tng_data->output_endianness_swap_func_32 == 2023-07-22T16:38:41,067 | ^~ 2023-07-22T16:38:41,071 mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 2023-07-22T16:38:41,071 9588 | if(tng_data->output_endianness_swap_func_64 == 2023-07-22T16:38:41,071 | ^~ 2023-07-22T16:38:41,076 mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 2023-07-22T16:38:41,076 9593 | else if(tng_data->output_endianness_swap_func_64 == 2023-07-22T16:38:41,076 | ^~ 2023-07-22T16:38:41,079 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: 2023-07-22T16:38:41,083 mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-22T16:38:41,083 9651 | tng_data->output_endianness_swap_func_32 = 2023-07-22T16:38:41,083 | ^ 2023-07-22T16:38:41,088 mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-22T16:38:41,088 9660 | tng_data->output_endianness_swap_func_64 = 2023-07-22T16:38:41,088 | ^ 2023-07-22T16:38:41,093 mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-22T16:38:41,093 9673 | tng_data->output_endianness_swap_func_32 = 2023-07-22T16:38:41,093 | ^ 2023-07-22T16:38:41,098 mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-22T16:38:41,098 9682 | tng_data->output_endianness_swap_func_64 = 2023-07-22T16:38:41,098 | ^ 2023-07-22T16:38:42,961 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: 2023-07-22T16:38:42,968 mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2023-07-22T16:38:42,968 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2023-07-22T16:38:42,968 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:38:42,975 mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 2023-07-22T16:38:42,975 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2023-07-22T16:38:42,975 | ^~~~~~~~~~~~~~~~~~ 2023-07-22T16:38:44,022 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: 2023-07-22T16:38:44,025 mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:44,025 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; 2023-07-22T16:38:44,026 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2023-07-22T16:38:44,027 mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:38:44,028 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, 2023-07-22T16:38:44,028 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:38:44,028 4309 | (int)n_frames, 2023-07-22T16:38:44,028 | ~~~~~~~~~~~~~~ 2023-07-22T16:38:44,028 4310 | f_precision, 2023-07-22T16:38:44,028 | ~~~~~~~~~~~~ 2023-07-22T16:38:44,028 4311 | 0, alt_algo, 2023-07-22T16:38:44,028 | ~~~~~~~~~~~~ 2023-07-22T16:38:44,029 4312 | &compressed_len); 2023-07-22T16:38:44,029 | ~~~~~~~~~~~~~~~~ 2023-07-22T16:38:44,032 mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 2023-07-22T16:38:44,032 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; 2023-07-22T16:38:44,032 | ^~~~~~~~~~~ 2023-07-22T16:38:54,980 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/tng.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/tng.o 2023-07-22T16:38:55,303 In file included from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-22T16:38:55,303 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-22T16:38:55,303 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-22T16:38:55,303 from mdtraj/formats/tng/tng.c:807: 2023-07-22T16:38:55,303 /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-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] 2023-07-22T16:38:55,303 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-22T16:38:55,304 | ^~~~~~~ 2023-07-22T16:38:55,383 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’: 2023-07-22T16:38:55,385 mdtraj/formats/tng/tng.c:3690:104: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,385 3690 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,386 | ^~ 2023-07-22T16:38:55,387 mdtraj/formats/tng/tng.c:3745:88: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,388 3745 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,388 | ^~ 2023-07-22T16:38:55,389 mdtraj/formats/tng/tng.c:3777:90: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,390 3777 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,390 | ^~ 2023-07-22T16:38:55,392 mdtraj/formats/tng/tng.c:3809:95: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,392 3809 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,392 | ^~ 2023-07-22T16:38:55,394 mdtraj/formats/tng/tng.c:3879:113: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,394 3879 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,395 | ^~ 2023-07-22T16:38:55,398 mdtraj/formats/tng/tng.c:3923:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,398 3923 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,398 | ^~ 2023-07-22T16:38:55,414 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’: 2023-07-22T16:38:55,416 mdtraj/formats/tng/tng.c:4719:106: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,416 4719 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,416 | ^~ 2023-07-22T16:38:55,419 mdtraj/formats/tng/tng.c:4764:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,419 4764 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,419 | ^~ 2023-07-22T16:38:55,424 mdtraj/formats/tng/tng.c:4871:115: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,425 4871 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,425 | ^~ 2023-07-22T16:38:55,427 mdtraj/formats/tng/tng.c:4901:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,427 4901 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,427 | ^~ 2023-07-22T16:38:55,433 