2024-05-29T16:37:19,096 Created temporary directory: /tmp/pip-build-tracker-fyzrg3wo 2024-05-29T16:37:19,098 Initialized build tracking at /tmp/pip-build-tracker-fyzrg3wo 2024-05-29T16:37:19,098 Created build tracker: /tmp/pip-build-tracker-fyzrg3wo 2024-05-29T16:37:19,098 Entered build tracker: /tmp/pip-build-tracker-fyzrg3wo 2024-05-29T16:37:19,099 Created temporary directory: /tmp/pip-wheel-g2xmm2m2 2024-05-29T16:37:19,103 Created temporary directory: /tmp/pip-ephem-wheel-cache-m9qq2emf 2024-05-29T16:37:19,130 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-29T16:37:19,133 2 location(s) to search for versions of mdtraj: 2024-05-29T16:37:19,133 * https://pypi.org/simple/mdtraj/ 2024-05-29T16:37:19,133 * https://www.piwheels.org/simple/mdtraj/ 2024-05-29T16:37:19,134 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2024-05-29T16:37:19,134 Getting page https://pypi.org/simple/mdtraj/ 2024-05-29T16:37:19,136 Found index url 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https://files.pythonhosted.org/packages/cd/9f/027fa58d4e93dd3d700e22d5766961c970f6882c2bffd33daef55219d078/mdtraj-1.8.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.8.0 2024-05-29T16:37:19,219 Found link https://files.pythonhosted.org/packages/4a/2e/5bb01aaa8cd2ea9d75dd2ac12fd9f04f7137a8c996bde0138ad1b5e54ecb/mdtraj-1.8.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.8.0 2024-05-29T16:37:19,219 Found link https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.1 2024-05-29T16:37:19,220 Found link https://files.pythonhosted.org/packages/e0/9e/857f613eae8af3fb8cc73904b3edf622c58de3884c5989e4466973c3c9ee/mdtraj-1.9.2.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.2 2024-05-29T16:37:19,220 Found link https://files.pythonhosted.org/packages/72/68/1efc74927df6fdaaa4816556a2534f4560cb69ed573ccac728e4fb8e3e09/mdtraj-1.9.3.tar.gz (from 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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/) 2024-05-29T16:37:19,221 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/) 2024-05-29T16:37:19,221 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 2024-05-29T16:37:19,222 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/) 2024-05-29T16:37:19,222 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/) 2024-05-29T16:37:19,222 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/) 2024-05-29T16:37:19,222 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/) 2024-05-29T16:37:19,222 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 2024-05-29T16:37:19,223 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 2024-05-29T16:37:19,223 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/) 2024-05-29T16:37:19,223 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 2024-05-29T16:37:19,223 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/) 2024-05-29T16:37:19,224 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 2024-05-29T16:37:19,224 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 2024-05-29T16:37:19,224 Found link https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.10.0rc2 2024-05-29T16:37:19,225 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2024-05-29T16:37:19,225 Getting page https://www.piwheels.org/simple/mdtraj/ 2024-05-29T16:37:19,226 Found index url https://www.piwheels.org/simple/ 2024-05-29T16:37:19,342 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2024-05-29T16:37:19,348 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp311-cp311-linux_armv6l.whl#sha256=bb4a20fe32bcfb564d4efcd3c10b2d6c88728eecacf8bd1b53dd402e387c444f (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T16:37:19,348 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp311-cp311-linux_armv7l.whl#sha256=bb4a20fe32bcfb564d4efcd3c10b2d6c88728eecacf8bd1b53dd402e387c444f (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T16:37:19,348 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp37-cp37m-linux_armv6l.whl#sha256=cb090c5366b7b76d938daa16ca5a431a4fe751344ec320479b3ba8134a6ff4bd (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T16:37:19,349 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp37-cp37m-linux_armv7l.whl#sha256=cb090c5366b7b76d938daa16ca5a431a4fe751344ec320479b3ba8134a6ff4bd (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T16:37:19,349 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/) 2024-05-29T16:37:19,349 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/) 2024-05-29T16:37:19,349 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/) 2024-05-29T16:37:19,349 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/) 2024-05-29T16:37:19,350 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv6l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T16:37:19,350 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-29T16:37:19,350 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/) 2024-05-29T16:37:19,350 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/) 2024-05-29T16:37:19,350 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/) 2024-05-29T16:37:19,351 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/) 2024-05-29T16:37:19,351 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/) 2024-05-29T16:37:19,351 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/) 2024-05-29T16:37:19,351 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/) 2024-05-29T16:37:19,351 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/) 2024-05-29T16:37:19,352 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/) 2024-05-29T16:37:19,352 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/) 2024-05-29T16:37:19,352 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2024-05-29T16:37:19,352 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2024-05-29T16:37:19,378 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2024-05-29T16:37:19,395 Collecting mdtraj==1.10.0rc2 2024-05-29T16:37:19,397 Created temporary directory: /tmp/pip-unpack-9ag04lzg 2024-05-29T16:37:19,442 Downloading mdtraj-1.10.0rc2.tar.gz (1.8 MB) 2024-05-29T16:37:20,542 Added mdtraj==1.10.0rc2 from https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz to build tracker '/tmp/pip-build-tracker-fyzrg3wo' 2024-05-29T16:37:20,549 Created temporary directory: /tmp/pip-build-env-cqkwedvw 2024-05-29T16:37:20,559 Installing build dependencies: started 2024-05-29T16:37:20,560 Running command pip subprocess to install build dependencies 2024-05-29T16:37:21,717 Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2024-05-29T16:37:22,230 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-29T16:37:23,771 Collecting setuptools 2024-05-29T16:37:23,788 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.0.0-py3-none-any.whl (863 kB) 2024-05-29T16:37:24,046 Collecting wheel 2024-05-29T16:37:24,063 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-05-29T16:37:25,094 Collecting numpy<2 2024-05-29T16:37:25,110 Using cached https://www.piwheels.org/simple/numpy/numpy-1.26.4-cp39-cp39-linux_armv7l.whl (5.6 MB) 2024-05-29T16:37:25,427 Collecting oldest-supported-numpy 2024-05-29T16:37:25,444 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2023.12.21-py3-none-any.whl (4.9 kB) 2024-05-29T16:37:26,840 Collecting Cython~=0.29.36 2024-05-29T16:37:26,884 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.37-cp39-cp39-linux_armv7l.whl (4.9 MB) 2024-05-29T16:37:27,458 Collecting numpy<2 2024-05-29T16:37:27,481 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB) 2024-05-29T16:37:29,600 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2024-05-29T16:37:29,820 Creating /tmp/pip-build-env-cqkwedvw/overlay/bin 2024-05-29T16:37:29,822 changing mode of /tmp/pip-build-env-cqkwedvw/overlay/bin/wheel to 755 2024-05-29T16:37:38,379 changing mode of /tmp/pip-build-env-cqkwedvw/overlay/bin/f2py to 755 2024-05-29T16:37:38,381 changing mode of /tmp/pip-build-env-cqkwedvw/overlay/bin/f2py3 to 755 2024-05-29T16:37:38,383 changing mode of /tmp/pip-build-env-cqkwedvw/overlay/bin/f2py3.9 to 755 2024-05-29T16:37:41,002 changing mode of /tmp/pip-build-env-cqkwedvw/overlay/bin/cygdb to 755 2024-05-29T16:37:41,004 changing mode of /tmp/pip-build-env-cqkwedvw/overlay/bin/cython to 755 2024-05-29T16:37:41,006 changing mode of /tmp/pip-build-env-cqkwedvw/overlay/bin/cythonize to 755 2024-05-29T16:37:41,050 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. 2024-05-29T16:37:41,051 scipy 1.13.0 requires numpy<2.3,>=1.22.4, but you have numpy 1.19.3 which is incompatible. 2024-05-29T16:37:41,051 Successfully installed Cython-0.29.37 numpy-1.19.3 oldest-supported-numpy-2023.12.21 setuptools-70.0.0 wheel-0.43.0 2024-05-29T16:37:41,700 Installing build dependencies: finished with status 'done' 2024-05-29T16:37:41,710 Getting requirements to build wheel: started 2024-05-29T16:37:41,711 Running command Getting requirements to build wheel 2024-05-29T16:37:42,427 Using built-in specs. 