2024-05-17T13:44:13,255 Created temporary directory: /tmp/pip-build-tracker-n39ep4mn 2024-05-17T13:44:13,256 Initialized build tracking at /tmp/pip-build-tracker-n39ep4mn 2024-05-17T13:44:13,257 Created build tracker: /tmp/pip-build-tracker-n39ep4mn 2024-05-17T13:44:13,257 Entered build tracker: /tmp/pip-build-tracker-n39ep4mn 2024-05-17T13:44:13,257 Created temporary directory: /tmp/pip-wheel-vvcs_07f 2024-05-17T13:44:13,261 Created temporary directory: /tmp/pip-ephem-wheel-cache-8qdxe4wr 2024-05-17T13:44:13,288 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-17T13:44:13,292 2 location(s) to search for versions of mdtraj: 2024-05-17T13:44:13,292 * https://pypi.org/simple/mdtraj/ 2024-05-17T13:44:13,292 * https://www.piwheels.org/simple/mdtraj/ 2024-05-17T13:44:13,292 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2024-05-17T13:44:13,293 Getting page https://pypi.org/simple/mdtraj/ 2024-05-17T13:44:13,295 Found index url 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https://files.pythonhosted.org/packages/3b/fd/4ffba665d0b0346072f61d0e8ef7ab281202db445d99136c717c89169a97/mdtraj-1.9.5-cp38-cp38-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T13:44:13,380 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/68/53/2f666107565f4735abd859b6af6867353eb08d0e9728d90fb0abc12d578e/mdtraj-1.9.5-cp39-cp39-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T13:44:13,380 Found link https://files.pythonhosted.org/packages/d8/cb/5dcc31c7e2c4485bd2aea66233def28954f2dc530607f5c43fefab71a963/mdtraj-1.9.5.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.5 2024-05-17T13:44:13,381 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/fe/a7/2a1392fe56ddd22a9cf5dcff7d684bdd7ce146d5c32839080dd8de7122dd/mdtraj-1.9.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T13:44:13,381 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/ce/ee/2015ff88cacb7c75b5e1cf6a57e8a089549b0e76bcd9474a08845f7ef12f/mdtraj-1.9.6-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T13:44:13,381 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/c0/61/2fb002b9b2ab90567eb1a837ed510152ddadd5b8358ac800b591e37675e0/mdtraj-1.9.6-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T13:44:13,381 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/09/49/85dc22a3c28108dfd0bce8a4268ae3937167b18fac531a0d801505cad7d9/mdtraj-1.9.6-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T13:44:13,381 Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.6 2024-05-17T13:44:13,382 Found link https://files.pythonhosted.org/packages/2f/03/c174bfb6471f796472ce1d8695f6c0d1a20ad6516cb789b70052df45b7a6/mdtraj-1.9.7.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.7 2024-05-17T13:44:13,382 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/5d/1c/75a4c0ec4fb42e5daafaf13a49c03194f76b7deb0134d894a5004d833446/mdtraj-1.9.8-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T13:44:13,382 Found link https://files.pythonhosted.org/packages/53/02/a30f67a8bd3dba6d6e4ecc02bee290f425bf30c504a8a959a04e2be321ac/mdtraj-1.9.8.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.8 2024-05-17T13:44:13,382 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/88/12/ecbe28c87bc3df8c4880cc742923a6f40633ca076c8f44b03533dfce0b66/mdtraj-1.9.9-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-17T13:44:13,382 Found link https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.9 2024-05-17T13:44:13,383 Found link https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.10.0rc1 2024-05-17T13:44:13,383 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2024-05-17T13:44:13,383 Getting page https://www.piwheels.org/simple/mdtraj/ 2024-05-17T13:44:13,384 Found index url https://www.piwheels.org/simple/ 2024-05-17T13:44:13,550 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2024-05-17T13:44:13,555 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp37-cp37m-linux_armv6l.whl#sha256=355ab9108c6d079032d3b97eaa3ad76e261893dcd45a07b62c5e8a493600e06d (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,555 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp37-cp37m-linux_armv7l.whl#sha256=355ab9108c6d079032d3b97eaa3ad76e261893dcd45a07b62c5e8a493600e06d (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,555 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv6l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,556 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,556 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv6l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,556 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv7l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,556 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv6l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,556 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,557 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv6l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,557 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,557 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,557 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv7l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,557 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv6l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,558 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-17T13:44:13,558 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2024-05-17T13:44:13,558 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2024-05-17T13:44:13,584 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2024-05-17T13:44:13,601 Collecting mdtraj==1.10.0rc1 2024-05-17T13:44:13,603 Created temporary directory: /tmp/pip-unpack-smg3v9h4 2024-05-17T13:44:13,647 Downloading mdtraj-1.10.0rc1.tar.gz (1.8 MB) 2024-05-17T13:44:14,709 Added mdtraj==1.10.0rc1 from https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz to build tracker '/tmp/pip-build-tracker-n39ep4mn' 2024-05-17T13:44:14,715 Created temporary directory: /tmp/pip-build-env-yz9spj33 2024-05-17T13:44:14,725 Installing build dependencies: started 2024-05-17T13:44:14,726 Running command pip subprocess to install build dependencies 2024-05-17T13:44:15,886 Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2024-05-17T13:44:16,405 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-17T13:44:17,891 Collecting setuptools 2024-05-17T13:44:17,909 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.5.1-py3-none-any.whl (894 kB) 2024-05-17T13:44:18,163 Collecting wheel 2024-05-17T13:44:18,179 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-05-17T13:44:18,307 Collecting oldest-supported-numpy 2024-05-17T13:44:18,345 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2023.12.21-py3-none-any.whl (4.9 kB) 2024-05-17T13:44:19,761 Collecting Cython~=0.29.36 2024-05-17T13:44:19,779 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.37-cp39-cp39-linux_armv7l.whl (4.9 MB) 2024-05-17T13:44:21,378 Collecting numpy==1.19.3 (from oldest-supported-numpy) 2024-05-17T13:44:21,396 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB) 2024-05-17T13:44:23,514 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2024-05-17T13:44:23,735 Creating /tmp/pip-build-env-yz9spj33/overlay/bin 2024-05-17T13:44:23,737 changing mode of /tmp/pip-build-env-yz9spj33/overlay/bin/wheel to 755 2024-05-17T13:44:33,729 changing mode of /tmp/pip-build-env-yz9spj33/overlay/bin/f2py to 755 2024-05-17T13:44:33,731 changing mode of /tmp/pip-build-env-yz9spj33/overlay/bin/f2py3 to 755 2024-05-17T13:44:33,733 changing mode of /tmp/pip-build-env-yz9spj33/overlay/bin/f2py3.9 to 755 2024-05-17T13:44:36,411 changing mode of /tmp/pip-build-env-yz9spj33/overlay/bin/cygdb to 755 2024-05-17T13:44:36,414 changing mode of /tmp/pip-build-env-yz9spj33/overlay/bin/cython to 755 2024-05-17T13:44:36,416 changing mode of /tmp/pip-build-env-yz9spj33/overlay/bin/cythonize to 755 2024-05-17T13:44:36,458 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. 2024-05-17T13:44:36,458 scipy 1.13.0 requires numpy<2.3,>=1.22.4, but you have numpy 1.19.3 which is incompatible. 2024-05-17T13:44:36,459 Successfully installed Cython-0.29.37 numpy-1.19.3 oldest-supported-numpy-2023.12.21 setuptools-69.5.1 wheel-0.43.0 2024-05-17T13:44:37,105 Installing build dependencies: finished with status 'done' 2024-05-17T13:44:37,115 Getting requirements to build wheel: started 2024-05-17T13:44:37,116 Running command Getting requirements to build wheel 2024-05-17T13:44:37,844 Using built-in specs. 