mdtraj/formats/tng/tng.c:5029:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,433 5029 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,433 | ^~ 2023-07-22T16:38:55,452 mdtraj/formats/tng/tng.c:5630:126: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,452 5630 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,453 | ^~ 2023-07-22T16:38:55,461 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’: 2023-07-22T16:38:55,464 mdtraj/formats/tng/tng.c:6040:152: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,464 6040 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,464 | ^~ 2023-07-22T16:38:55,479 mdtraj/formats/tng/tng.c:6308:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,479 6308 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,479 | ^~ 2023-07-22T16:38:55,485 mdtraj/formats/tng/tng.c:6410:304: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,485 6410 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,485 | ^~ 2023-07-22T16:38:55,556 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’: 2023-07-22T16:38:55,561 mdtraj/formats/tng/tng.c:8902:94: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,561 8902 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,561 | ^~ 2023-07-22T16:38:55,566 mdtraj/formats/tng/tng.c:8934:75: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,566 8934 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,566 | ^~ 2023-07-22T16:38:55,571 mdtraj/formats/tng/tng.c:8966:81: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,571 8966 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,571 | ^~ 2023-07-22T16:38:55,586 mdtraj/formats/tng/tng.c:9289:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,586 9289 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,586 | ^~ 2023-07-22T16:38:55,607 mdtraj/formats/tng/tng.c:9480:372: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,608 9480 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,608 | ^~ 2023-07-22T16:38:55,627 mdtraj/formats/tng/tng.c:9532:378: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,627 9532 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,627 | ^~ 2023-07-22T16:38:55,634 mdtraj/formats/tng/tng.c:9594:89: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-22T16:38:55,634 9594 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-22T16:38:55,634 | ^~ 2023-07-22T16:39:11,609 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:39:11,856 building 'mdtraj.formats.dcd' extension 2023-07-22T16:39:11,857 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd 2023-07-22T16:39:11,858 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src 2023-07-22T16:39:11,859 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:39:12,190 In file included from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-22T16:39:12,190 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-22T16:39:12,190 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-22T16:39:12,190 from mdtraj/formats/dcd/dcd.c:779: 2023-07-22T16:39:12,191 /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-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] 2023-07-22T16:39:12,191 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-22T16:39:12,191 | ^~~~~~~ 2023-07-22T16:39:19,481 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2023-07-22T16:39:19,481 mdtraj/formats/dcd/dcd.c:691:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:39:19,482 691 | #define PyInt_FromLong PyLong_FromLong 2023-07-22T16:39:19,482 | ^~~~~~~~~~~~~~~ 2023-07-22T16:39:19,484 mdtraj/formats/dcd/dcd.c:5449:7: note: ‘__pyx_v_i’ was declared here 2023-07-22T16:39:19,484 5449 | int __pyx_v_i; 2023-07-22T16:39:19,484 | ^~~~~~~~~ 2023-07-22T16:39:22,569 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:39:23,903 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:39:24,050 building 'mdtraj.formats.binpos' extension 2023-07-22T16:39:24,051 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos 2023-07-22T16:39:24,051 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src 2023-07-22T16:39:24,052 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:39:24,390 In file included from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-22T16:39:24,390 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-22T16:39:24,390 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-22T16:39:24,391 from mdtraj/formats/binpos/binpos.c:779: 2023-07-22T16:39:24,391 /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-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] 2023-07-22T16:39:24,391 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-22T16:39:24,391 | ^~~~~~~ 2023-07-22T16:39:32,302 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2023-07-22T16:39:32,305 mdtraj/formats/binpos/binpos.c:5510:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:39:32,305 5510 | if (__pyx_t_2) { 2023-07-22T16:39:32,305 | ^ 2023-07-22T16:39:32,308 mdtraj/formats/binpos/binpos.c:4990:7: note: ‘__pyx_v_status’ was declared here 2023-07-22T16:39:32,308 4990 | int __pyx_v_status; 2023-07-22T16:39:32,308 | ^~~~~~~~~~~~~~ 2023-07-22T16:39:32,308 mdtraj/formats/binpos/binpos.c:691:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:39:32,308 691 | #define PyInt_FromLong PyLong_FromLong 2023-07-22T16:39:32,309 | ^~~~~~~~~~~~~~~ 2023-07-22T16:39:32,311 mdtraj/formats/binpos/binpos.c:4987:7: note: ‘__pyx_v_i’ was declared here 2023-07-22T16:39:32,311 4987 | int __pyx_v_i; 2023-07-22T16:39:32,311 | ^~~~~~~~~ 2023-07-22T16:39:33,758 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:39:34,067 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/binpos.