2024-05-29T16:37:42,428 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-29T16:37:42,428 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-29T16:37:42,429 Target: arm-linux-gnueabihf 2024-05-29T16:37:42,429 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 2024-05-29T16:37:42,429 Thread model: posix 2024-05-29T16:37:42,429 Supported LTO compression algorithms: zlib zstd 2024-05-29T16:37:42,429 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-29T16:37:46,503 C compiler: 2024-05-29T16:37:46,503 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-29T16:37:46,503 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-29T16:37:46,503 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-29T16:37:46,504 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-29T16:37:46,504 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-29T16:37:46,504 running egg_info 2024-05-29T16:37:46,510 writing mdtraj.egg-info/PKG-INFO 2024-05-29T16:37:46,513 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-29T16:37:46,514 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-29T16:37:46,516 writing requirements to mdtraj.egg-info/requires.txt 2024-05-29T16:37:46,517 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-29T16:37:46,558 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-29T16:37:46,579 reading manifest template 'MANIFEST.in' 2024-05-29T16:37:47,192 no previously-included directories found matching '__pycache__' 2024-05-29T16:37:47,192 no previously-included directories found matching '*.pyc' 2024-05-29T16:37:47,193 adding license file 'LICENSE' 2024-05-29T16:37:47,207 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-29T16:37:47,290 Getting requirements to build wheel: finished with status 'done' 2024-05-29T16:37:47,301 Created temporary directory: /tmp/pip-modern-metadata-rl5ywapb 2024-05-29T16:37:47,306 Preparing metadata (pyproject.toml): started 2024-05-29T16:37:47,307 Running command Preparing metadata (pyproject.toml) 2024-05-29T16:37:48,012 Using built-in specs. 2024-05-29T16:37:48,013 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-29T16:37:48,013 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-29T16:37:48,013 Target: arm-linux-gnueabihf 2024-05-29T16:37:48,013 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 2024-05-29T16:37:48,013 Thread model: posix 2024-05-29T16:37:48,013 Supported LTO compression algorithms: zlib zstd 2024-05-29T16:37:48,013 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-29T16:37:51,948 /tmp/pip-wheel-g2xmm2m2/mdtraj_cb5838667e234fd1a83af0927729f5d6/basesetup.py:518: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-rl5ywapb --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2024-05-29T16:37:51,948 warnings.warn( 2024-05-29T16:37:53,812 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. 2024-05-29T16:37:53,812 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. 2024-05-29T16:37:53,812 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. 2024-05-29T16:38:17,580 C compiler: 2024-05-29T16:38:17,581 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-29T16:38:17,581 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-29T16:38:17,581 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-29T16:38:17,581 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-29T16:38:17,581 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-29T16:38:17,582 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-29T16:38:17,582 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-29T16:38:17,582 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-29T16:38:17,582 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-29T16:38:17,582 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-29T16:38:17,582 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-29T16:38:17,583 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-29T16:38:17,583 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-29T16:38:17,583 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-29T16:38:17,583 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-29T16:38:17,683 running dist_info 2024-05-29T16:38:17,690 creating /tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info 2024-05-29T16:38:17,697 writing /tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info/PKG-INFO 2024-05-29T16:38:17,700 writing dependency_links to /tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info/dependency_links.txt 2024-05-29T16:38:17,702 writing entry points to /tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info/entry_points.txt 2024-05-29T16:38:17,703 writing requirements to /tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info/requires.txt 2024-05-29T16:38:17,704 writing top-level names to /tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info/top_level.txt 2024-05-29T16:38:17,706 writing manifest file '/tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info/SOURCES.txt' 2024-05-29T16:38:17,755 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,755 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,756 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,756 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,756 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,756 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,756 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,756 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,757 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,757 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,758 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,758 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:38:17,772 reading manifest file '/tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info/SOURCES.txt' 2024-05-29T16:38:17,774 reading manifest template 'MANIFEST.in' 2024-05-29T16:38:18,337 no previously-included directories found matching '__pycache__' 2024-05-29T16:38:18,338 no previously-included directories found matching '*.pyc' 2024-05-29T16:38:18,339 adding license file 'LICENSE' 2024-05-29T16:38:18,350 writing manifest file '/tmp/pip-modern-metadata-rl5ywapb/mdtraj.egg-info/SOURCES.txt' 2024-05-29T16:38:18,351 creating '/tmp/pip-modern-metadata-rl5ywapb/mdtraj-1.10.0rc2.dist-info' 2024-05-29T16:38:19,135 Preparing metadata (pyproject.toml): finished with status 'done' 2024-05-29T16:38:19,141 Source in /tmp/pip-wheel-g2xmm2m2/mdtraj_cb5838667e234fd1a83af0927729f5d6 has version 1.10.0rc2, which satisfies requirement mdtraj==1.10.0rc2 from https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz 2024-05-29T16:38:19,142 Removed mdtraj==1.10.0rc2 from https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz from build tracker '/tmp/pip-build-tracker-fyzrg3wo' 2024-05-29T16:38:19,146 Created temporary directory: /tmp/pip-unpack-xy3ahw7c 2024-05-29T16:38:19,147 Created temporary directory: /tmp/pip-unpack-3p6clr4k 2024-05-29T16:38:19,155 Building wheels for collected packages: mdtraj 2024-05-29T16:38:19,160 Created temporary directory: /tmp/pip-wheel-hcs33agr 2024-05-29T16:38:19,160 Destination directory: /tmp/pip-wheel-hcs33agr 2024-05-29T16:38:19,162 Building wheel for mdtraj (pyproject.toml): started 2024-05-29T16:38:19,163 Running command Building wheel for mdtraj (pyproject.toml) 2024-05-29T16:38:19,897 Using built-in specs. 2024-05-29T16:38:19,898 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-29T16:38:19,898 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-29T16:38:19,898 Target: arm-linux-gnueabihf 2024-05-29T16:38:19,899 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 2024-05-29T16:38:19,899 Thread model: posix 2024-05-29T16:38:19,899 Supported LTO compression algorithms: zlib zstd 2024-05-29T16:38:19,899 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-29T16:38:25,546 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. 2024-05-29T16:38:25,546 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. 2024-05-29T16:38:25,546 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. 