2024-05-17T13:44:37,844 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-17T13:44:37,845 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-17T13:44:37,845 Target: arm-linux-gnueabihf 2024-05-17T13:44:37,845 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 2024-05-17T13:44:37,845 Thread model: posix 2024-05-17T13:44:37,845 Supported LTO compression algorithms: zlib zstd 2024-05-17T13:44:37,845 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-17T13:44:41,984 C compiler: 2024-05-17T13:44:41,984 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-17T13:44:41,984 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-17T13:44:41,985 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-17T13:44:41,985 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-17T13:44:41,985 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-17T13:44:41,985 running egg_info 2024-05-17T13:44:41,991 writing mdtraj.egg-info/PKG-INFO 2024-05-17T13:44:41,994 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-17T13:44:41,996 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-17T13:44:41,997 writing requirements to mdtraj.egg-info/requires.txt 2024-05-17T13:44:41,998 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-17T13:44:42,041 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-17T13:44:42,064 reading manifest template 'MANIFEST.in' 2024-05-17T13:44:42,685 no previously-included directories found matching '__pycache__' 2024-05-17T13:44:42,687 no previously-included directories found matching '*.pyc' 2024-05-17T13:44:42,687 adding license file 'LICENSE' 2024-05-17T13:44:42,701 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-17T13:44:42,786 Getting requirements to build wheel: finished with status 'done' 2024-05-17T13:44:42,795 Created temporary directory: /tmp/pip-modern-metadata-2gyj7mkz 2024-05-17T13:44:42,798 Preparing metadata (pyproject.toml): started 2024-05-17T13:44:42,799 Running command Preparing metadata (pyproject.toml) 2024-05-17T13:44:43,516 Using built-in specs. 2024-05-17T13:44:43,516 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-17T13:44:43,517 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-17T13:44:43,517 Target: arm-linux-gnueabihf 2024-05-17T13:44:43,517 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 2024-05-17T13:44:43,517 Thread model: posix 2024-05-17T13:44:43,517 Supported LTO compression algorithms: zlib zstd 2024-05-17T13:44:43,517 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-17T13:44:47,494 /tmp/pip-wheel-vvcs_07f/mdtraj_e4327fcf02b84bbcb069eb6e70cb76e6/basesetup.py:503: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-2gyj7mkz --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2024-05-17T13:44:47,495 warnings.warn( 2024-05-17T13:44:49,394 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T13:44:49,394 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T13:44:49,394 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T13:45:13,077 C compiler: 2024-05-17T13:45:13,077 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-17T13:45:13,077 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-17T13:45:13,078 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-17T13:45:13,078 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-17T13:45:13,078 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-17T13:45:13,078 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-17T13:45:13,078 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-17T13:45:13,078 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-17T13:45:13,079 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-17T13:45:13,079 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-17T13:45:13,079 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-17T13:45:13,079 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-17T13:45:13,079 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-17T13:45:13,079 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-17T13:45:13,079 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-17T13:45:13,176 running dist_info 2024-05-17T13:45:13,183 creating /tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info 2024-05-17T13:45:13,189 writing /tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info/PKG-INFO 2024-05-17T13:45:13,193 writing dependency_links to /tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info/dependency_links.txt 2024-05-17T13:45:13,194 writing entry points to /tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info/entry_points.txt 2024-05-17T13:45:13,196 writing requirements to /tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info/requires.txt 2024-05-17T13:45:13,197 writing top-level names to /tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info/top_level.txt 2024-05-17T13:45:13,198 writing manifest file '/tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info/SOURCES.txt' 2024-05-17T13:45:13,247 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,247 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,248 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,248 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,248 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,248 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,248 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,248 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,249 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,249 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,250 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,250 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:45:13,264 reading manifest file '/tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info/SOURCES.txt' 2024-05-17T13:45:13,266 reading manifest template 'MANIFEST.in' 2024-05-17T13:45:13,842 no previously-included directories found matching '__pycache__' 2024-05-17T13:45:13,843 no previously-included directories found matching '*.pyc' 2024-05-17T13:45:13,843 adding license file 'LICENSE' 2024-05-17T13:45:13,854 writing manifest file '/tmp/pip-modern-metadata-2gyj7mkz/mdtraj.egg-info/SOURCES.txt' 2024-05-17T13:45:13,856 creating '/tmp/pip-modern-metadata-2gyj7mkz/mdtraj-1.10.0rc1.dist-info' 2024-05-17T13:45:14,641 Preparing metadata (pyproject.toml): finished with status 'done' 2024-05-17T13:45:14,648 Source in /tmp/pip-wheel-vvcs_07f/mdtraj_e4327fcf02b84bbcb069eb6e70cb76e6 has version 1.10.0rc1, which satisfies requirement mdtraj==1.10.0rc1 from https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz 2024-05-17T13:45:14,649 Removed mdtraj==1.10.0rc1 from https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz from build tracker '/tmp/pip-build-tracker-n39ep4mn' 2024-05-17T13:45:14,653 Created temporary directory: /tmp/pip-unpack-ruumrfei 2024-05-17T13:45:14,654 Created temporary directory: /tmp/pip-unpack-1o168tol 2024-05-17T13:45:14,663 Building wheels for collected packages: mdtraj 2024-05-17T13:45:14,667 Created temporary directory: /tmp/pip-wheel-9or1if6t 2024-05-17T13:45:14,667 Destination directory: /tmp/pip-wheel-9or1if6t 2024-05-17T13:45:14,669 Building wheel for mdtraj (pyproject.toml): started 2024-05-17T13:45:14,670 Running command Building wheel for mdtraj (pyproject.toml) 2024-05-17T13:45:15,377 Using built-in specs. 2024-05-17T13:45:15,378 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-17T13:45:15,378 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-17T13:45:15,378 Target: arm-linux-gnueabihf 2024-05-17T13:45:15,378 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 2024-05-17T13:45:15,379 Thread model: posix 2024-05-17T13:45:15,379 Supported LTO compression algorithms: zlib zstd 2024-05-17T13:45:15,379 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-17T13:45:21,050 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T13:45:21,050 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T13:45:21,050 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-17T13:45:47,022 C compiler: 2024-05-17T13:45:47,022 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-17T13:45:47,022 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-17T13:45:47,022 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-17T13:45:47,023 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-17T13:45:47,023 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-17T13:45:47,023 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-17T13:45:47,023 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-17T13:45:47,023 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-17T13:45:47,023 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-17T13:45:47,024 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-17T13:45:47,024 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-17T13:45:47,024 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-17T13:45:47,024 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-17T13:45:47,024 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-17T13:45:47,024 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-17T13:45:47,147 running bdist_wheel 2024-05-17T13:45:47,186 running build 2024-05-17T13:45:47,186 running build_py 2024-05-17T13:45:47,196 creating