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:39:34,201 building 'mdtraj.formats.dtr' extension 2023-07-22T16:39:34,202 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr 2023-07-22T16:39:34,203 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src 2023-07-22T16:39:34,204 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -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-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:39:34,466 In file included from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-22T16:39:34,466 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-22T16:39:34,466 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-22T16:39:34,467 from mdtraj/formats/dtr/dtr.cpp:800: 2023-07-22T16:39:34,467 /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-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] 2023-07-22T16:39:34,467 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-22T16:39:34,467 | ^~~~~~~ 2023-07-22T16:39:46,736 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -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-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:39:48,405 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2023-07-22T16:39:48,405 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=] 2023-07-22T16:39:48,405 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2023-07-22T16:39:48,406 | ~~^ ~ 2023-07-22T16:39:48,406 | | | 2023-07-22T16:39:48,406 | | size_t {aka unsigned int} 2023-07-22T16:39:48,406 | long int 2023-07-22T16:39:48,406 | %d 2023-07-22T16:39:48,406 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=] 2023-07-22T16:39:48,407 487 | printf("size %d framesize %d\n\n", 2023-07-22T16:39:48,407 | ~^ 2023-07-22T16:39:48,407 | | 2023-07-22T16:39:48,407 | int 2023-07-22T16:39:48,407 | %lld 2023-07-22T16:39:48,407 488 | keys[i].size(), m_framesize); 2023-07-22T16:39:48,408 | ~~~~~~~~~~~~~~ 2023-07-22T16:39:48,408 | | 2023-07-22T16:39:48,408 | uint64_t {aka long long unsigned int} 2023-07-22T16:39:48,408 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=] 2023-07-22T16:39:48,408 487 | printf("size %d framesize %d\n\n", 2023-07-22T16:39:48,408 | ~^ 2023-07-22T16:39:48,408 | | 2023-07-22T16:39:48,409 | int 2023-07-22T16:39:48,409 | %lld 2023-07-22T16:39:48,409 488 | keys[i].size(), m_framesize); 2023-07-22T16:39:48,409 | ~~~~~~~~~~~ 2023-07-22T16:39:48,409 | | 2023-07-22T16:39:48,409 | uint64_t {aka long long unsigned int} 2023-07-22T16:39:48,409 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=] 2023-07-22T16:39:48,410 494 | "non-constant time interval at frame %ld\n", i); 2023-07-22T16:39:48,410 | ~~^ ~ 2023-07-22T16:39:48,410 | | | 2023-07-22T16:39:48,410 | | size_t {aka unsigned int} 2023-07-22T16:39:48,410 | long int 2023-07-22T16:39:48,410 | %d 2023-07-22T16:39:48,410 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=] 2023-07-22T16:39:48,411 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2023-07-22T16:39:48,411 | ~~^ ~ 2023-07-22T16:39:48,411 | | | 2023-07-22T16:39:48,411 | | size_t {aka unsigned int} 2023-07-22T16:39:48,411 | long int 2023-07-22T16:39:48,411 | %d 2023-07-22T16:39:48,536 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2023-07-22T16:39:48,536 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=] 2023-07-22T16:39:48,536 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2023-07-22T16:39:48,537 | ~~^ 2023-07-22T16:39:48,537 | | 2023-07-22T16:39:48,537 | long int 2023-07-22T16:39:48,537 | %lld 2023-07-22T16:39:48,537 1302 | 3*natoms, pos.count); 2023-07-22T16:39:48,537 | ~~~~~~~~~ 2023-07-22T16:39:48,538 | | 2023-07-22T16:39:48,538 | uint64_t {aka long long unsigned int} 2023-07-22T16:39:48,538 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=] 2023-07-22T16:39:48,538 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2023-07-22T16:39:48,538 | ~~^ 2023-07-22T16:39:48,538 | | 2023-07-22T16:39:48,539 | long int 2023-07-22T16:39:48,539 | %lld 2023-07-22T16:39:48,539 1311 | 3*natoms, vel.count); 2023-07-22T16:39:48,539 | ~~~~~~~~~ 2023-07-22T16:39:48,539 | | 2023-07-22T16:39:48,539 | uint64_t {aka long long unsigned int} 2023-07-22T16:39:48,562 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2023-07-22T16:39:48,562 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=] 2023-07-22T16:39:48,562 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2023-07-22T16:39:48,562 | ~~^ 2023-07-22T16:39:48,563 | | 2023-07-22T16:39:48,563 | long int 2023-07-22T16:39:48,563 | %lld 2023-07-22T16:39:48,563 1573 | velblob.count, 3*natoms); 2023-07-22T16:39:48,563 | ~~~~~~~~~~~~~ 2023-07-22T16:39:48,563 | | 2023-07-22T16:39:48,563 | uint64_t {aka long long unsigned int} 2023-07-22T16:39:49,599 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: 2023-07-22T16:39:49,599 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 2023-07-22T16:39:49,599 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2023-07-22T16:39:49,599 | ~~~~~~~~^~~~~ 2023-07-22T16:39:51,830 In file included from /usr/include/c++/10/map:60, 2023-07-22T16:39:51,830 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2023-07-22T16:39:51,831 /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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> >]’: 2023-07-22T16:39:51,831 /usr/include/c++/10/bits/stl_tree.h:2193:5: 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 