2024-05-29T16:38:49,306 C compiler: 2024-05-29T16:38:49,306 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-29T16:38:49,307 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-29T16:38:49,307 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-29T16:38:49,307 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-29T16:38:49,307 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-29T16:38:49,307 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-29T16:38:49,308 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-29T16:38:49,308 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-29T16:38:49,308 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-29T16:38:49,308 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-29T16:38:49,308 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-29T16:38:49,308 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-29T16:38:49,309 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-29T16:38:49,309 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-29T16:38:49,309 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-29T16:38:49,431 running bdist_wheel 2024-05-29T16:38:49,470 running build 2024-05-29T16:38:49,470 running build_py 2024-05-29T16:38:49,479 creating build 2024-05-29T16:38:49,480 creating build/lib.linux-armv7l-cpython-39 2024-05-29T16:38:49,481 creating build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-29T16:38:49,482 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-29T16:38:49,484 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-29T16:38:49,486 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-29T16:38:49,489 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,490 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,492 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,494 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,496 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,498 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,501 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,502 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,505 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-29T16:38:49,507 creating build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-29T16:38:49,508 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-29T16:38:49,510 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-29T16:38:49,513 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-29T16:38:49,515 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-29T16:38:49,518 creating build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-29T16:38:49,519 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-29T16:38:49,521 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-29T16:38:49,522 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-29T16:38:49,526 creating build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-29T16:38:49,527 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-29T16:38:49,529 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-29T16:38:49,532 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-29T16:38:49,533 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-29T16:38:49,537 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-29T16:38:49,540 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-29T16:38:49,544 creating build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-29T16:38:49,545 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-29T16:38:49,547 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-29T16:38:49,549 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-29T16:38:49,551 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-29T16:38:49,553 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-29T16:38:49,555 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-29T16:38:49,558 creating build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-29T16:38:49,559 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-29T16:38:49,561 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-29T16:38:49,563 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-29T16:38:49,567 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,568 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,571 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,573 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,576 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,577 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,580 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,583 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,585 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,588 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,591 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,593 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,596 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,598 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,601 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,602 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,605 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,607 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,609 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,613 creating build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,614 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,617 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,619 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,621 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,624 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,626 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,628 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,631 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,632 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,634 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,637 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,638 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,641 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,643 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,645 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:38:49,648 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,649 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,651 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,654 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,656 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,659 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,661 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,664 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,665 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,667 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,669 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,671 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,674 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,676 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-29T16:38:49,679 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-29T16:38:49,680 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-29T16:38:49,683 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-29T16:38:49,685 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-29T16:38:49,693 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-29T16:38:49,694 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-29T16:38:49,697 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-29T16:38:49,707 running build_ext 2024-05-29T16:38:49,710 building 'mdtraj.formats.xtc' extension 2024-05-29T16:38:49,711 creating build/temp.linux-armv7l-cpython-39 2024-05-29T16:38:49,712 creating build/temp.linux-armv7l-cpython-39/mdtraj 2024-05-29T16:38:49,713 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats 2024-05-29T16:38:49,713 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc 2024-05-29T16:38:49,714 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src 2024-05-29T16:38:49,715 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-cqkwedvw/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 2024-05-29T16:38:49,843 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-cqkwedvw/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 2024-05-29T16:38:49,984 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-29T16:38:49,984 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:38:49,984 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-29T16:38:49,985 | ^~~~~~ 2024-05-29T16:38:49,985 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:38:49,985 785 | int smallidx, minidx, maxidx; 2024-05-29T16:38:49,985 | ^~~~~~ 2024-05-29T16:38:49,992 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-29T16:38:49,993 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:38:49,993 1016 | int errval=1; 2024-05-29T16:38:49,993 | ^~~~~~ 2024-05-29T16:38:49,998 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-29T16:38:49,999 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:38:49,999 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-29T16:38:49,999 | ^~~~~~ 2024-05-29T16:38:50,000 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:38:50,000 1302 | int smallidx, minidx, maxidx; 2024-05-29T16:38:50,000 | ^~~~~~ 2024-05-29T16:38:50,009 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-29T16:38:50,010 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:38:50,010 1509 | int errval=1; 2024-05-29T16:38:50,010 | ^~~~~~ 2024-05-29T16:38:52,115 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-cqkwedvw/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 2024-05-29T16:38:52,192 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2024-05-29T16:38:52,193 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2024-05-29T16:38:52,193 