2024-05-30T15:26:23,459 Created temporary directory: /tmp/pip-build-tracker-28yh7p3q 2024-05-30T15:26:23,460 Initialized build tracking at /tmp/pip-build-tracker-28yh7p3q 2024-05-30T15:26:23,461 Created build tracker: /tmp/pip-build-tracker-28yh7p3q 2024-05-30T15:26:23,461 Entered build tracker: /tmp/pip-build-tracker-28yh7p3q 2024-05-30T15:26:23,462 Created temporary directory: /tmp/pip-wheel-9fhva0p7 2024-05-30T15:26:23,465 Created temporary directory: /tmp/pip-ephem-wheel-cache-kcow35va 2024-05-30T15:26:23,487 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-30T15:26:23,491 2 location(s) to search for versions of mdtraj: 2024-05-30T15:26:23,491 * https://pypi.org/simple/mdtraj/ 2024-05-30T15:26:23,491 * https://www.piwheels.org/simple/mdtraj/ 2024-05-30T15:26:23,492 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2024-05-30T15:26:23,492 Getting page https://pypi.org/simple/mdtraj/ 2024-05-30T15:26:23,494 Found index url 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https://files.pythonhosted.org/packages/3b/fd/4ffba665d0b0346072f61d0e8ef7ab281202db445d99136c717c89169a97/mdtraj-1.9.5-cp38-cp38-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T15:26:23,771 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/) 2024-05-30T15:26:23,772 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 2024-05-30T15:26:23,773 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/) 2024-05-30T15:26:23,773 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/) 2024-05-30T15:26:23,774 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/) 2024-05-30T15:26:23,774 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/) 2024-05-30T15:26:23,774 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 2024-05-30T15:26:23,775 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 2024-05-30T15:26:23,776 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/) 2024-05-30T15:26:23,776 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 2024-05-30T15:26:23,777 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/) 2024-05-30T15:26:23,778 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 2024-05-30T15:26:23,778 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 2024-05-30T15:26:23,779 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 2024-05-30T15:26:23,780 Found link https://files.pythonhosted.org/packages/5a/a0/645d6a0156a982c410f61533d96cdb9c5086f0ac55ea97be1fc87a7d95f6/mdtraj-1.10.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.10.0 2024-05-30T15:26:23,781 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2024-05-30T15:26:23,781 Getting page https://www.piwheels.org/simple/mdtraj/ 2024-05-30T15:26:23,783 Found index url https://www.piwheels.org/simple/ 2024-05-30T15:26:23,950 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2024-05-30T15:26:23,957 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/) 2024-05-30T15:26:23,958 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/) 2024-05-30T15:26:23,958 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/) 2024-05-30T15:26:23,958 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/) 2024-05-30T15:26:23,959 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv6l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T15:26:23,959 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv7l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T15:26:23,960 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/) 2024-05-30T15:26:23,960 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/) 2024-05-30T15:26:23,961 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/) 2024-05-30T15:26:23,961 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/) 2024-05-30T15:26:23,962 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/) 2024-05-30T15:26:23,962 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/) 2024-05-30T15:26:23,963 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/) 2024-05-30T15:26:23,963 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/) 2024-05-30T15:26:23,964 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/) 2024-05-30T15:26:23,965 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/) 2024-05-30T15:26:23,965 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/) 2024-05-30T15:26:23,966 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/) 2024-05-30T15:26:23,966 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/) 2024-05-30T15:26:23,966 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/) 2024-05-30T15:26:23,967 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/) 2024-05-30T15:26:23,967 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/) 2024-05-30T15:26:23,968 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2024-05-30T15:26:23,968 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2024-05-30T15:26:23,993 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2024-05-30T15:26:24,011 Collecting mdtraj==1.10.0 2024-05-30T15:26:24,014 Created temporary directory: /tmp/pip-unpack-ych7lkjp 2024-05-30T15:26:24,230 Downloading mdtraj-1.10.0.tar.gz (1.8 MB) 2024-05-30T15:26:25,331 Added mdtraj==1.10.0 from https://files.pythonhosted.org/packages/5a/a0/645d6a0156a982c410f61533d96cdb9c5086f0ac55ea97be1fc87a7d95f6/mdtraj-1.10.0.tar.gz to build tracker '/tmp/pip-build-tracker-28yh7p3q' 2024-05-30T15:26:25,338 Created temporary directory: /tmp/pip-build-env-dj600ech 2024-05-30T15:26:25,343 Installing build dependencies: started 2024-05-30T15:26:25,344 Running command pip subprocess to install build dependencies 2024-05-30T15:26:26,514 Using pip 24.0 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-05-30T15:26:27,011 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-30T15:26:28,452 Collecting setuptools 2024-05-30T15:26:28,481 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.0.0-py3-none-any.whl (863 kB) 2024-05-30T15:26:28,706 Collecting wheel 2024-05-30T15:26:28,721 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-05-30T15:26:29,356 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-30T15:26:29,360 