2023-07-22T16:39:51,831 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-07-22T16:39:51,831 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:51,893 /usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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> >]’: 2023-07-22T16:39:51,893 /usr/include/c++/10/bits/stl_tree.h:2458:7: 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 2023-07-22T16:39:51,893 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-07-22T16:39:51,893 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:51,894 /usr/include/c++/10/bits/stl_tree.h:2458:7: 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 2023-07-22T16:39:51,948 In file included from /usr/include/c++/10/map:61, 2023-07-22T16:39:51,949 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2023-07-22T16:39:51,949 /usr/include/c++/10/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2023-07-22T16:39:51,949 /usr/include/c++/10/bits/stl_map.h:520:37: 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 2023-07-22T16:39:51,949 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-07-22T16:39:51,949 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:51,949 521 | std::forward_as_tuple(std::move(__k)), 2023-07-22T16:39:51,949 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:51,949 522 | std::tuple<>()); 2023-07-22T16:39:51,950 | ~~~~~~~~~~~~~~~ 2023-07-22T16:39:52,723 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: 2023-07-22T16:39:52,724 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2023-07-22T16:39:52,724 706 | sprintf(sub, "%03x/", i); 2023-07-22T16:39:52,724 | ^~~~ 2023-07-22T16:39:52,724 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 2023-07-22T16:39:52,724 706 | sprintf(sub, "%03x/", i); 2023-07-22T16:39:52,724 | ^~~~~~~ 2023-07-22T16:39:52,725 mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2023-07-22T16:39:52,725 706 | sprintf(sub, "%03x/", i); 2023-07-22T16:39:52,725 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2023-07-22T16:39:52,725 mdtraj/formats/dtr/src/dtrplugin.cxx:714:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2023-07-22T16:39:52,725 714 | sprintf(subsub, "%03x", j); 2023-07-22T16:39:52,725 | ^~~~ 2023-07-22T16:39:52,725 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 2023-07-22T16:39:52,726 714 | sprintf(subsub, "%03x", j); 2023-07-22T16:39:52,726 | ^~~~~~ 2023-07-22T16:39:52,726 mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2023-07-22T16:39:52,726 714 | sprintf(subsub, "%03x", j); 2023-07-22T16:39:52,726 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:53,137 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: 2023-07-22T16:39:53,137 mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2023-07-22T16:39:53,138 667 | sprintf(answer, "%03x/", d1); 2023-07-22T16:39:53,138 | ^ 2023-07-22T16:39:53,138 mdtraj/formats/dtr/src/dtrplugin.cxx:667:13: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2023-07-22T16:39:53,138 667 | sprintf(answer, "%03x/", d1); 2023-07-22T16:39:53,138 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:53,138 mdtraj/formats/dtr/src/dtrplugin.cxx:665:28: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 2023-07-22T16:39:53,139 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-07-22T16:39:53,139 | ^~~~ 2023-07-22T16:39:53,139 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2023-07-22T16:39:53,139 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-07-22T16:39:53,139 | ^~~~~~~~~~~~ 2023-07-22T16:39:53,139 mdtraj/formats/dtr/src/dtrplugin.cxx:665:13: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2023-07-22T16:39:53,139 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-07-22T16:39:53,140 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:55,853 In file included from /usr/include/c++/10/map:61, 2023-07-22T16:39:55,854 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2023-07-22T16:39:55,854 /usr/include/c++/10/bits/stl_map.h: In member function ‘int desres::molfile::DtrReader::frame_from_bytes(const void*, uint64_t, molfile_timestep_t*) const’: 2023-07-22T16:39:55,854 /usr/include/c++/10/bits/stl_map.h:520:37: 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 2023-07-22T16:39:55,854 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-07-22T16:39:55,854 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:55,855 521 | std::forward_as_tuple(std::move(__k)), 2023-07-22T16:39:55,855 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:39:55,855 522 | std::tuple<>()); 2023-07-22T16:39:55,855 | ~~~~~~~~~~~~~~~ 2023-07-22T16:40:00,974 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:40:01,352 building 'mdtraj._rmsd' extension 2023-07-22T16:40:01,353 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd 2023-07-22T16:40:01,354 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src 2023-07-22T16:40:01,356 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:40:35,661 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:40:35,863 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:40:36,114 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:40:36,812 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:40:37,224 building 'mdtraj._lprmsd' extension 2023-07-22T16:40:37,225 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:40:37,494 In file included from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-22T16:40:37,495 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-22T16:40:37,495 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-22T16:40:37,495 from mdtraj/rmsd/_lprmsd.cpp:809: 2023-07-22T16:40:37,495 /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-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] 2023-07-22T16:40:37,495 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-22T16:40:37,495 | ^~~~~~~ 2023-07-22T16:40:48,153 mdtraj/rmsd/_lprmsd.