build 2024-05-17T13:45:47,197 creating build/lib.linux-armv7l-cpython-39 2024-05-17T13:45:47,198 creating build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-17T13:45:47,199 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-17T13:45:47,201 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-17T13:45:47,203 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-17T13:45:47,206 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,207 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,209 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,211 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,213 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,215 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,218 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,219 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,222 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-17T13:45:47,224 creating build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-17T13:45:47,225 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-17T13:45:47,227 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-17T13:45:47,229 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-17T13:45:47,231 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-17T13:45:47,234 creating build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-17T13:45:47,235 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-17T13:45:47,237 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-17T13:45:47,239 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-17T13:45:47,242 creating build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-17T13:45:47,243 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-17T13:45:47,246 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-17T13:45:47,248 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-17T13:45:47,250 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-17T13:45:47,254 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-17T13:45:47,256 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-17T13:45:47,260 creating build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-17T13:45:47,261 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-17T13:45:47,263 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-17T13:45:47,266 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-17T13:45:47,268 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-17T13:45:47,270 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-17T13:45:47,272 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-17T13:45:47,275 creating build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-17T13:45:47,276 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-17T13:45:47,278 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-17T13:45:47,280 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-17T13:45:47,283 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,285 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,287 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,290 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,293 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,295 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,298 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,301 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,304 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,306 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,309 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,313 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,316 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,319 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,322 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,324 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,327 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,329 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,332 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,336 creating build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,337 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,340 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,343 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,345 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,348 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,350 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,353 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,356 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,358 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,360 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,363 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,365 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,367 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,370 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,372 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:45:47,376 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,377 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,380 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,383 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,385 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,388 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,391 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,393 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,395 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,398 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,400 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,402 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,405 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,408 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-17T13:45:47,411 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-17T13:45:47,413 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-17T13:45:47,416 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-17T13:45:47,418 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-17T13:45:47,426 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-17T13:45:47,428 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-17T13:45:47,431 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-17T13:45:47,441 running build_ext 2024-05-17T13:45:47,445 building 'mdtraj.formats.xtc' extension 2024-05-17T13:45:47,446 creating build/temp.linux-armv7l-cpython-39 2024-05-17T13:45:47,447 creating build/temp.linux-armv7l-cpython-39/mdtraj 2024-05-17T13:45:47,448 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats 2024-05-17T13:45:47,449 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc 2024-05-17T13:45:47,449 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src 2024-05-17T13:45:47,451 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-yz9spj33/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 2024-05-17T13:45:47,575 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-yz9spj33/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 2024-05-17T13:45:47,717 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-17T13:45:47,718 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:45:47,718 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-17T13:45:47,718 | ^~~~~~ 2024-05-17T13:45:47,718 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:45:47,718 785 | int smallidx, minidx, maxidx; 2024-05-17T13:45:47,718 | ^~~~~~ 2024-05-17T13:45:47,725 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-17T13:45:47,725 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:45:47,725 1016 | int errval=1; 2024-05-17T13:45:47,725 | ^~~~~~ 2024-05-17T13:45:47,729 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-17T13:45:47,730 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:45:47,730 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-17T13:45:47,730 | ^~~~~~ 2024-05-17T13:45:47,730 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:45:47,731 1302 | int smallidx, minidx, maxidx; 2024-05-17T13:45:47,731 | ^~~~~~ 2024-05-17T13:45:47,739 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-17T13:45:47,740 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:45:47,740 1509 | int errval=1; 2024-05-17T13:45:47,740 | ^~~~~~ 2024-05-17T13:45:50,088 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-yz9spj33/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 2024-05-17T13:45:50,167 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2024-05-17T13:45:50,167 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2024-05-17T13:45:50,167 66 | int i,j,result; 2024-05-17T13:45:50,168 | ^ 2024-05-17T13:45:50,168 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2024-05-17T13:45:50,168 66 | int i,j,result; 2024-05-17T13:45:50,168 | ^ 2024-05-17T13:45:50,169 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2024-05-17T13:45:50,169 