66 | int i,j,result; 2024-05-29T16:38:52,193 | ^ 2024-05-29T16:38:52,193 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2024-05-29T16:38:52,193 66 | int i,j,result; 2024-05-29T16:38:52,193 | ^ 2024-05-29T16:38:52,194 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2024-05-29T16:38:52,195 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2024-05-29T16:38:52,195 119 | if (NULL == xd) 2024-05-29T16:38:52,195 | ^~ 2024-05-29T16:38:52,195 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’ 2024-05-29T16:38:52,195 122 | do { 2024-05-29T16:38:52,195 | ^~ 2024-05-29T16:38:52,335 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-cqkwedvw/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 2024-05-29T16:38:52,658 In file included from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-29T16:38:52,658 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T16:38:52,658 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-29T16:38:52,658 from mdtraj/formats/xtc/xtc.c:781: 2024-05-29T16:38:52,658 /tmp/pip-build-env-cqkwedvw/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] 2024-05-29T16:38:52,659 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T16:38:52,659 | ^~~~~~~ 2024-05-29T16:38:59,153 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2024-05-29T16:38:59,153 mdtraj/formats/xtc/xtc.c:693:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:38:59,153 693 | #define PyInt_FromLong PyLong_FromLong 2024-05-29T16:38:59,153 | ^~~~~~~~~~~~~~~ 2024-05-29T16:38:59,159 mdtraj/formats/xtc/xtc.c:9547:7: note: ‘__pyx_v_status’ was declared here 2024-05-29T16:38:59,159 9547 | int __pyx_v_status; 2024-05-29T16:38:59,159 | ^~~~~~~~~~~~~~ 2024-05-29T16:39:08,588 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2024-05-29T16:39:08,592 mdtraj/formats/xtc/xtc.c:8066:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,593 8066 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-29T16:39:08,593 | ^ 2024-05-29T16:39:08,597 mdtraj/formats/xtc/xtc.c:8062:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,597 8062 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-29T16:39:08,598 | ^ 2024-05-29T16:39:08,602 mdtraj/formats/xtc/xtc.c:8058:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,602 8058 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T16:39:08,602 | ^ 2024-05-29T16:39:08,607 mdtraj/formats/xtc/xtc.c:8018:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,607 8018 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T16:39:08,607 | ^ 2024-05-29T16:39:08,612 mdtraj/formats/xtc/xtc.c:8000:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,612 8000 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T16:39:08,612 | ^ 2024-05-29T16:39:08,616 mdtraj/formats/xtc/xtc.c:8076:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,616 8076 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T16:39:08,616 | ^ 2024-05-29T16:39:08,621 mdtraj/formats/xtc/xtc.c:8038:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,621 8038 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-29T16:39:08,621 | ^ 2024-05-29T16:39:08,625 mdtraj/formats/xtc/xtc.c:8034:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,626 8034 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-29T16:39:08,626 | ^ 2024-05-29T16:39:08,630 mdtraj/formats/xtc/xtc.c:8030:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,630 8030 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T16:39:08,631 | ^ 2024-05-29T16:39:08,635 mdtraj/formats/xtc/xtc.c:7653:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,635 7653 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-29T16:39:08,635 | ^ 2024-05-29T16:39:08,639 mdtraj/formats/xtc/xtc.c:7649:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:08,640 7649 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-29T16:39:08,640 | ^ 2024-05-29T16:39:13,208 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 2024-05-29T16:39:13,380 building 'mdtraj.formats.trr' extension 2024-05-29T16:39:13,381 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-cqkwedvw/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 2024-05-29T16:39:13,495 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-cqkwedvw/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 2024-05-29T16:39:13,625 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-29T16:39:13,626 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:39:13,626 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-29T16:39:13,626 | ^~~~~~ 2024-05-29T16:39:13,626 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:39:13,626 785 | int smallidx, minidx, maxidx; 2024-05-29T16:39:13,626 | ^~~~~~ 2024-05-29T16:39:13,633 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-29T16:39:13,633 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:39:13,633 1016 | int errval=1; 2024-05-29T16:39:13,633 | ^~~~~~ 2024-05-29T16:39:13,638 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-29T16:39:13,638 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:39:13,638 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-29T16:39:13,639 | ^~~~~~ 2024-05-29T16:39:13,639 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:39:13,639 1302 | int smallidx, minidx, maxidx; 2024-05-29T16:39:13,639 | ^~~~~~ 2024-05-29T16:39:13,652 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-29T16:39:13,653 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-29T16:39:13,653 1509 | int errval=1; 2024-05-29T16:39:13,653 | ^~~~~~ 2024-05-29T16:39:15,786 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-cqkwedvw/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 2024-05-29T16:39:16,441 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-cqkwedvw/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 2024-05-29T16:39:16,747 In file included from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-29T16:39:16,747 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T16:39:16,747 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-29T16:39:16,747 from mdtraj/formats/xtc/trr.c:781: 2024-05-29T16:39:16,748 /tmp/pip-build-env-cqkwedvw/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] 2024-05-29T16:39:16,748 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T16:39:16,748 | ^~~~~~~ 2024-05-29T16:39:23,524 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2024-05-29T16:39:23,524 mdtraj/formats/xtc/trr.c:693:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:23,524 693 | #define PyInt_FromLong PyLong_FromLong 2024-05-29T16:39:23,524 | ^~~~~~~~~~~~~~~ 2024-05-29T16:39:23,531 mdtraj/formats/xtc/trr.c:11073:7: note: ‘__pyx_v_status’ was declared here 2024-05-29T16:39:23,531 11073 | int __pyx_v_status; 2024-05-29T16:39:23,531 | ^~~~~~~~~~~~~~ 2024-05-29T16:39:33,221 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2024-05-29T16:39:33,226 mdtraj/formats/xtc/trr.c:8426:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,227 8426 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-29T16:39:33,227 | ^ 2024-05-29T16:39:33,232 mdtraj/formats/xtc/trr.c:8422:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,232 8422 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T16:39:33,232 | ^ 2024-05-29T16:39:33,232 mdtraj/formats/xtc/trr.c:1929:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,233 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-29T16:39:33,233 | ^ 2024-05-29T16:39:33,236 mdtraj/formats/xtc/trr.c:6963:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-05-29T16:39:33,237 6963 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-29T16:39:33,237 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:39:33,241 mdtraj/formats/xtc/trr.c:8416:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,241 8416 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-05-29T16:39:33,241 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-29T16:39:33,246 mdtraj/formats/xtc/trr.c:8369:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,246 8369 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-29T16:39:33,246 | ^ 2024-05-29T16:39:33,251 mdtraj/formats/xtc/trr.c:8365:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,251 8365 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T16:39:33,251 | ^ 2024-05-29T16:39:33,252 mdtraj/formats/xtc/trr.c:1929:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,252 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-29T16:39:33,252 | ^ 2024-05-29T16:39:33,256 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-05-29T16:39:33,256 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-29T16:39:33,256 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:39:33,260 mdtraj/formats/xtc/trr.c:8359:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,260 8359 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-05-29T16:39:33,261 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-29T16:39:33,265 