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: 2023-07-22T16:40:48,153 mdtraj/rmsd/_lprmsd.cpp:4099:14: warning: ‘__pyx_pybuffernd_ref_xyz_frame_dis.__Pyx_LocalBuf_ND::diminfo[0].__Pyx_Buf_DimInfo::shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:40:48,153 4099 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; 2023-07-22T16:40:48,153 | ^~ 2023-07-22T16:40:58,684 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:01,089 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:01,294 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:02,321 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:02,614 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:02,860 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:03,560 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:41:03,885 building 'mdtraj.core.lib.libtheobald' extension 2023-07-22T16:41:03,886 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2023-07-22T16:41:04,547 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2023-07-22T16:41:04,751 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o 2023-07-22T16:41:04,789 building 'mdtraj.geometry._geometry' extension 2023-07-22T16:41:04,790 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-22T16:41:04,791 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src 2023-07-22T16:41:04,792 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:05,054 In file included from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-22T16:41:05,054 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-22T16:41:05,054 from /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-22T16:41:05,054 from mdtraj/geometry/src/_geometry.cpp:811: 2023-07-22T16:41:05,054 /tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-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] 2023-07-22T16:41:05,055 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-22T16:41:05,055 | ^~~~~~~ 2023-07-22T16:41:10,340 mdtraj/geometry/src/_geometry.cpp: In function ‘void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’: 2023-07-22T16:41:10,340 mdtraj/geometry/src/_geometry.cpp:6099:224: warning: ‘__pyx_v_delta[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:41:10,340 6099 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); 2023-07-22T16:41:10,341 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:41:10,341 mdtraj/geometry/src/_geometry.cpp:6113:277: warning: ‘__pyx_v_delta[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:41:10,341 6113 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); 2023-07-22T16:41:10,341 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-07-22T16:41:10,341 mdtraj/geometry/src/_geometry.cpp:6113:277: warning: ‘__pyx_v_offset[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:41:34,108 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:50,434 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:53,931 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:41:54,944 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/sasa.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:41:55,368 building 'mdtraj.geometry.drid' extension 2023-07-22T16:41:55,369 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:42:19,751 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:42:20,332 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:42:20,451 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/moments.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:42:20,784 building 'mdtraj.geometry.neighbors' extension 2023-07-22T16:42:20,785 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:42:43,714 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:42:44,850 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighbors.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:42:45,174 building 'mdtraj.geometry.neighborlist' extension 2023-07-22T16:42:45,175 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:43:05,504 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-_vmb_5d0/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-22T16:43:09,772 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2023-07-22T16:43:09,772 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors[0][0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:43:09,773 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2023-07-22T16:43:09,773 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-07-22T16:43:09,773 mdtraj/geometry/src/neighborlist.cpp:51:53: warning: ‘periodicBoxVectors[1][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:43:09,773 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; 2023-07-22T16:43:09,773 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-07-22T16:43:09,773 mdtraj/geometry/src/neighborlist.cpp:52:53: warning: ‘periodicBoxVectors[2][2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:43:09,774 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; 2023-07-22T16:43:09,774 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-07-22T16:43:09,774 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors[0][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-22T16:43:09,774 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2023-07-22T16:43:09,774 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-07-22T16:43:10,767 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighborlist.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so 2023-07-22T16:43:11,155 installing to build/bdist.linux-armv7l/wheel 2023-07-22T16:43:11,155 running install 2023-07-22T16:43:11,180 running install_lib 2023-07-22T16:43:11,189 creating build/bdist.linux-armv7l 2023-07-22T16:43:11,190 creating build/bdist.linux-armv7l/wheel 2023-07-22T16:43:11,192 creating build/bdist.linux-armv7l/wheel/mdtraj 2023-07-22T16:43:11,193 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-07-22T16:43:11,194 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-07-22T16:43:11,197 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-07-22T16:43:11,199 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-07-22T16:43:11,202 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,202 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,205 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/six.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,207 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,209 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,211 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,213 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,216 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,218 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,219 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,221 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,223 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,226 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,228 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,230 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,233 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,235 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,238 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,241 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,243 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,245 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,247 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-22T16:43:11,249 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,251 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-22T16:43:11,254 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,255 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,257 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,260 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,291 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,293 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,296 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,340 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,342 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,345 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,408 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,410 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,412 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,434 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,437 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,439 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,442 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,444 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,446 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,448 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-22T16:43:11,451 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-22T16:43:11,452 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-22T16:43:11,454 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-22T16:43:11,456 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-22T16:43:11,458 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-22T16:43:11,460 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-22T16:43:11,462 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-22T16:43:11,464 copying build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-22T16:43:11,495 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-22T16:43:11,496 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-22T16:43:11,499 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-22T16:43:11,502 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-22T16:43:11,506 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-22T16:43:11,508 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-22T16:43:11,511 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-07-22T16:43:11,512 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-07-22T16:43:11,514 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-07-22T16:43:11,516 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-07-22T16:43:11,519 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-22T16:43:11,521 copying build/lib.linux-armv7l-cpython-39/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-22T16:43:11,524 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,525 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,542 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,561 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,598 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,601 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,604 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,608 