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2024-05-17T13:45:50,169 119 | if (NULL == xd) 2024-05-17T13:45:50,169 | ^~ 2024-05-17T13:45:50,169 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’ 2024-05-17T13:45:50,170 122 | do { 2024-05-17T13:45:50,170 | ^~ 2024-05-17T13:45:50,308 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-yz9spj33/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 2024-05-17T13:45:50,639 In file included from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-17T13:45:50,640 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T13:45:50,640 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-17T13:45:50,640 from mdtraj/formats/xtc/xtc.c:781: 2024-05-17T13:45:50,640 /tmp/pip-build-env-yz9spj33/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] 2024-05-17T13:45:50,640 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T13:45:50,640 | ^~~~~~~ 2024-05-17T13:45:57,147 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2024-05-17T13:45:57,148 mdtraj/formats/xtc/xtc.c:693:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:45:57,148 693 | #define PyInt_FromLong PyLong_FromLong 2024-05-17T13:45:57,148 | ^~~~~~~~~~~~~~~ 2024-05-17T13:45:57,153 mdtraj/formats/xtc/xtc.c:9547:7: note: ‘__pyx_v_status’ was declared here 2024-05-17T13:45:57,153 9547 | int __pyx_v_status; 2024-05-17T13:45:57,153 | ^~~~~~~~~~~~~~ 2024-05-17T13:46:06,536 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2024-05-17T13:46:06,541 mdtraj/formats/xtc/xtc.c:8066:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,541 8066 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-17T13:46:06,541 | ^ 2024-05-17T13:46:06,546 mdtraj/formats/xtc/xtc.c:8062:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,546 8062 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-17T13:46:06,546 | ^ 2024-05-17T13:46:06,550 mdtraj/formats/xtc/xtc.c:8058:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,551 8058 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T13:46:06,551 | ^ 2024-05-17T13:46:06,555 mdtraj/formats/xtc/xtc.c:8018:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,555 8018 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T13:46:06,556 | ^ 2024-05-17T13:46:06,560 mdtraj/formats/xtc/xtc.c:8000:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,560 8000 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T13:46:06,560 | ^ 2024-05-17T13:46:06,564 mdtraj/formats/xtc/xtc.c:8076:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,564 8076 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T13:46:06,564 | ^ 2024-05-17T13:46:06,569 mdtraj/formats/xtc/xtc.c:8038:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,569 8038 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-17T13:46:06,569 | ^ 2024-05-17T13:46:06,574 mdtraj/formats/xtc/xtc.c:8034:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,574 8034 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-17T13:46:06,574 | ^ 2024-05-17T13:46:06,578 mdtraj/formats/xtc/xtc.c:8030:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,579 8030 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T13:46:06,579 | ^ 2024-05-17T13:46:06,583 mdtraj/formats/xtc/xtc.c:7653:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,583 7653 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-17T13:46:06,583 | ^ 2024-05-17T13:46:06,588 mdtraj/formats/xtc/xtc.c:7649:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:06,588 7649 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-17T13:46:06,588 | ^ 2024-05-17T13:46:11,145 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 2024-05-17T13:46:11,308 building 'mdtraj.formats.trr' extension 2024-05-17T13:46:11,309 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-yz9spj33/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 2024-05-17T13:46:11,422 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-yz9spj33/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 2024-05-17T13:46:11,551 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-17T13:46:11,552 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:46:11,552 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-17T13:46:11,552 | ^~~~~~ 2024-05-17T13:46:11,552 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:46:11,553 785 | int smallidx, minidx, maxidx; 2024-05-17T13:46:11,553 | ^~~~~~ 2024-05-17T13:46:11,560 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-17T13:46:11,561 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:46:11,561 1016 | int errval=1; 2024-05-17T13:46:11,561 | ^~~~~~ 2024-05-17T13:46:11,566 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-17T13:46:11,566 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:46:11,567 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-17T13:46:11,567 | ^~~~~~ 2024-05-17T13:46:11,567 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:46:11,568 1302 | int smallidx, minidx, maxidx; 2024-05-17T13:46:11,568 | ^~~~~~ 2024-05-17T13:46:11,577 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-17T13:46:11,578 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-17T13:46:11,578 1509 | int errval=1; 2024-05-17T13:46:11,578 | ^~~~~~ 2024-05-17T13:46:13,689 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-yz9spj33/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 2024-05-17T13:46:14,336 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-yz9spj33/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 2024-05-17T13:46:14,647 In file included from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-17T13:46:14,647 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T13:46:14,647 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-17T13:46:14,647 from mdtraj/formats/xtc/trr.c:781: 2024-05-17T13:46:14,647 /tmp/pip-build-env-yz9spj33/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] 2024-05-17T13:46:14,648 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T13:46:14,648 | ^~~~~~~ 2024-05-17T13:46:21,431 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2024-05-17T13:46:21,431 mdtraj/formats/xtc/trr.c:693:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:21,431 693 | #define PyInt_FromLong PyLong_FromLong 2024-05-17T13:46:21,431 | ^~~~~~~~~~~~~~~ 2024-05-17T13:46:21,437 mdtraj/formats/xtc/trr.c:11073:7: note: ‘__pyx_v_status’ was declared here 2024-05-17T13:46:21,438 11073 | int __pyx_v_status; 2024-05-17T13:46:21,438 | ^~~~~~~~~~~~~~ 2024-05-17T13:46:31,147 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2024-05-17T13:46:31,152 mdtraj/formats/xtc/trr.c:8426:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,152 8426 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-17T13:46:31,153 | ^ 2024-05-17T13:46:31,157 mdtraj/formats/xtc/trr.c:8422:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,158 8422 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T13:46:31,158 | ^ 2024-05-17T13:46:31,158 mdtraj/formats/xtc/trr.c:1929:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,158 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-17T13:46:31,159 | ^ 2024-05-17T13:46:31,162 mdtraj/formats/xtc/trr.c:6963:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-05-17T13:46:31,162 6963 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-17T13:46:31,162 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:46:31,167 mdtraj/formats/xtc/trr.c:8416:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,167 8416 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-05-17T13:46:31,167 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-17T13:46:31,172 mdtraj/formats/xtc/trr.c:8369:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,172 8369 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-17T13:46:31,172 | ^ 2024-05-17T13:46:31,177 mdtraj/formats/xtc/trr.c:8365:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,177 8365 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T13:46:31,177 | ^ 2024-05-17T13:46:31,177 mdtraj/formats/xtc/trr.c:1929:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,178 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-17T13:46:31,178 | ^ 2024-05-17T13:46:31,181 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-05-17T13:46:31,181 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-17T13:46:31,182 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:46:31,186 mdtraj/formats/xtc/trr.c:8359:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,186 8359 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-05-17T13:46:31,186 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-17T13:46:31,190 mdtraj/formats/xtc/trr.c:8759:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,190 8759 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T13:46:31,190 | ^ 2024-05-17T13:46:31,195 mdtraj/formats/xtc/trr.c:8755:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,196 