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-30T15:26:29,363 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-30T15:26:29,366 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-30T15:26:29,370 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-05-30T15:26:29,718 Collecting numpy<2 2024-05-30T15:26:29,742 Using cached https://www.piwheels.org/simple/numpy/numpy-1.26.4-cp311-cp311-linux_armv7l.whl (5.6 MB) 2024-05-30T15:26:30,037 Collecting oldest-supported-numpy 2024-05-30T15:26:30,054 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2023.12.21-py3-none-any.whl (4.9 kB) 2024-05-30T15:26:31,340 Collecting Cython~=0.29.36 2024-05-30T15:26:31,360 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.37-cp311-cp311-linux_armv7l.whl (5.0 MB) 2024-05-30T15:26:31,869 Collecting numpy<2 2024-05-30T15:26:31,885 Using cached https://www.piwheels.org/simple/numpy/numpy-1.23.2-cp311-cp311-linux_armv7l.whl (12.4 MB) 2024-05-30T15:26:34,800 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2024-05-30T15:26:35,027 Creating /tmp/pip-build-env-dj600ech/overlay/local/bin 2024-05-30T15:26:35,029 changing mode of /tmp/pip-build-env-dj600ech/overlay/local/bin/wheel to 755 2024-05-30T15:26:45,866 changing mode of /tmp/pip-build-env-dj600ech/overlay/local/bin/f2py to 755 2024-05-30T15:26:45,869 changing mode of /tmp/pip-build-env-dj600ech/overlay/local/bin/f2py3 to 755 2024-05-30T15:26:45,871 changing mode of /tmp/pip-build-env-dj600ech/overlay/local/bin/f2py3.11 to 755 2024-05-30T15:26:48,640 changing mode of /tmp/pip-build-env-dj600ech/overlay/local/bin/cygdb to 755 2024-05-30T15:26:48,642 changing mode of /tmp/pip-build-env-dj600ech/overlay/local/bin/cython to 755 2024-05-30T15:26:48,644 changing mode of /tmp/pip-build-env-dj600ech/overlay/local/bin/cythonize to 755 2024-05-30T15:26:48,700 Successfully installed Cython-0.29.37 numpy-1.23.2 oldest-supported-numpy-2023.12.21 setuptools-70.0.0 wheel-0.43.0 2024-05-30T15:26:49,441 Installing build dependencies: finished with status 'done' 2024-05-30T15:26:49,452 Getting requirements to build wheel: started 2024-05-30T15:26:49,454 Running command Getting requirements to build wheel 2024-05-30T15:26:50,161 Using built-in specs. 2024-05-30T15:26:50,161 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-30T15:26:50,162 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-30T15:26:50,162 Target: arm-linux-gnueabihf 2024-05-30T15:26:50,163 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-30T15:26:50,164 Thread model: posix 2024-05-30T15:26:50,164 Supported LTO compression algorithms: zlib zstd 2024-05-30T15:26:50,165 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-30T15:26:54,413 C compiler: 2024-05-30T15:26:54,413 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-30T15:26:54,414 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-30T15:26:54,414 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-30T15:26:54,415 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-30T15:26:54,415 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-30T15:26:54,416 running egg_info 2024-05-30T15:26:54,420 writing mdtraj.egg-info/PKG-INFO 2024-05-30T15:26:54,423 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-30T15:26:54,425 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-30T15:26:54,427 writing requirements to mdtraj.egg-info/requires.txt 2024-05-30T15:26:54,428 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-30T15:26:54,468 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-30T15:26:54,493 reading manifest template 'MANIFEST.in' 2024-05-30T15:26:55,123 no previously-included directories found matching '__pycache__' 2024-05-30T15:26:55,124 no previously-included directories found matching '*.pyc' 2024-05-30T15:26:55,124 adding license file 'LICENSE' 2024-05-30T15:26:55,136 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-30T15:26:55,234 Getting requirements to build wheel: finished with status 'done' 2024-05-30T15:26:55,243 Created temporary directory: /tmp/pip-modern-metadata-b2zuvqui 2024-05-30T15:26:55,245 Preparing metadata (pyproject.toml): started 2024-05-30T15:26:55,246 Running command Preparing metadata (pyproject.toml) 2024-05-30T15:26:55,901 Using built-in specs. 2024-05-30T15:26:55,902 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-30T15:26:55,903 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-30T15:26:55,903 Target: arm-linux-gnueabihf 2024-05-30T15:26:55,904 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-30T15:26:55,904 Thread model: posix 2024-05-30T15:26:55,905 Supported LTO compression algorithms: zlib zstd 2024-05-30T15:26:55,905 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-30T15:27:00,031 /tmp/pip-wheel-9fhva0p7/mdtraj_2e376ad532df4bdd9aa33396fbcb5a36/basesetup.py:518: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-b2zuvqui --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2024-05-30T15:27:00,032 warnings.warn( 2024-05-30T15:27:01,793 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. 2024-05-30T15:27:01,794 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. 2024-05-30T15:27:01,795 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. 