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-07-22T16:43:11,609 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-07-22T16:43:11,613 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-07-22T16:43:11,614 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-07-22T16:43:11,616 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-07-22T16:43:11,619 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-07-22T16:43:11,622 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-07-22T16:43:11,623 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,625 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,628 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,631 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,655 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,689 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,691 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,693 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,695 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,723 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,726 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,728 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,730 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,732 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,734 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,737 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,739 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,742 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-22T16:43:11,744 copying build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-22T16:43:11,764 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-22T16:43:11,766 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-22T16:43:11,768 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-22T16:43:11,771 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-22T16:43:11,773 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-22T16:43:11,775 copying build/lib.linux-armv7l-cpython-39/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-22T16:43:11,777 copying build/lib.linux-armv7l-cpython-39/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-22T16:43:11,780 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-07-22T16:43:11,781 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-07-22T16:43:11,785 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-07-22T16:43:11,788 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-07-22T16:43:11,790 running install_egg_info 2023-07-22T16:43:11,832 running egg_info 2023-07-22T16:43:11,841 writing mdtraj.egg-info/PKG-INFO 2023-07-22T16:43:11,843 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2023-07-22T16:43:11,846 writing entry points to mdtraj.egg-info/entry_points.txt 2023-07-22T16:43:11,848 writing requirements to mdtraj.egg-info/requires.txt 2023-07-22T16:43:11,850 writing top-level names to mdtraj.egg-info/top_level.txt 2023-07-22T16:43:11,907 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-07-22T16:43:11,933 reading manifest template 'MANIFEST.in' 2023-07-22T16:43:12,720 no previously-included directories found matching '__pycache__' 2023-07-22T16:43:12,722 no previously-included directories found matching '*.pyc' 2023-07-22T16:43:12,723 adding license file 'LICENSE' 2023-07-22T16:43:12,741 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-07-22T16:43:12,743 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.9.9-py3.9.egg-info 2023-07-22T16:43:12,757 running install_scripts 2023-07-22T16:43:12,809 creating build/bdist.linux-armv7l/wheel/mdtraj-1.9.9.dist-info/WHEEL 2023-07-22T16:43:12,813 creating '/tmp/pip-wheel-5x0w5wg8/.tmp-xtkhbxyl/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-07-22T16:43:12,815 adding 'mdtraj/__init__.py' 2023-07-22T16:43:13,063 adding 'mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:13,442 adding 'mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:13,456 adding 'mdtraj/io.py' 2023-07-22T16:43:13,458 adding 'mdtraj/version.py' 2023-07-22T16:43:13,460 adding 'mdtraj/core/__init__.py' 2023-07-22T16:43:13,463 adding 'mdtraj/core/element.py' 2023-07-22T16:43:13,466 adding 'mdtraj/core/residue_names.py' 2023-07-22T16:43:13,469 adding 'mdtraj/core/selection.py' 2023-07-22T16:43:13,477 adding 'mdtraj/core/topology.py' 2023-07-22T16:43:13,487 adding 'mdtraj/core/trajectory.py' 2023-07-22T16:43:13,489 adding 'mdtraj/core/lib/center.h' 2023-07-22T16:43:13,499 adding 'mdtraj/core/lib/libtheobald.a' 2023-07-22T16:43:13,502 adding 'mdtraj/core/lib/theobald_rmsd.h' 2023-07-22T16:43:13,504 adding 'mdtraj/formats/__init__.py' 2023-07-22T16:43:13,508 adding 'mdtraj/formats/amberrst.py' 2023-07-22T16:43:13,511 adding 'mdtraj/formats/arc.py' 2023-07-22T16:43:13,652 adding 'mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:13,817 adding 'mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:14,247 adding 'mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:14,265 adding 'mdtraj/formats/gro.py' 2023-07-22T16:43:14,267 adding 'mdtraj/formats/gsd.py' 2023-07-22T16:43:14,272 adding 'mdtraj/formats/hdf5.py' 2023-07-22T16:43:14,274 adding 'mdtraj/formats/hoomdxml.py' 2023-07-22T16:43:14,278 adding 'mdtraj/formats/lammpstrj.py' 2023-07-22T16:43:14,281 adding 'mdtraj/formats/lh5.py' 2023-07-22T16:43:14,284 adding 'mdtraj/formats/mdcrd.py' 2023-07-22T16:43:14,286 adding 'mdtraj/formats/mol2.py' 2023-07-22T16:43:14,289 adding 'mdtraj/formats/netcdf.py' 