mdtraj/formats/xtc/trr.c:8759:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,265 8759 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T16:39:33,265 | ^ 2024-05-29T16:39:33,270 mdtraj/formats/xtc/trr.c:8755:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,270 8755 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-29T16:39:33,270 | ^ 2024-05-29T16:39:33,275 mdtraj/formats/xtc/trr.c:8600:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,275 8600 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T16:39:33,276 | ^ 2024-05-29T16:39:33,280 mdtraj/formats/xtc/trr.c:8596:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,281 8596 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-29T16:39:33,281 | ^ 2024-05-29T16:39:33,285 mdtraj/formats/xtc/trr.c:8652:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,285 8652 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-29T16:39:33,285 | ^ 2024-05-29T16:39:33,290 mdtraj/formats/xtc/trr.c:8648:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:33,290 8648 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-29T16:39:33,291 | ^ 2024-05-29T16:39:39,658 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 2024-05-29T16:39:39,829 building 'mdtraj.formats.dcd' extension 2024-05-29T16:39:39,830 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd 2024-05-29T16:39:39,831 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src 2024-05-29T16:39:39,832 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-cqkwedvw/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 2024-05-29T16:39:40,161 In file included from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-29T16:39:40,161 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T16:39:40,161 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-29T16:39:40,161 from mdtraj/formats/dcd/dcd.c:779: 2024-05-29T16:39:40,161 /tmp/pip-build-env-cqkwedvw/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] 2024-05-29T16:39:40,161 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T16:39:40,162 | ^~~~~~~ 2024-05-29T16:39:47,429 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2024-05-29T16:39:47,429 mdtraj/formats/dcd/dcd.c:691:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:39:47,429 691 | #define PyInt_FromLong PyLong_FromLong 2024-05-29T16:39:47,429 | ^~~~~~~~~~~~~~~ 2024-05-29T16:39:47,431 mdtraj/formats/dcd/dcd.c:5442:7: note: ‘__pyx_v_i’ was declared here 2024-05-29T16:39:47,432 5442 | int __pyx_v_i; 2024-05-29T16:39:47,432 | ^~~~~~~~~ 2024-05-29T16:39:50,524 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-cqkwedvw/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 2024-05-29T16:39:51,843 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 2024-05-29T16:39:51,978 building 'mdtraj.formats.dtr' extension 2024-05-29T16:39:51,979 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr 2024-05-29T16:39:51,979 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src 2024-05-29T16:39:51,980 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:39:52,239 In file included from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-29T16:39:52,239 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T16:39:52,239 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-29T16:39:52,240 from mdtraj/formats/dtr/dtr.cpp:800: 2024-05-29T16:39:52,240 /tmp/pip-build-env-cqkwedvw/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] 2024-05-29T16:39:52,240 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T16:39:52,240 | ^~~~~~~ 2024-05-29T16:40:04,441 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-cqkwedvw/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 2024-05-29T16:40:06,119 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2024-05-29T16:40:06,119 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=] 2024-05-29T16:40:06,120 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2024-05-29T16:40:06,120 | ~~^ ~ 2024-05-29T16:40:06,120 | | | 2024-05-29T16:40:06,120 | | size_t {aka unsigned int} 2024-05-29T16:40:06,120 | long int 2024-05-29T16:40:06,120 | %d 2024-05-29T16:40:06,121 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=] 2024-05-29T16:40:06,121 487 | printf("size %d framesize %d\n\n", 2024-05-29T16:40:06,121 | ~^ 2024-05-29T16:40:06,121 | | 2024-05-29T16:40:06,121 | int 2024-05-29T16:40:06,121 | %lld 2024-05-29T16:40:06,121 488 | keys[i].size(), m_framesize); 2024-05-29T16:40:06,121 | ~~~~~~~~~~~~~~ 2024-05-29T16:40:06,122 | | 2024-05-29T16:40:06,122 | uint64_t {aka long long unsigned int} 2024-05-29T16:40:06,122 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=] 2024-05-29T16:40:06,122 487 | printf("size %d framesize %d\n\n", 2024-05-29T16:40:06,122 | ~^ 2024-05-29T16:40:06,122 | | 2024-05-29T16:40:06,123 | int 2024-05-29T16:40:06,123 | %lld 2024-05-29T16:40:06,123 488 | keys[i].size(), m_framesize); 2024-05-29T16:40:06,123 | ~~~~~~~~~~~ 2024-05-29T16:40:06,123 | | 2024-05-29T16:40:06,123 | uint64_t {aka long long unsigned int} 2024-05-29T16:40:06,123 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=] 2024-05-29T16:40:06,124 494 | "non-constant time interval at frame %ld\n", i); 2024-05-29T16:40:06,124 | ~~^ ~ 2024-05-29T16:40:06,124 | | | 2024-05-29T16:40:06,124 | | size_t {aka unsigned int} 2024-05-29T16:40:06,124 | long int 2024-05-29T16:40:06,124 | %d 2024-05-29T16:40:06,124 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=] 2024-05-29T16:40:06,125 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2024-05-29T16:40:06,125 | ~~^ ~ 2024-05-29T16:40:06,125 | | | 2024-05-29T16:40:06,125 | | size_t {aka unsigned int} 2024-05-29T16:40:06,125 | long int 2024-05-29T16:40:06,125 | %d 2024-05-29T16:40:06,248 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-29T16:40:06,248 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=] 2024-05-29T16:40:06,248 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2024-05-29T16:40:06,248 | ~~^ 2024-05-29T16:40:06,248 | | 2024-05-29T16:40:06,248 | long int 2024-05-29T16:40:06,249 | %lld 2024-05-29T16:40:06,249 1302 | 3*natoms, pos.count); 2024-05-29T16:40:06,249 | ~~~~~~~~~ 2024-05-29T16:40:06,249 | | 2024-05-29T16:40:06,249 | uint64_t {aka long long unsigned int} 2024-05-29T16:40:06,249 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=] 2024-05-29T16:40:06,249 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2024-05-29T16:40:06,250 | ~~^ 2024-05-29T16:40:06,250 | | 2024-05-29T16:40:06,250 | long int 2024-05-29T16:40:06,250 | %lld 2024-05-29T16:40:06,250 1311 | 3*natoms, vel.count); 2024-05-29T16:40:06,250 | ~~~~~~~~~ 2024-05-29T16:40:06,250 | | 2024-05-29T16:40:06,251 | uint64_t {aka long long unsigned int} 2024-05-29T16:40:06,273 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-29T16:40:06,273 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=] 2024-05-29T16:40:06,273 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2024-05-29T16:40:06,273 | ~~^ 2024-05-29T16:40:06,273 | | 2024-05-29T16:40:06,274 | long int 2024-05-29T16:40:06,274 | %lld 2024-05-29T16:40:06,274 1573 | velblob.count, 3*natoms); 2024-05-29T16:40:06,274 | ~~~~~~~~~~~~~ 2024-05-29T16:40:06,274 | | 2024-05-29T16:40:06,274 | uint64_t {aka long long unsigned int} 2024-05-29T16:40:07,290 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: 2024-05-29T16:40:07,290 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 2024-05-29T16:40:07,290 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2024-05-29T16:40:07,291 | ~~~~~~~~^~~~~ 2024-05-29T16:40:09,506 In file included from /usr/include/c++/10/map:60, 2024-05-29T16:40:09,506 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-29T16:40:09,506 /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> >]’: 2024-05-29T16:40:09,507 /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 2024-05-29T16:40:09,507 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-29T16:40:09,507 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:09,568 /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> >]’: 2024-05-29T16:40:09,568 /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 2024-05-29T16:40:09,569 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-29T16:40:09,569 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:09,569 /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 2024-05-29T16:40:09,623 In file included from /usr/include/c++/10/map:61, 2024-05-29T16:40:09,624 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-29T16:40:09,624 /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> >]’: 2024-05-29T16:40:09,624 /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 2024-05-29T16:40:09,624 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-29T16:40:09,624 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:09,624 521 | std::forward_as_tuple(std::move(__k)), 2024-05-29T16:40:09,625 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:09,625 522 | std::tuple<>()); 2024-05-29T16:40:09,625 | ~~~~~~~~~~~~~~~ 2024-05-29T16:40:10,393 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: 2024-05-29T16:40:10,394 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=] 2024-05-29T16:40:10,394 706 | sprintf(sub, "%03x/", i); 2024-05-29T16:40:10,394 | ^~~~ 2024-05-29T16:40:10,394 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 2024-05-29T16:40:10,394 706 | sprintf(sub, "%03x/", i); 2024-05-29T16:40:10,395 | ^~~~~~~ 2024-05-29T16:40:10,395 mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2024-05-29T16:40:10,395 706 | sprintf(sub, "%03x/", i); 2024-05-29T16:40:10,395 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2024-05-29T16:40:10,395 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=] 2024-05-29T16:40:10,395 714 | sprintf(subsub, "%03x", j); 2024-05-29T16:40:10,395 | ^~~~ 2024-05-29T16:40:10,396 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 2024-05-29T16:40:10,396 714 | sprintf(subsub, "%03x", j); 2024-05-29T16:40:10,396 | ^~~~~~ 2024-05-29T16:40:10,396 mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2024-05-29T16:40:10,396 714 | sprintf(subsub, "%03x", j); 2024-05-29T16:40:10,396 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:10,804 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: 2024-05-29T16:40:10,804 mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-29T16:40:10,805 667 | sprintf(answer, "%03x/", d1); 2024-05-29T16:40:10,805 | ^ 2024-05-29T16:40:10,805 mdtraj/formats/dtr/src/dtrplugin.cxx:667:13: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2024-05-29T16:40:10,805 667 | sprintf(answer, "%03x/", d1); 2024-05-29T16:40:10,805 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:10,806 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=] 2024-05-29T16:40:10,806 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-29T16:40:10,806 | ^~~~ 2024-05-29T16:40:10,806 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2024-05-29T16:40:10,806 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-29T16:40:10,806 | ^~~~~~~~~~~~ 2024-05-29T16:40:10,806 mdtraj/formats/dtr/src/dtrplugin.cxx:665:13: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2024-05-29T16:40:10,806 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-29T16:40:10,807 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:13,505 In file included from /usr/include/c++/10/map:61, 2024-05-29T16:40:13,505 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-29T16:40:13,505 /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’: 2024-05-29T16:40:13,506 /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 2024-05-29T16:40:13,506 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-29T16:40:13,506 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:13,506 521 | std::forward_as_tuple(std::move(__k)), 2024-05-29T16:40:13,506 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-29T16:40:13,506 522 | std::tuple<>()); 2024-05-29T16:40:13,506 | ~~~~~~~~~~~~~~~ 2024-05-29T16:40:18,665 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 2024-05-29T16:40:19,032 building 'mdtraj._rmsd' extension 2024-05-29T16:40:19,033 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd 2024-05-29T16:40:19,034 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src 2024-05-29T16:40:19,035 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-cqkwedvw/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 2024-05-29T16:40:53,338 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-cqkwedvw/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 2024-05-29T16:40:53,540 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-cqkwedvw/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 2024-05-29T16:40:53,787 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-cqkwedvw/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 2024-05-29T16:40:54,477 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 2024-05-29T16:40:54,829 building 'mdtraj._lprmsd' extension 2024-05-29T16:40:54,831 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-cqkwedvw/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 2024-05-29T16:40:55,067 In file included from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-29T16:40:55,068 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T16:40:55,068 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-29T16:40:55,068 from mdtraj/rmsd/_lprmsd.cpp:809: 2024-05-29T16:40:55,068 /tmp/pip-build-env-cqkwedvw/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] 2024-05-29T16:40:55,068 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T16:40:55,068 | ^~~~~~~ 2024-05-29T16:41:05,712 mdtraj/rmsd/_lprmsd.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: 2024-05-29T16:41:05,713 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] 2024-05-29T16:41:05,713 4099 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; 2024-05-29T16:41:05,713 | ^~ 2024-05-29T16:41:16,213 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-cqkwedvw/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 2024-05-29T16:41:18,574 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-cqkwedvw/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 2024-05-29T16:41:18,772 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-cqkwedvw/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 2024-05-29T16:41:19,797 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-cqkwedvw/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 2024-05-29T16:41:20,082 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-cqkwedvw/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 2024-05-29T16:41:20,327 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-cqkwedvw/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 2024-05-29T16:41:20,987 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 2024-05-29T16:41:21,305 building 'mdtraj.core.lib.libtheobald' extension 2024-05-29T16:41:21,306 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-cqkwedvw/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 2024-05-29T16:41:21,960 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-cqkwedvw/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 2024-05-29T16:41:22,158 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 2024-05-29T16:41:22,194 building 'mdtraj.geometry._geometry' extension 2024-05-29T16:41:22,195 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-29T16:41:22,196 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src 2024-05-29T16:41:22,198 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-cqkwedvw/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 2024-05-29T16:41:22,466 In file included from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-29T16:41:22,467 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-29T16:41:22,467 from /tmp/pip-build-env-cqkwedvw/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-29T16:41:22,467 from mdtraj/geometry/src/_geometry.cpp:811: 2024-05-29T16:41:22,467 /tmp/pip-build-env-cqkwedvw/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] 2024-05-29T16:41:22,468 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-29T16:41:22,468 | ^~~~~~~ 2024-05-29T16:41:51,760 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-cqkwedvw/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 2024-05-29T16:42:08,086 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-cqkwedvw/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 2024-05-29T16:42:11,561 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-cqkwedvw/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 2024-05-29T16:42:12,530 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 2024-05-29T16:42:12,964 building 'mdtraj.geometry.drid' extension 2024-05-29T16:42:12,965 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-cqkwedvw/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 2024-05-29T16:42:37,336 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/geometry/include -I/tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:42:37,916 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-cqkwedvw/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 2024-05-29T16:42:38,025 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 2024-05-29T16:42:38,357 building 'mdtraj.geometry.neighbors' extension 2024-05-29T16:42:38,359 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-cqkwedvw/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 2024-05-29T16:43:01,185 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-cqkwedvw/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 2024-05-29T16:43:02,320 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 2024-05-29T16:43:02,640 building 'mdtraj.geometry.neighborlist' extension 2024-05-29T16:43:02,641 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-cqkwedvw/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 