2024-05-30T15:27:23,016 C compiler: 2024-05-30T15:27:23,017 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-30T15:27:23,017 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-30T15:27:23,017 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-30T15:27:23,018 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-30T15:27:23,018 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-30T15:27:23,019 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-30T15:27:23,020 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-30T15:27:23,020 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-30T15:27:23,021 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-30T15:27:23,021 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-30T15:27:23,022 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-30T15:27:23,022 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-30T15:27:23,023 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-30T15:27:23,024 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-30T15:27:23,024 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-30T15:27:23,106 running dist_info 2024-05-30T15:27:23,113 creating /tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info 2024-05-30T15:27:23,119 writing /tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info/PKG-INFO 2024-05-30T15:27:23,123 writing dependency_links to /tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info/dependency_links.txt 2024-05-30T15:27:23,124 writing entry points to /tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info/entry_points.txt 2024-05-30T15:27:23,126 writing requirements to /tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info/requires.txt 2024-05-30T15:27:23,127 writing top-level names to /tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info/top_level.txt 2024-05-30T15:27:23,128 writing manifest file '/tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info/SOURCES.txt' 2024-05-30T15:27:23,174 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,174 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,175 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,175 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,176 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,177 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,177 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,178 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,179 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,179 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,180 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,180 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,180 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,181 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,181 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,182 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,182 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,183 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,183 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,183 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,184 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,185 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,185 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,185 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,186 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,186 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,187 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,188 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,188 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,188 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:27:23,194 reading manifest file '/tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info/SOURCES.txt' 2024-05-30T15:27:23,196 reading manifest template 'MANIFEST.in' 2024-05-30T15:27:23,784 no previously-included directories found matching '__pycache__' 2024-05-30T15:27:23,785 no previously-included directories found matching '*.pyc' 2024-05-30T15:27:23,785 adding license file 'LICENSE' 2024-05-30T15:27:23,794 writing manifest file '/tmp/pip-modern-metadata-b2zuvqui/mdtraj.egg-info/SOURCES.txt' 2024-05-30T15:27:23,796 creating '/tmp/pip-modern-metadata-b2zuvqui/mdtraj-1.10.0.dist-info' 2024-05-30T15:27:24,687 Preparing metadata (pyproject.toml): finished with status 'done' 2024-05-30T15:27:24,691 Source in /tmp/pip-wheel-9fhva0p7/mdtraj_2e376ad532df4bdd9aa33396fbcb5a36 has version 1.10.0, which satisfies requirement mdtraj==1.10.0 from https://files.pythonhosted.org/packages/5a/a0/645d6a0156a982c410f61533d96cdb9c5086f0ac55ea97be1fc87a7d95f6/mdtraj-1.10.0.tar.gz 2024-05-30T15:27:24,692 Removed mdtraj==1.10.0 from https://files.pythonhosted.org/packages/5a/a0/645d6a0156a982c410f61533d96cdb9c5086f0ac55ea97be1fc87a7d95f6/mdtraj-1.10.0.tar.gz from build tracker '/tmp/pip-build-tracker-28yh7p3q' 2024-05-30T15:27:24,696 Created temporary directory: /tmp/pip-unpack-ndeqn9d1 2024-05-30T15:27:24,697 Created temporary directory: /tmp/pip-unpack-7klp54x_ 2024-05-30T15:27:24,705 Building wheels for collected packages: mdtraj 2024-05-30T15:27:24,711 Created temporary directory: /tmp/pip-wheel-alrjb9wl 2024-05-30T15:27:24,712 Destination directory: /tmp/pip-wheel-alrjb9wl 2024-05-30T15:27:24,714 Building wheel for mdtraj (pyproject.toml): started 2024-05-30T15:27:24,715 Running command Building wheel for mdtraj (pyproject.toml) 2024-05-30T15:27:25,400 Using built-in specs. 2024-05-30T15:27:25,401 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-30T15:27:25,402 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2024-05-30T15:27:25,402 Target: arm-linux-gnueabihf 2024-05-30T15:27:25,403 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-30T15:27:25,403 Thread model: posix 2024-05-30T15:27:25,404 Supported LTO compression algorithms: zlib zstd 2024-05-30T15:27:25,404 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2024-05-30T15:27:31,115 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. 2024-05-30T15:27:31,115 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. 2024-05-30T15:27:31,116 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. 