8755 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-17T13:46:31,196 | ^ 2024-05-17T13:46:31,200 mdtraj/formats/xtc/trr.c:8600:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,201 8600 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T13:46:31,201 | ^ 2024-05-17T13:46:31,206 mdtraj/formats/xtc/trr.c:8596:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,206 8596 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-17T13:46:31,206 | ^ 2024-05-17T13:46:31,210 mdtraj/formats/xtc/trr.c:8652:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,210 8652 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-17T13:46:31,210 | ^ 2024-05-17T13:46:31,215 mdtraj/formats/xtc/trr.c:8648:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:31,215 8648 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-17T13:46:31,216 | ^ 2024-05-17T13:46:37,599 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 2024-05-17T13:46:37,773 building 'mdtraj.formats.dcd' extension 2024-05-17T13:46:37,774 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd 2024-05-17T13:46:37,774 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src 2024-05-17T13:46:37,775 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-yz9spj33/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 2024-05-17T13:46:38,091 In file included from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-17T13:46:38,091 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T13:46:38,091 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-17T13:46:38,091 from mdtraj/formats/dcd/dcd.c:779: 2024-05-17T13:46:38,091 /tmp/pip-build-env-yz9spj33/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] 2024-05-17T13:46:38,091 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T13:46:38,092 | ^~~~~~~ 2024-05-17T13:46:45,354 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2024-05-17T13:46:45,355 mdtraj/formats/dcd/dcd.c:691:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:46:45,355 691 | #define PyInt_FromLong PyLong_FromLong 2024-05-17T13:46:45,355 | ^~~~~~~~~~~~~~~ 2024-05-17T13:46:45,357 mdtraj/formats/dcd/dcd.c:5442:7: note: ‘__pyx_v_i’ was declared here 2024-05-17T13:46:45,358 5442 | int __pyx_v_i; 2024-05-17T13:46:45,358 | ^~~~~~~~~ 2024-05-17T13:46:48,450 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-yz9spj33/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 2024-05-17T13:46:49,769 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 2024-05-17T13:46:49,904 building 'mdtraj.formats.dtr' extension 2024-05-17T13:46:49,904 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr 2024-05-17T13:46:49,905 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src 2024-05-17T13:46:49,906 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-yz9spj33/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 2024-05-17T13:46:50,159 In file included from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-17T13:46:50,159 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T13:46:50,159 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-17T13:46:50,160 from mdtraj/formats/dtr/dtr.cpp:800: 2024-05-17T13:46:50,160 /tmp/pip-build-env-yz9spj33/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] 2024-05-17T13:46:50,160 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T13:46:50,160 | ^~~~~~~ 2024-05-17T13:47:02,717 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-yz9spj33/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 2024-05-17T13:47:04,423 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2024-05-17T13:47:04,423 mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-17T13:47:04,424 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2024-05-17T13:47:04,424 | ~~^ ~ 2024-05-17T13:47:04,424 | | | 2024-05-17T13:47:04,424 | | size_t {aka unsigned int} 2024-05-17T13:47:04,424 | long int 2024-05-17T13:47:04,424 | %d 2024-05-17T13:47:04,425 mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-17T13:47:04,425 487 | printf("size %d framesize %d\n\n", 2024-05-17T13:47:04,425 | ~^ 2024-05-17T13:47:04,425 | | 2024-05-17T13:47:04,425 | int 2024-05-17T13:47:04,425 | %lld 2024-05-17T13:47:04,425 488 | keys[i].size(), m_framesize); 2024-05-17T13:47:04,426 | ~~~~~~~~~~~~~~ 2024-05-17T13:47:04,426 | | 2024-05-17T13:47:04,426 | uint64_t {aka long long unsigned int} 2024-05-17T13:47:04,426 mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-17T13:47:04,426 487 | printf("size %d framesize %d\n\n", 2024-05-17T13:47:04,426 | ~^ 2024-05-17T13:47:04,426 | | 2024-05-17T13:47:04,427 | int 2024-05-17T13:47:04,427 | %lld 2024-05-17T13:47:04,427 488 | keys[i].size(), m_framesize); 2024-05-17T13:47:04,427 | ~~~~~~~~~~~ 2024-05-17T13:47:04,427 | | 2024-05-17T13:47:04,427 | uint64_t {aka long long unsigned int} 2024-05-17T13:47:04,427 mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-17T13:47:04,428 494 | "non-constant time interval at frame %ld\n", i); 2024-05-17T13:47:04,428 | ~~^ ~ 2024-05-17T13:47:04,428 | | | 2024-05-17T13:47:04,428 | | size_t {aka unsigned int} 2024-05-17T13:47:04,428 | long int 2024-05-17T13:47:04,428 | %d 2024-05-17T13:47:04,428 mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-17T13:47:04,429 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2024-05-17T13:47:04,429 | ~~^ ~ 2024-05-17T13:47:04,429 | | | 2024-05-17T13:47:04,429 | | size_t {aka unsigned int} 2024-05-17T13:47:04,429 | long int 2024-05-17T13:47:04,429 | %d 2024-05-17T13:47:04,552 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-17T13:47:04,553 mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-17T13:47:04,553 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2024-05-17T13:47:04,553 | ~~^ 2024-05-17T13:47:04,553 | | 2024-05-17T13:47:04,553 | long int 2024-05-17T13:47:04,553 | %lld 2024-05-17T13:47:04,554 1302 | 3*natoms, pos.count); 2024-05-17T13:47:04,554 | ~~~~~~~~~ 2024-05-17T13:47:04,554 | | 2024-05-17T13:47:04,554 | uint64_t {aka long long unsigned int} 2024-05-17T13:47:04,554 mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-17T13:47:04,554 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2024-05-17T13:47:04,555 | ~~^ 2024-05-17T13:47:04,555 | | 2024-05-17T13:47:04,555 | long int 2024-05-17T13:47:04,555 | %lld 2024-05-17T13:47:04,555 1311 | 3*natoms, vel.count); 2024-05-17T13:47:04,555 | ~~~~~~~~~ 2024-05-17T13:47:04,555 | | 2024-05-17T13:47:04,556 | uint64_t {aka long long unsigned int} 2024-05-17T13:47:04,578 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-17T13:47:04,578 mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-17T13:47:04,578 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2024-05-17T13:47:04,578 | ~~^ 2024-05-17T13:47:04,578 | | 2024-05-17T13:47:04,578 | long int 2024-05-17T13:47:04,579 | %lld 2024-05-17T13:47:04,579 1573 | velblob.count, 3*natoms); 2024-05-17T13:47:04,579 | ~~~~~~~~~~~~~ 2024-05-17T13:47:04,579 | | 2024-05-17T13:47:04,579 | uint64_t {aka long long unsigned int} 2024-05-17T13:47:05,598 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: 2024-05-17T13:47:05,599 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 2024-05-17T13:47:05,599 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2024-05-17T13:47:05,599 | ~~~~~~~~^~~~~ 2024-05-17T13:47:07,811 In file included from /usr/include/c++/10/map:60, 2024-05-17T13:47:07,811 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-17T13:47:07,811 /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> >]’: 2024-05-17T13:47:07,812 /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 2024-05-17T13:47:07,812 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-17T13:47:07,812 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:07,873 /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> >]’: 2024-05-17T13:47:07,873 /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 2024-05-17T13:47:07,873 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-17T13:47:07,873 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:07,874 /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 2024-05-17T13:47:07,928 In file included from /usr/include/c++/10/map:61, 2024-05-17T13:47:07,928 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-17T13:47:07,929 /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> >]’: 2024-05-17T13:47:07,929 /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 2024-05-17T13:47:07,929 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-17T13:47:07,929 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:07,929 521 | std::forward_as_tuple(std::move(__k)), 2024-05-17T13:47:07,929 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:07,929 522 | std::tuple<>()); 2024-05-17T13:47:07,930 | ~~~~~~~~~~~~~~~ 2024-05-17T13:47:08,696 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: 2024-05-17T13:47:08,696 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=] 