2024-05-29T16:43:22,856 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-cqkwedvw/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 2024-05-29T16:43:27,149 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-29T16:43:27,149 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors[0][0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:43:27,149 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2024-05-29T16:43:27,149 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-29T16:43:27,150 mdtraj/geometry/src/neighborlist.cpp:51:53: warning: ‘periodicBoxVectors[1][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:43:27,150 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; 2024-05-29T16:43:27,150 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-29T16:43:27,150 mdtraj/geometry/src/neighborlist.cpp:52:53: warning: ‘periodicBoxVectors[2][2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:43:27,150 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; 2024-05-29T16:43:27,150 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-29T16:43:27,151 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors[0][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-29T16:43:27,151 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2024-05-29T16:43:27,151 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-29T16:43:28,150 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 2024-05-29T16:43:28,517 installing to build/bdist.linux-armv7l/wheel 2024-05-29T16:43:28,517 running install 2024-05-29T16:43:28,544 running install_lib 2024-05-29T16:43:28,554 creating build/bdist.linux-armv7l 2024-05-29T16:43:28,555 creating build/bdist.linux-armv7l/wheel 2024-05-29T16:43:28,557 creating build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T16:43:28,558 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,559 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,561 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,564 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,567 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,568 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,571 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,573 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,576 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,578 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,581 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,583 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,584 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,586 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,588 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,590 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,593 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,595 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-29T16:43:28,597 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,600 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,602 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,603 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,606 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-29T16:43:28,608 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T16:43:28,609 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T16:43:28,610 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T16:43:28,613 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T16:43:28,615 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-29T16:43:28,617 copying build/lib.linux-armv7l-cpython-39/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T16:43:28,619 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-29T16:43:28,620 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-29T16:43:28,622 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-29T16:43:28,624 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-29T16:43:28,626 copying build/lib.linux-armv7l-cpython-39/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T16:43:28,628 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T16:43:28,629 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-29T16:43:28,630 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-29T16:43:28,633 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-29T16:43:28,635 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-29T16:43:28,637 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T16:43:28,639 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T16:43:28,642 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T16:43:28,643 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T16:43:28,646 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T16:43:28,648 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-29T16:43:28,653 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T16:43:28,653 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T16:43:28,655 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T16:43:28,658 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T16:43:28,659 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T16:43:28,661 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T16:43:28,663 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-29T16:43:28,665 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-29T16:43:28,666 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-29T16:43:28,668 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-29T16:43:28,670 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-29T16:43:28,672 copying build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T16:43:28,692 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,693 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,696 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,698 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,701 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-29T16:43:28,702 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-29T16:43:28,706 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-29T16:43:28,707 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-29T16:43:28,710 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-29T16:43:28,712 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-29T16:43:28,714 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-29T16:43:28,717 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,718 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,740 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,743 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,779 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,782 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,784 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,787 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,809 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,811 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,814 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,816 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,819 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,821 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,823 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,825 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,827 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,839 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,842 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-29T16:43:28,844 copying build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T16:43:28,878 copying build/lib.linux-armv7l-cpython-39/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-29T16:43:28,881 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,882 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,884 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,910 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,913 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,975 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,977 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,980 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,982 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,985 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,988 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,990 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,992 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:28,995 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:29,024 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:29,062 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:29,064 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:29,067 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:29,070 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:29,072 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-29T16:43:29,075 running install_egg_info 2024-05-29T16:43:29,092 running egg_info 2024-05-29T16:43:29,100 writing