2024-05-30T15:27:52,272 C compiler: 2024-05-30T15:27:52,273 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-30T15:27:52,273 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-30T15:27:52,274 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-30T15:27:52,275 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-30T15:27:52,276 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-30T15:27:52,277 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-30T15:27:52,277 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-30T15:27:52,278 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-30T15:27:52,278 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-30T15:27:52,279 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-30T15:27:52,279 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-30T15:27:52,280 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-30T15:27:52,280 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-30T15:27:52,281 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-30T15:27:52,282 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-30T15:27:52,391 running bdist_wheel 2024-05-30T15:27:52,428 running build 2024-05-30T15:27:52,429 running build_py 2024-05-30T15:27:52,438 creating build 2024-05-30T15:27:52,439 creating build/lib.linux-armv7l-cpython-311 2024-05-30T15:27:52,440 creating build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-30T15:27:52,441 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-30T15:27:52,444 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-30T15:27:52,445 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2024-05-30T15:27:52,449 creating build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,450 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,452 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,454 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,457 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,459 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,461 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,463 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,466 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,468 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,470 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,472 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,475 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,477 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,479 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,481 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:27:52,484 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,485 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,487 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,489 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,491 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,493 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,495 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,497 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,500 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,502 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,505 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,507 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,510 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,512 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,514 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,517 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,520 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,522 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,525 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,528 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,529 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,531 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,533 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,535 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,537 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,539 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,542 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,544 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2024-05-30T15:27:52,547 creating build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-30T15:27:52,547 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-30T15:27:52,549 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-30T15:27:52,552 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2024-05-30T15:27:52,555 creating build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-30T15:27:52,556 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-30T15:27:52,559 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-30T15:27:52,560 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-30T15:27:52,564 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-30T15:27:52,566 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-30T15:27:52,570 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2024-05-30T15:27:52,573 creating build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-30T15:27:52,574 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-30T15:27:52,576 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-30T15:27:52,578 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-30T15:27:52,580 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-30T15:27:52,582 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-30T15:27:52,584 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2024-05-30T15:27:52,587 creating build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-30T15:27:52,588 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-30T15:27:52,590 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-30T15:27:52,592 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-30T15:27:52,595 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2024-05-30T15:27:52,597 creating build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-30T15:27:52,598 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-30T15:27:52,600 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-30T15:27:52,602 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2024-05-30T15:27:52,605 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-30T15:27:52,606 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-30T15:27:52,608 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-30T15:27:52,611 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2024-05-30T15:27:52,615 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,616 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,618 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,621 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,623 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,625 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,628 