2023-07-22T16:43:14,291 adding 'mdtraj/formats/openmmxml.py' 2023-07-22T16:43:14,294 adding 'mdtraj/formats/pdbx.py' 2023-07-22T16:43:14,297 adding 'mdtraj/formats/prmtop.py' 2023-07-22T16:43:14,299 adding 'mdtraj/formats/psf.py' 2023-07-22T16:43:14,301 adding 'mdtraj/formats/registry.py' 2023-07-22T16:43:14,721 adding 'mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:15,011 adding 'mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:15,285 adding 'mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:15,296 adding 'mdtraj/formats/xyzfile.py' 2023-07-22T16:43:15,298 adding 'mdtraj/formats/pdb/__init__.py' 2023-07-22T16:43:15,303 adding 'mdtraj/formats/pdb/pdbfile.py' 2023-07-22T16:43:15,308 adding 'mdtraj/formats/pdb/pdbstructure.py' 2023-07-22T16:43:15,311 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2023-07-22T16:43:15,313 adding 'mdtraj/formats/pdb/data/residues.xml' 2023-07-22T16:43:15,316 adding 'mdtraj/geometry/__init__.py' 2023-07-22T16:43:15,850 adding 'mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:15,871 adding 'mdtraj/geometry/alignment.py' 2023-07-22T16:43:15,873 adding 'mdtraj/geometry/angle.py' 2023-07-22T16:43:15,876 adding 'mdtraj/geometry/contact.py' 2023-07-22T16:43:15,878 adding 'mdtraj/geometry/dihedral.py' 2023-07-22T16:43:15,881 adding 'mdtraj/geometry/distance.py' 2023-07-22T16:43:16,169 adding 'mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:16,180 adding 'mdtraj/geometry/dssp.py' 2023-07-22T16:43:16,183 adding 'mdtraj/geometry/hbond.py' 2023-07-22T16:43:16,186 adding 'mdtraj/geometry/internal.py' 2023-07-22T16:43:16,492 adding 'mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:16,783 adding 'mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so' 2023-07-22T16:43:16,794 adding 'mdtraj/geometry/order.py' 2023-07-22T16:43:16,796 adding 'mdtraj/geometry/rdf.py' 2023-07-22T16:43:16,798 adding 'mdtraj/geometry/rg.py' 2023-07-22T16:43:16,801 adding 'mdtraj/geometry/sasa.py' 2023-07-22T16:43:16,802 adding 'mdtraj/geometry/shape.py' 2023-07-22T16:43:16,805 adding 'mdtraj/geometry/thermodynamic_properties.py' 2023-07-22T16:43:16,807 adding 'mdtraj/nmr/__init__.py' 2023-07-22T16:43:16,809 adding 'mdtraj/nmr/scalar_couplings.py' 2023-07-22T16:43:16,811 adding 'mdtraj/nmr/shift_wrappers.py' 2023-07-22T16:43:16,814 adding 'mdtraj/reporters/__init__.py' 2023-07-22T16:43:16,816 adding 'mdtraj/reporters/basereporter.py' 2023-07-22T16:43:16,818 adding 'mdtraj/reporters/dcdreporter.py' 2023-07-22T16:43:16,820 adding 'mdtraj/reporters/hdf5reporter.py' 2023-07-22T16:43:16,821 adding 'mdtraj/reporters/netcdfreporter.py' 2023-07-22T16:43:16,823 adding 'mdtraj/reporters/xtcreporter.py' 2023-07-22T16:43:16,825 adding 'mdtraj/scripts/__init__.py' 2023-07-22T16:43:16,828 adding 'mdtraj/scripts/mdconvert.py' 2023-07-22T16:43:16,831 adding 'mdtraj/scripts/mdinspect.py' 2023-07-22T16:43:16,833 adding 'mdtraj/testing/__init__.py' 2023-07-22T16:43:16,836 adding 'mdtraj/testing/docscrape.py' 2023-07-22T16:43:16,838 adding 'mdtraj/testing/docstrings.py' 2023-07-22T16:43:16,840 adding 'mdtraj/testing/testing.py' 2023-07-22T16:43:16,843 adding 'mdtraj/utils/__init__.py' 2023-07-22T16:43:16,846 adding 'mdtraj/utils/contextmanagers.py' 2023-07-22T16:43:16,848 adding 'mdtraj/utils/delay_import.py' 2023-07-22T16:43:16,850 adding 'mdtraj/utils/rotation.py' 2023-07-22T16:43:16,851 adding 'mdtraj/utils/singleton.py' 2023-07-22T16:43:16,854 adding 'mdtraj/utils/six.py' 2023-07-22T16:43:16,856 adding 'mdtraj/utils/unitcell.py' 2023-07-22T16:43:16,859 adding 'mdtraj/utils/validation.py' 2023-07-22T16:43:16,860 adding 'mdtraj/utils/zipped.py' 2023-07-22T16:43:16,863 adding 'mdtraj/utils/unit/__init__.py' 2023-07-22T16:43:16,865 adding 'mdtraj/utils/unit/basedimension.py' 2023-07-22T16:43:16,867 adding 'mdtraj/utils/unit/baseunit.py' 2023-07-22T16:43:16,869 adding 'mdtraj/utils/unit/constants.py' 2023-07-22T16:43:16,872 adding 'mdtraj/utils/unit/doctests.py' 2023-07-22T16:43:16,875 adding 'mdtraj/utils/unit/mymatrix.py' 2023-07-22T16:43:16,877 adding 'mdtraj/utils/unit/prefix.py' 2023-07-22T16:43:16,881 adding 'mdtraj/utils/unit/quantity.py' 2023-07-22T16:43:16,883 adding 'mdtraj/utils/unit/standard_dimensions.py' 2023-07-22T16:43:16,887 adding 'mdtraj/utils/unit/unit.py' 2023-07-22T16:43:16,890 adding 'mdtraj/utils/unit/unit_definitions.py' 2023-07-22T16:43:16,892 adding 'mdtraj/utils/unit/unit_math.py' 2023-07-22T16:43:16,894 adding 'mdtraj/utils/unit/unit_operators.py' 2023-07-22T16:43:16,899 adding 'mdtraj-1.9.9.dist-info/LICENSE' 2023-07-22T16:43:16,901 adding 'mdtraj-1.9.9.dist-info/METADATA' 2023-07-22T16:43:16,902 adding 'mdtraj-1.9.9.dist-info/WHEEL' 2023-07-22T16:43:16,903 adding 'mdtraj-1.9.9.dist-info/entry_points.txt' 2023-07-22T16:43:16,905 adding 'mdtraj-1.9.9.dist-info/top_level.txt' 2023-07-22T16:43:16,907 adding 'mdtraj-1.9.9.dist-info/RECORD' 2023-07-22T16:43:16,983 removing build/bdist.linux-armv7l/wheel 2023-07-22T16:43:17,750 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2023-07-22T16:43:17,887 Created wheel for mdtraj: filename=mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl size=7084028 sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac 2023-07-22T16:43:17,888 Stored in directory: /tmp/pip-ephem-wheel-cache-qlvw2l2r/wheels/3b/ee/4a/ecfa133b4736856518fe1312dad4fa1dcfc24f718086bbbfa3 2023-07-22T16:43:17,905 Successfully built mdtraj 2023-07-22T16:43:18,066 Removed build tracker: '/tmp/pip-build-tracker-l9pb_0if'