2024-05-17T13:47:08,697 706 | sprintf(sub, "%03x/", i); 2024-05-17T13:47:08,697 | ^~~~ 2024-05-17T13:47:08,697 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 2024-05-17T13:47:08,697 706 | sprintf(sub, "%03x/", i); 2024-05-17T13:47:08,697 | ^~~~~~~ 2024-05-17T13:47:08,697 mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2024-05-17T13:47:08,698 706 | sprintf(sub, "%03x/", i); 2024-05-17T13:47:08,698 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2024-05-17T13:47:08,698 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=] 2024-05-17T13:47:08,698 714 | sprintf(subsub, "%03x", j); 2024-05-17T13:47:08,698 | ^~~~ 2024-05-17T13:47:08,698 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 2024-05-17T13:47:08,698 714 | sprintf(subsub, "%03x", j); 2024-05-17T13:47:08,699 | ^~~~~~ 2024-05-17T13:47:08,699 mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2024-05-17T13:47:08,699 714 | sprintf(subsub, "%03x", j); 2024-05-17T13:47:08,699 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:09,106 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: 2024-05-17T13:47:09,106 mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-17T13:47:09,107 667 | sprintf(answer, "%03x/", d1); 2024-05-17T13:47:09,107 | ^ 2024-05-17T13:47:09,107 mdtraj/formats/dtr/src/dtrplugin.cxx:667:13: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2024-05-17T13:47:09,107 667 | sprintf(answer, "%03x/", d1); 2024-05-17T13:47:09,107 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:09,107 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=] 2024-05-17T13:47:09,107 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-17T13:47:09,108 | ^~~~ 2024-05-17T13:47:09,108 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2024-05-17T13:47:09,108 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-17T13:47:09,108 | ^~~~~~~~~~~~ 2024-05-17T13:47:09,108 mdtraj/formats/dtr/src/dtrplugin.cxx:665:13: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2024-05-17T13:47:09,108 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-17T13:47:09,108 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:11,800 In file included from /usr/include/c++/10/map:61, 2024-05-17T13:47:11,800 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-17T13:47:11,801 /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’: 2024-05-17T13:47:11,801 /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 2024-05-17T13:47:11,801 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-17T13:47:11,801 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:11,801 521 | std::forward_as_tuple(std::move(__k)), 2024-05-17T13:47:11,802 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-17T13:47:11,802 522 | std::tuple<>()); 2024-05-17T13:47:11,802 | ~~~~~~~~~~~~~~~ 2024-05-17T13:47:16,937 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 2024-05-17T13:47:18,031 building 'mdtraj._rmsd' extension 2024-05-17T13:47:18,033 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd 2024-05-17T13:47:18,037 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src 2024-05-17T13:47:18,041 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-yz9spj33/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 2024-05-17T13:47:52,205 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-yz9spj33/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 2024-05-17T13:47:52,406 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-yz9spj33/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 2024-05-17T13:47:52,652 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-yz9spj33/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 2024-05-17T13:47:53,307 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 2024-05-17T13:47:53,660 building 'mdtraj._lprmsd' extension 2024-05-17T13:47:53,661 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 -Imdtraj/rmsd/include -I/tmp/pip-build-env-yz9spj33/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 2024-05-17T13:47:53,921 In file included from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-17T13:47:53,922 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T13:47:53,922 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-17T13:47:53,922 from mdtraj/rmsd/_lprmsd.cpp:809: 2024-05-17T13:47:53,922 /tmp/pip-build-env-yz9spj33/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] 2024-05-17T13:47:53,923 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T13:47:53,923 | ^~~~~~~ 2024-05-17T13:48:04,578 mdtraj/rmsd/_lprmsd.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: 2024-05-17T13:48:04,579 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] 2024-05-17T13:48:04,579 4099 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; 2024-05-17T13:48:04,579 | ^~ 2024-05-17T13:48:15,063 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-yz9spj33/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 2024-05-17T13:48:17,725 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-yz9spj33/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 2024-05-17T13:48:17,984 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-yz9spj33/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 2024-05-17T13:48:22,204 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-yz9spj33/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 2024-05-17T13:48:22,828 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-yz9spj33/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 2024-05-17T13:48:23,584 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-yz9spj33/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 2024-05-17T13:48:24,478 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 2024-05-17T13:48:25,902 building 'mdtraj.core.lib.libtheobald' extension 2024-05-17T13:48:25,914 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-yz9spj33/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 2024-05-17T13:48:27,464 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-yz9spj33/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 2024-05-17T13:48:27,872 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 2024-05-17T13:48:27,924 building 'mdtraj.geometry._geometry' extension 2024-05-17T13:48:27,925 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-17T13:48:27,926 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src 2024-05-17T13:48:27,927 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-yz9spj33/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 2024-05-17T13:48:28,778 In file included from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-17T13:48:28,778 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-17T13:48:28,779 from /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-17T13:48:28,779 from mdtraj/geometry/src/_geometry.cpp:811: 2024-05-17T13:48:28,779 /tmp/pip-build-env-yz9spj33/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] 2024-05-17T13:48:28,779 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-17T13:48:28,779 | ^~~~~~~ 2024-05-17T13:48:58,138 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-yz9spj33/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 2024-05-17T13:49:14,423 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-yz9spj33/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 2024-05-17T13:49:17,895 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-yz9spj33/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 2024-05-17T13:49:19,789 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 2024-05-17T13:49:20,320 building 'mdtraj.geometry.drid' extension 2024-05-17T13:49:20,321 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/geometry/include -I/tmp/pip-build-env-yz9spj33/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 2024-05-17T13:49:44,555 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-yz9spj33/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 2024-05-17T13:49:45,283 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-yz9spj33/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 2024-05-17T13:49:45,449 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 2024-05-17T13:49:46,003 building 'mdtraj.geometry.neighbors' extension 2024-05-17T13:49:46,004 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-yz9spj33/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 2024-05-17T13:50:08,753 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-yz9spj33/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 2024-05-17T13:50:09,891 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 2024-05-17T13:50:10,209 building 'mdtraj.geometry.neighborlist' extension 2024-05-17T13:50:10,209 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-yz9spj33/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 2024-05-17T13:50:30,447 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-yz9spj33/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 