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,630 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,633 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,635 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,637 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,639 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,641 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,644 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2024-05-30T15:27:52,651 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-30T15:27:52,652 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-30T15:27:52,655 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2024-05-30T15:27:52,664 running build_ext 2024-05-30T15:27:52,667 building 'mdtraj.formats.xtc' extension 2024-05-30T15:27:52,667 creating build/temp.linux-armv7l-cpython-311 2024-05-30T15:27:52,668 creating build/temp.linux-armv7l-cpython-311/mdtraj 2024-05-30T15:27:52,669 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats 2024-05-30T15:27:52,669 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc 2024-05-30T15:27:52,670 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src 2024-05-30T15:27:52,671 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:27:52,789 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:27:52,938 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-30T15:27:52,938 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:27:52,939 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-30T15:27:52,940 | ^~~~~~ 2024-05-30T15:27:52,941 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:27:52,941 785 | int smallidx, minidx, maxidx; 2024-05-30T15:27:52,942 | ^~~~~~ 2024-05-30T15:27:52,948 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-30T15:27:52,948 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:27:52,949 1016 | int errval=1; 2024-05-30T15:27:52,949 | ^~~~~~ 2024-05-30T15:27:52,954 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-30T15:27:52,955 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:27:52,955 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-30T15:27:52,956 | ^~~~~~ 2024-05-30T15:27:52,957 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:27:52,958 1302 | int smallidx, minidx, maxidx; 2024-05-30T15:27:52,958 | ^~~~~~ 2024-05-30T15:27:52,966 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-30T15:27:52,967 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:27:52,968 1509 | int errval=1; 2024-05-30T15:27:52,968 | ^~~~~~ 2024-05-30T15:27:55,549 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:27:55,627 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2024-05-30T15:27:55,628 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 2024-05-30T15:27:55,628 66 | int i,j,result; 2024-05-30T15:27:55,629 | ^ 2024-05-30T15:27:55,630 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 2024-05-30T15:27:55,630 66 | int i,j,result; 2024-05-30T15:27:55,631 | ^ 2024-05-30T15:27:55,631 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2024-05-30T15:27:55,632 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2024-05-30T15:27:55,633 119 | if (NULL == xd) 2024-05-30T15:27:55,633 | ^~ 2024-05-30T15:27:55,634 mdtraj/formats/xtc/src/xdrfile_xtc.c:122:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2024-05-30T15:27:55,635 122 | do { 2024-05-30T15:27:55,635 | ^~ 2024-05-30T15:27:55,769 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:27:56,162 In file included from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-30T15:27:56,162 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T15:27:56,163 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-30T15:27:56,164 from mdtraj/formats/xtc/xtc.c:784: 2024-05-30T15:27:56,164 /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-30T15:27:56,165 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T15:27:56,165 | ^~~~~~~ 2024-05-30T15:28:04,626 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2024-05-30T15:28:04,627 mdtraj/formats/xtc/xtc.c:696:40: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:04,628 696 | #define PyInt_FromLong PyLong_FromLong 2024-05-30T15:28:04,628 | ^~~~~~~~~~~~~~~ 2024-05-30T15:28:04,636 mdtraj/formats/xtc/xtc.c:9563:7: note: ‘__pyx_v_status’ was declared here 2024-05-30T15:28:04,637 9563 | int __pyx_v_status; 2024-05-30T15:28:04,638 | ^~~~~~~~~~~~~~ 2024-05-30T15:28:15,564 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2024-05-30T15:28:15,572 mdtraj/formats/xtc/xtc.c:8082:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,573 8082 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-30T15:28:15,573 | ^ 2024-05-30T15:28:15,579 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 2024-05-30T15:28:15,579 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-30T15:28:15,580 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,587 mdtraj/formats/xtc/xtc.c:8078:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,587 8078 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-30T15:28:15,588 | ^ 2024-05-30T15:28:15,593 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 2024-05-30T15:28:15,594 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-30T15:28:15,594 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,601 mdtraj/formats/xtc/xtc.c:8074:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,602 8074 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T15:28:15,602 | ^ 2024-05-30T15:28:15,608 mdtraj/formats/xtc/xtc.c:6485:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 2024-05-30T15:28:15,609 6485 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2024-05-30T15:28:15,609 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,616 mdtraj/formats/xtc/xtc.c:8034:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,616 8034 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T15:28:15,617 | ^ 2024-05-30T15:28:15,622 mdtraj/formats/xtc/xtc.c:6481:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 2024-05-30T15:28:15,623 6481 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; 