mdtraj.egg-info/PKG-INFO 2024-05-29T16:43:29,104 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-29T16:43:29,106 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-29T16:43:29,107 writing requirements to mdtraj.egg-info/requires.txt 2024-05-29T16:43:29,109 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-29T16:43:29,142 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,142 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,142 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,142 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,143 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,143 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,143 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,143 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,144 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,144 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,145 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,145 dependency /tmp/pip-build-env-cqkwedvw/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 2024-05-29T16:43:29,160 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-29T16:43:29,177 reading manifest template 'MANIFEST.in' 2024-05-29T16:43:29,746 no previously-included directories found matching '__pycache__' 2024-05-29T16:43:29,747 no previously-included directories found matching '*.pyc' 2024-05-29T16:43:29,748 adding license file 'LICENSE' 2024-05-29T16:43:29,763 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-29T16:43:29,765 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.10.0rc2-py3.9.egg-info 2024-05-29T16:43:29,779 running install_scripts 2024-05-29T16:43:29,832 creating build/bdist.linux-armv7l/wheel/mdtraj-1.10.0rc2.dist-info/WHEEL 2024-05-29T16:43:29,835 creating '/tmp/pip-wheel-hcs33agr/.tmp-w54kva70/mdtraj-1.10.0rc2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-29T16:43:29,838 adding 'mdtraj/__init__.py' 2024-05-29T16:43:30,074 adding 'mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:30,440 adding 'mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:30,453 adding 'mdtraj/io.py' 2024-05-29T16:43:30,454 adding 'mdtraj/version.py' 2024-05-29T16:43:30,456 adding 'mdtraj/core/__init__.py' 2024-05-29T16:43:30,459 adding 'mdtraj/core/element.py' 2024-05-29T16:43:30,461 adding 'mdtraj/core/residue_names.py' 2024-05-29T16:43:30,464 adding 'mdtraj/core/selection.py' 2024-05-29T16:43:30,471 adding 'mdtraj/core/topology.py' 2024-05-29T16:43:30,481 adding 'mdtraj/core/trajectory.py' 2024-05-29T16:43:30,483 adding 'mdtraj/core/lib/center.h' 2024-05-29T16:43:30,492 adding 'mdtraj/core/lib/libtheobald.a' 2024-05-29T16:43:30,494 adding 'mdtraj/core/lib/theobald_rmsd.h' 2024-05-29T16:43:30,496 adding 'mdtraj/formats/__init__.py' 2024-05-29T16:43:30,499 adding 'mdtraj/formats/amberrst.py' 2024-05-29T16:43:30,502 adding 'mdtraj/formats/arc.py' 2024-05-29T16:43:30,655 adding 'mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:31,069 adding 'mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:31,086 adding 'mdtraj/formats/gro.py' 2024-05-29T16:43:31,088 adding 'mdtraj/formats/gsd.py' 2024-05-29T16:43:31,093 adding 'mdtraj/formats/hdf5.py' 2024-05-29T16:43:31,094 adding 'mdtraj/formats/hoomdxml.py' 2024-05-29T16:43:31,097 adding 'mdtraj/formats/lammpstrj.py' 2024-05-29T16:43:31,100 adding 'mdtraj/formats/lh5.py' 2024-05-29T16:43:31,103 adding 'mdtraj/formats/mdcrd.py' 2024-05-29T16:43:31,105 adding 'mdtraj/formats/mol2.py' 2024-05-29T16:43:31,108 adding 'mdtraj/formats/netcdf.py' 2024-05-29T16:43:31,109 adding 'mdtraj/formats/openmmxml.py' 2024-05-29T16:43:31,111 adding 'mdtraj/formats/pdbx.py' 2024-05-29T16:43:31,113 adding 'mdtraj/formats/prmtop.py' 2024-05-29T16:43:31,115 adding 'mdtraj/formats/psf.py' 2024-05-29T16:43:31,116 adding 'mdtraj/formats/registry.py' 2024-05-29T16:43:31,380 adding 'mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:31,640 adding 'mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:31,650 adding 'mdtraj/formats/xyzfile.py' 2024-05-29T16:43:31,652 adding 'mdtraj/formats/pdb/__init__.py' 2024-05-29T16:43:31,656 adding 'mdtraj/formats/pdb/pdbfile.py' 2024-05-29T16:43:31,661 adding 'mdtraj/formats/pdb/pdbstructure.py' 2024-05-29T16:43:31,664 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2024-05-29T16:43:31,666 adding 'mdtraj/formats/pdb/data/residues.xml' 2024-05-29T16:43:31,668 adding 'mdtraj/geometry/__init__.py' 2024-05-29T16:43:32,184 adding 'mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:32,205 adding 'mdtraj/geometry/alignment.py' 2024-05-29T16:43:32,207 adding 'mdtraj/geometry/angle.py' 2024-05-29T16:43:32,209 adding 'mdtraj/geometry/contact.py' 2024-05-29T16:43:32,211 adding 'mdtraj/geometry/dihedral.py' 2024-05-29T16:43:32,214 adding 'mdtraj/geometry/distance.py' 2024-05-29T16:43:32,488 adding 'mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:32,498 adding 'mdtraj/geometry/dssp.py' 2024-05-29T16:43:32,501 adding 'mdtraj/geometry/hbond.py' 2024-05-29T16:43:32,503 adding 'mdtraj/geometry/internal.py' 2024-05-29T16:43:32,798 adding 'mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:33,076 adding 'mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so' 2024-05-29T16:43:33,087 adding 'mdtraj/geometry/order.py' 2024-05-29T16:43:33,088 adding 'mdtraj/geometry/rdf.py' 2024-05-29T16:43:33,090 adding 'mdtraj/geometry/rg.py' 2024-05-29T16:43:33,092 adding 'mdtraj/geometry/sasa.py' 2024-05-29T16:43:33,093 adding 'mdtraj/geometry/shape.py' 2024-05-29T16:43:33,095 adding 'mdtraj/geometry/thermodynamic_properties.py' 2024-05-29T16:43:33,097 adding 'mdtraj/nmr/__init__.py' 2024-05-29T16:43:33,099 adding 'mdtraj/nmr/scalar_couplings.py' 2024-05-29T16:43:33,101 adding 'mdtraj/nmr/shift_wrappers.py' 2024-05-29T16:43:33,102 adding 'mdtraj/reporters/__init__.py' 2024-05-29T16:43:33,104 adding 'mdtraj/reporters/basereporter.py' 2024-05-29T16:43:33,106 adding 'mdtraj/reporters/dcdreporter.py' 2024-05-29T16:43:33,107 adding 'mdtraj/reporters/hdf5reporter.py' 2024-05-29T16:43:33,109 adding 'mdtraj/reporters/netcdfreporter.py' 2024-05-29T16:43:33,110 adding 'mdtraj/reporters/xtcreporter.py' 2024-05-29T16:43:33,112 adding 'mdtraj/scripts/__init__.py' 2024-05-29T16:43:33,114 adding 'mdtraj/scripts/mdconvert.py' 2024-05-29T16:43:33,116 adding 'mdtraj/scripts/mdinspect.py' 2024-05-29T16:43:33,118 adding 'mdtraj/testing/__init__.py' 2024-05-29T16:43:33,121 adding 'mdtraj/testing/docscrape.py' 2024-05-29T16:43:33,122 adding 'mdtraj/testing/docstrings.py' 2024-05-29T16:43:33,124 adding 'mdtraj/testing/testing.py' 2024-05-29T16:43:33,126 adding 'mdtraj/utils/__init__.py' 2024-05-29T16:43:33,127 adding 'mdtraj/utils/contextmanagers.py' 2024-05-29T16:43:33,129 adding 'mdtraj/utils/delay_import.py' 2024-05-29T16:43:33,131 adding 'mdtraj/utils/rotation.py' 2024-05-29T16:43:33,132 adding 'mdtraj/utils/singleton.py' 2024-05-29T16:43:33,134 adding 'mdtraj/utils/unitcell.py' 2024-05-29T16:43:33,135 adding 'mdtraj/utils/validation.py' 2024-05-29T16:43:33,137 adding 'mdtraj/utils/zipped.py' 2024-05-29T16:43:33,139 adding 'mdtraj/utils/unit/__init__.py' 2024-05-29T16:43:33,141 adding 'mdtraj/utils/unit/basedimension.py' 2024-05-29T16:43:33,142 adding 'mdtraj/utils/unit/baseunit.py' 2024-05-29T16:43:33,144 adding 'mdtraj/utils/unit/constants.py' 2024-05-29T16:43:33,147 adding 'mdtraj/utils/unit/doctests.py' 2024-05-29T16:43:33,149 adding 'mdtraj/utils/unit/mymatrix.py' 2024-05-29T16:43:33,151 adding 'mdtraj/utils/unit/prefix.py' 2024-05-29T16:43:33,154 adding 'mdtraj/utils/unit/quantity.py' 2024-05-29T16:43:33,156 adding 'mdtraj/utils/unit/standard_dimensions.py' 2024-05-29T16:43:33,159 adding 'mdtraj/utils/unit/unit.py' 2024-05-29T16:43:33,162 adding 'mdtraj/utils/unit/unit_definitions.py' 2024-05-29T16:43:33,164 adding 'mdtraj/utils/unit/unit_math.py' 2024-05-29T16:43:33,166 adding 'mdtraj/utils/unit/unit_operators.py' 2024-05-29T16:43:33,171 adding 'mdtraj-1.10.0rc2.dist-info/LICENSE' 2024-05-29T16:43:33,172 adding 'mdtraj-1.10.0rc2.dist-info/METADATA' 2024-05-29T16:43:33,173 adding 'mdtraj-1.10.0rc2.dist-info/WHEEL' 2024-05-29T16:43:33,174 adding 'mdtraj-1.10.0rc2.dist-info/entry_points.txt' 2024-05-29T16:43:33,175 adding 'mdtraj-1.10.0rc2.dist-info/top_level.txt' 2024-05-29T16:43:33,177 adding 'mdtraj-1.10.0rc2.dist-info/RECORD' 2024-05-29T16:43:33,242 removing build/bdist.linux-armv7l/wheel 2024-05-29T16:43:34,001 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2024-05-29T16:43:34,127 Created wheel for mdtraj: filename=mdtraj-1.10.0rc2-cp39-cp39-linux_armv7l.whl size=6060012 sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b 2024-05-29T16:43:34,128 Stored in directory: /tmp/pip-ephem-wheel-cache-m9qq2emf/wheels/36/f4/2c/876a103cbbfe96e4f90896bf051c40ff3a0fd32079daab4dcd 2024-05-29T16:43:34,145 Successfully built mdtraj 2024-05-29T16:43:34,299 Removed build tracker: '/tmp/pip-build-tracker-fyzrg3wo'