2024-05-17T13:50:34,711 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-17T13:50:34,711 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors[0][0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:50:34,712 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2024-05-17T13:50:34,712 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-17T13:50:34,712 mdtraj/geometry/src/neighborlist.cpp:51:53: warning: ‘periodicBoxVectors[1][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:50:34,712 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; 2024-05-17T13:50:34,712 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-17T13:50:34,712 mdtraj/geometry/src/neighborlist.cpp:52:53: warning: ‘periodicBoxVectors[2][2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:50:34,713 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; 2024-05-17T13:50:34,713 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-17T13:50:34,713 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors[0][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-17T13:50:34,713 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2024-05-17T13:50:34,713 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-17T13:50:35,707 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 2024-05-17T13:50:36,073 installing to build/bdist.linux-armv7l/wheel 2024-05-17T13:50:36,074 running install 2024-05-17T13:50:36,099 running install_lib 2024-05-17T13:50:36,108 creating build/bdist.linux-armv7l 2024-05-17T13:50:36,109 creating build/bdist.linux-armv7l/wheel 2024-05-17T13:50:36,111 creating build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T13:50:36,112 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,113 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,115 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,117 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,119 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,120 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,123 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,125 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,127 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,130 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,132 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,134 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,136 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,138 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,140 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,142 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,145 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,147 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-17T13:50:36,149 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,151 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,154 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,156 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,158 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-17T13:50:36,161 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T13:50:36,161 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T13:50:36,163 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T13:50:36,166 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T13:50:36,168 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-17T13:50:36,170 copying build/lib.linux-armv7l-cpython-39/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T13:50:36,173 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-17T13:50:36,174 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-17T13:50:36,177 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-17T13:50:36,178 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-17T13:50:36,181 copying build/lib.linux-armv7l-cpython-39/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T13:50:36,183 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T13:50:36,184 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-17T13:50:36,185 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-17T13:50:36,189 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-17T13:50:36,190 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-17T13:50:36,192 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T13:50:36,195 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T13:50:36,197 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T13:50:36,198 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T13:50:36,201 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T13:50:36,204 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-17T13:50:36,208 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T13:50:36,209 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T13:50:36,211 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T13:50:36,213 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T13:50:36,215 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T13:50:36,217 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T13:50:36,219 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-17T13:50:36,221 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-17T13:50:36,222 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-17T13:50:36,224 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-17T13:50:36,226 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-17T13:50:36,228 copying build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T13:50:36,249 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,250 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,253 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,255 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,258 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-17T13:50:36,259 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-17T13:50:36,263 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-17T13:50:36,264 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-17T13:50:36,267 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-17T13:50:36,269 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-17T13:50:36,271 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-17T13:50:36,274 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,275 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,311 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,314 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,357 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,361 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,363 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,366 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,386 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,389 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,392 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,395 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,397 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,400 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,402 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,405 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,408 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,421 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,424 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-17T13:50:36,426 copying build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T13:50:36,458 copying build/lib.linux-armv7l-cpython-39/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-17T13:50:36,461 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,462 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,464 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,495 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,499 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,548 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,551 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,554 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,557 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,560 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,563 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,565 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,568 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,571 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,597 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,620 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,622 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,625 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,629 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,631 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-17T13:50:36,634 running install_egg_info 2024-05-17T13:50:36,655 running egg_info 2024-05-17T13:50:36,663 writing mdtraj.egg-info/PKG-INFO 2024-05-17T13:50:36,668 