2024-05-30T15:28:15,623 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,630 mdtraj/formats/xtc/xtc.c:8016:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,631 8016 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T15:28:15,631 | ^ 2024-05-30T15:28:15,637 mdtraj/formats/xtc/xtc.c:6477:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 2024-05-30T15:28:15,637 6477 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; 2024-05-30T15:28:15,638 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,644 mdtraj/formats/xtc/xtc.c:8092:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,645 8092 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T15:28:15,646 | ^ 2024-05-30T15:28:15,651 mdtraj/formats/xtc/xtc.c:6473:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 2024-05-30T15:28:15,652 6473 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; 2024-05-30T15:28:15,652 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,659 mdtraj/formats/xtc/xtc.c:8054:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,659 8054 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-30T15:28:15,660 | ^ 2024-05-30T15:28:15,665 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 2024-05-30T15:28:15,666 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-30T15:28:15,666 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,673 mdtraj/formats/xtc/xtc.c:8050:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,674 8050 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-30T15:28:15,674 | ^ 2024-05-30T15:28:15,680 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 2024-05-30T15:28:15,680 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-30T15:28:15,681 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,688 mdtraj/formats/xtc/xtc.c:8046:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,688 8046 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T15:28:15,689 | ^ 2024-05-30T15:28:15,694 mdtraj/formats/xtc/xtc.c:6467:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 2024-05-30T15:28:15,695 6467 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2024-05-30T15:28:15,695 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,701 mdtraj/formats/xtc/xtc.c:7669:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,702 7669 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-30T15:28:15,703 | ^ 2024-05-30T15:28:15,708 mdtraj/formats/xtc/xtc.c:6469:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 2024-05-30T15:28:15,709 6469 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2024-05-30T15:28:15,709 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:15,715 mdtraj/formats/xtc/xtc.c:7665:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:15,716 7665 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T15:28:15,717 | ^ 2024-05-30T15:28:15,722 mdtraj/formats/xtc/xtc.c:6469:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 2024-05-30T15:28:15,723 6469 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2024-05-30T15:28:15,723 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:20,375 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/xtc.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:28:20,520 building 'mdtraj.formats.trr' extension 2024-05-30T15:28:20,521 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:28:20,632 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:28:20,776 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-30T15:28:20,777 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:28:20,777 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-30T15:28:20,778 | ^~~~~~ 2024-05-30T15:28:20,778 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:28:20,779 785 | int smallidx, minidx, maxidx; 2024-05-30T15:28:20,779 | ^~~~~~ 2024-05-30T15:28:20,786 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-30T15:28:20,786 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:28:20,787 1016 | int errval=1; 2024-05-30T15:28:20,788 | ^~~~~~ 2024-05-30T15:28:20,792 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-30T15:28:20,793 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:28:20,793 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-30T15:28:20,794 | ^~~~~~ 2024-05-30T15:28:20,795 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:28:20,795 1302 | int smallidx, minidx, maxidx; 2024-05-30T15:28:20,796 | ^~~~~~ 2024-05-30T15:28:20,804 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-30T15:28:20,805 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-30T15:28:20,806 1509 | int errval=1; 2024-05-30T15:28:20,807 | ^~~~~~ 2024-05-30T15:28:23,387 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:28:24,181 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:28:24,564 In file included from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-30T15:28:24,565 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T15:28:24,566 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-30T15:28:24,566 from mdtraj/formats/xtc/trr.c:784: 2024-05-30T15:28:24,567 /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-30T15:28:24,567 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T15:28:24,567 | ^~~~~~~ 2024-05-30T15:28:33,758 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2024-05-30T15:28:33,758 mdtraj/formats/xtc/trr.c:696:40: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:33,759 696 | #define PyInt_FromLong PyLong_FromLong 2024-05-30T15:28:33,759 | ^~~~~~~~~~~~~~~ 2024-05-30T15:28:33,769 mdtraj/formats/xtc/trr.c:11089:7: note: ‘__pyx_v_status’ was declared here 2024-05-30T15:28:33,770 11089 | int __pyx_v_status; 2024-05-30T15:28:33,770 | ^~~~~~~~~~~~~~ 2024-05-30T15:28:45,036 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2024-05-30T15:28:45,044 mdtraj/formats/xtc/trr.c:8442:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,045 8442 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-30T15:28:45,046 | ^ 2024-05-30T15:28:45,051 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2024-05-30T15:28:45,052 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-30T15:28:45,053 