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-17T13:50:36,669 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-17T13:50:36,671 writing requirements to mdtraj.egg-info/requires.txt 2024-05-17T13:50:36,673 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-17T13:50:36,723 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,723 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,723 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,723 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,723 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,724 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,724 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,724 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,725 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,725 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,726 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,726 dependency /tmp/pip-build-env-yz9spj33/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-17T13:50:36,744 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-17T13:50:36,766 reading manifest template 'MANIFEST.in' 2024-05-17T13:50:37,476 no previously-included directories found matching '__pycache__' 2024-05-17T13:50:37,478 no previously-included directories found matching '*.pyc' 2024-05-17T13:50:37,478 adding license file 'LICENSE' 2024-05-17T13:50:37,501 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-17T13:50:37,503 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.10.0rc1-py3.9.egg-info 2024-05-17T13:50:37,519 running install_scripts 2024-05-17T13:50:37,575 creating build/bdist.linux-armv7l/wheel/mdtraj-1.10.0rc1.dist-info/WHEEL 2024-05-17T13:50:37,579 creating '/tmp/pip-wheel-9or1if6t/.tmp-7uzeoqjj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-17T13:50:37,581 adding 'mdtraj/__init__.py' 2024-05-17T13:50:37,818 adding 'mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:38,183 adding 'mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:38,196 adding 'mdtraj/io.py' 2024-05-17T13:50:38,198 adding 'mdtraj/version.py' 2024-05-17T13:50:38,199 adding 'mdtraj/core/__init__.py' 2024-05-17T13:50:38,202 adding 'mdtraj/core/element.py' 2024-05-17T13:50:38,205 adding 'mdtraj/core/residue_names.py' 2024-05-17T13:50:38,207 adding 'mdtraj/core/selection.py' 2024-05-17T13:50:38,215 adding 'mdtraj/core/topology.py' 2024-05-17T13:50:38,224 adding 'mdtraj/core/trajectory.py' 2024-05-17T13:50:38,227 adding 'mdtraj/core/lib/center.h' 2024-05-17T13:50:38,236 adding 'mdtraj/core/lib/libtheobald.a' 2024-05-17T13:50:38,238 adding 'mdtraj/core/lib/theobald_rmsd.h' 2024-05-17T13:50:38,240 adding 'mdtraj/formats/__init__.py' 2024-05-17T13:50:38,244 adding 'mdtraj/formats/amberrst.py' 2024-05-17T13:50:38,246 adding 'mdtraj/formats/arc.py' 2024-05-17T13:50:38,400 adding 'mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:38,813 adding 'mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:38,830 adding 'mdtraj/formats/gro.py' 2024-05-17T13:50:38,832 adding 'mdtraj/formats/gsd.py' 2024-05-17T13:50:38,836 adding 'mdtraj/formats/hdf5.py' 2024-05-17T13:50:38,838 adding 'mdtraj/formats/hoomdxml.py' 2024-05-17T13:50:38,841 adding 'mdtraj/formats/lammpstrj.py' 2024-05-17T13:50:38,844 adding 'mdtraj/formats/lh5.py' 2024-05-17T13:50:38,846 adding 'mdtraj/formats/mdcrd.py' 2024-05-17T13:50:38,849 adding 'mdtraj/formats/mol2.py' 2024-05-17T13:50:38,852 adding 'mdtraj/formats/netcdf.py' 2024-05-17T13:50:38,853 adding 'mdtraj/formats/openmmxml.py' 2024-05-17T13:50:38,855 adding 'mdtraj/formats/pdbx.py' 2024-05-17T13:50:38,857 adding 'mdtraj/formats/prmtop.py' 2024-05-17T13:50:38,859 adding 'mdtraj/formats/psf.py' 2024-05-17T13:50:38,861 adding 'mdtraj/formats/registry.py' 2024-05-17T13:50:39,123 adding 'mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:39,388 adding 'mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:39,401 adding 'mdtraj/formats/xyzfile.py' 2024-05-17T13:50:39,408 adding 'mdtraj/formats/pdb/__init__.py' 2024-05-17T13:50:39,415 adding 'mdtraj/formats/pdb/pdbfile.py' 2024-05-17T13:50:39,424 adding 'mdtraj/formats/pdb/pdbstructure.py' 2024-05-17T13:50:39,429 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2024-05-17T13:50:39,431 adding 'mdtraj/formats/pdb/data/residues.xml' 2024-05-17T13:50:39,437 adding 'mdtraj/geometry/__init__.py' 2024-05-17T13:50:39,956 adding 'mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:39,979 adding 'mdtraj/geometry/alignment.py' 2024-05-17T13:50:39,983 adding 'mdtraj/geometry/angle.py' 2024-05-17T13:50:39,988 adding 'mdtraj/geometry/contact.py' 2024-05-17T13:50:39,993 adding 'mdtraj/geometry/dihedral.py' 2024-05-17T13:50:39,999 adding 'mdtraj/geometry/distance.py' 2024-05-17T13:50:40,276 adding 'mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:40,286 adding 'mdtraj/geometry/dssp.py' 2024-05-17T13:50:40,289 adding 'mdtraj/geometry/hbond.py' 2024-05-17T13:50:40,291 adding 'mdtraj/geometry/internal.py' 2024-05-17T13:50:40,586 adding 'mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:40,863 adding 'mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so' 2024-05-17T13:50:40,874 adding 'mdtraj/geometry/order.py' 2024-05-17T13:50:40,876 adding 'mdtraj/geometry/rdf.py' 2024-05-17T13:50:40,877 adding 'mdtraj/geometry/rg.py' 2024-05-17T13:50:40,879 adding 'mdtraj/geometry/sasa.py' 2024-05-17T13:50:40,881 adding 'mdtraj/geometry/shape.py' 2024-05-17T13:50:40,882 adding 'mdtraj/geometry/thermodynamic_properties.py' 2024-05-17T13:50:40,884 adding 'mdtraj/nmr/__init__.py' 2024-05-17T13:50:40,886 adding 'mdtraj/nmr/scalar_couplings.py' 2024-05-17T13:50:40,888 adding 'mdtraj/nmr/shift_wrappers.py' 2024-05-17T13:50:40,890 adding 'mdtraj/reporters/__init__.py' 2024-05-17T13:50:40,892 adding 'mdtraj/reporters/basereporter.py' 2024-05-17T13:50:40,893 adding 'mdtraj/reporters/dcdreporter.py' 2024-05-17T13:50:40,895 adding 'mdtraj/reporters/hdf5reporter.py' 2024-05-17T13:50:40,896 adding 'mdtraj/reporters/netcdfreporter.py' 2024-05-17T13:50:40,898 adding 'mdtraj/reporters/xtcreporter.py' 2024-05-17T13:50:40,900 adding 'mdtraj/scripts/__init__.py' 2024-05-17T13:50:40,902 adding 'mdtraj/scripts/mdconvert.py' 2024-05-17T13:50:40,904 adding 'mdtraj/scripts/mdinspect.py' 2024-05-17T13:50:40,906 adding 'mdtraj/testing/__init__.py' 2024-05-17T13:50:40,908 adding 'mdtraj/testing/docscrape.py' 2024-05-17T13:50:40,910 adding 'mdtraj/testing/docstrings.py' 2024-05-17T13:50:40,912 adding 'mdtraj/testing/testing.py' 2024-05-17T13:50:40,914 adding 'mdtraj/utils/__init__.py' 2024-05-17T13:50:40,915 adding 'mdtraj/utils/contextmanagers.py' 2024-05-17T13:50:40,917 adding 'mdtraj/utils/delay_import.py' 2024-05-17T13:50:40,919 adding 'mdtraj/utils/rotation.py' 2024-05-17T13:50:40,920 adding 'mdtraj/utils/singleton.py' 2024-05-17T13:50:40,922 adding 'mdtraj/utils/unitcell.py' 2024-05-17T13:50:40,923 adding 'mdtraj/utils/validation.py' 2024-05-17T13:50:40,925 adding 'mdtraj/utils/zipped.py' 2024-05-17T13:50:40,927 adding 'mdtraj/utils/unit/__init__.py' 2024-05-17T13:50:40,929 adding 'mdtraj/utils/unit/basedimension.py' 2024-05-17T13:50:40,930 adding 'mdtraj/utils/unit/baseunit.py' 2024-05-17T13:50:40,932 adding 'mdtraj/utils/unit/constants.py' 2024-05-17T13:50:40,935 adding 'mdtraj/utils/unit/doctests.py' 2024-05-17T13:50:40,937 adding 'mdtraj/utils/unit/mymatrix.py' 2024-05-17T13:50:40,939 adding 'mdtraj/utils/unit/prefix.py' 2024-05-17T13:50:40,942 adding 'mdtraj/utils/unit/quantity.py' 2024-05-17T13:50:40,944 adding 'mdtraj/utils/unit/standard_dimensions.py' 2024-05-17T13:50:40,947 adding 'mdtraj/utils/unit/unit.py' 2024-05-17T13:50:40,950 adding 'mdtraj/utils/unit/unit_definitions.py' 2024-05-17T13:50:40,951 adding 'mdtraj/utils/unit/unit_math.py' 2024-05-17T13:50:40,953 adding 'mdtraj/utils/unit/unit_operators.py' 2024-05-17T13:50:40,958 adding 'mdtraj-1.10.0rc1.dist-info/LICENSE' 2024-05-17T13:50:40,959 adding 'mdtraj-1.10.0rc1.dist-info/METADATA' 2024-05-17T13:50:40,960 adding 'mdtraj-1.10.0rc1.dist-info/WHEEL' 2024-05-17T13:50:40,961 adding 'mdtraj-1.10.0rc1.dist-info/entry_points.txt' 2024-05-17T13:50:40,962 adding 'mdtraj-1.10.0rc1.dist-info/top_level.txt' 2024-05-17T13:50:40,964 adding 'mdtraj-1.10.0rc1.dist-info/RECORD' 2024-05-17T13:50:41,025 removing build/bdist.linux-armv7l/wheel 2024-05-17T13:50:41,793 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2024-05-17T13:50:41,926 Created wheel for mdtraj: filename=mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl size=6059964 sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 2024-05-17T13:50:41,927 Stored in directory: /tmp/pip-ephem-wheel-cache-8qdxe4wr/wheels/09/4e/30/8b6074d92f6ce8af208e9b6f7556ae070de485f36a899d71da 2024-05-17T13:50:41,945 Successfully built mdtraj 2024-05-17T13:50:42,112 Removed build tracker: '/tmp/pip-build-tracker-n39ep4mn'