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,060 mdtraj/formats/xtc/trr.c:8438:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,060 8438 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T15:28:45,061 | ^ 2024-05-30T15:28:45,067 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2024-05-30T15:28:45,067 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-30T15:28:45,068 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,068 mdtraj/formats/xtc/trr.c:1935:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,069 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-30T15:28:45,070 | ^ 2024-05-30T15:28:45,075 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-05-30T15:28:45,076 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-30T15:28:45,077 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,084 mdtraj/formats/xtc/trr.c:8432:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,084 8432 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-05-30T15:28:45,085 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-30T15:28:45,091 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2024-05-30T15:28:45,092 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-30T15:28:45,092 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,099 mdtraj/formats/xtc/trr.c:8385:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,099 8385 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-30T15:28:45,100 | ^ 2024-05-30T15:28:45,106 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2024-05-30T15:28:45,107 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-30T15:28:45,107 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,114 mdtraj/formats/xtc/trr.c:8381:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,115 8381 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T15:28:45,115 | ^ 2024-05-30T15:28:45,121 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2024-05-30T15:28:45,122 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-30T15:28:45,122 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,123 mdtraj/formats/xtc/trr.c:1935:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,124 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-30T15:28:45,124 | ^ 2024-05-30T15:28:45,130 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-05-30T15:28:45,131 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-30T15:28:45,132 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,138 mdtraj/formats/xtc/trr.c:8375:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,139 8375 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-05-30T15:28:45,140 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-30T15:28:45,146 mdtraj/formats/xtc/trr.c:6995:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2024-05-30T15:28:45,146 6995 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-30T15:28:45,147 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,154 mdtraj/formats/xtc/trr.c:8775:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,155 8775 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T15:28:45,155 | ^ 2024-05-30T15:28:45,161 mdtraj/formats/xtc/trr.c:7001:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2024-05-30T15:28:45,162 7001 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-05-30T15:28:45,162 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,170 mdtraj/formats/xtc/trr.c:8771:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,170 8771 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-30T15:28:45,171 | ^ 2024-05-30T15:28:45,177 mdtraj/formats/xtc/trr.c:7001:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2024-05-30T15:28:45,178 7001 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2024-05-30T15:28:45,178 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,185 mdtraj/formats/xtc/trr.c:8616:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,186 8616 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T15:28:45,186 | ^ 2024-05-30T15:28:45,192 mdtraj/formats/xtc/trr.c:6997:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2024-05-30T15:28:45,193 6997 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-05-30T15:28:45,193 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,201 mdtraj/formats/xtc/trr.c:8612:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,201 8612 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-30T15:28:45,202 | ^ 2024-05-30T15:28:45,208 mdtraj/formats/xtc/trr.c:6997:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2024-05-30T15:28:45,208 6997 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2024-05-30T15:28:45,209 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,216 mdtraj/formats/xtc/trr.c:8668:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,217 8668 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T15:28:45,217 | ^ 2024-05-30T15:28:45,223 mdtraj/formats/xtc/trr.c:6981:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2024-05-30T15:28:45,224 6981 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-05-30T15:28:45,225 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:45,232 mdtraj/formats/xtc/trr.c:8664:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:28:45,232 8664 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-30T15:28:45,233 | ^ 2024-05-30T15:28:45,239 mdtraj/formats/xtc/trr.c:6981:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2024-05-30T15:28:45,240 6981 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2024-05-30T15:28:45,240 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:28:51,833 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/trr.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:28:51,979 building 'mdtraj.formats.dcd' extension 2024-05-30T15:28:51,980 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd 2024-05-30T15:28:51,981 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src 2024-05-30T15:28:51,982 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:28:52,452 In file included from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-30T15:28:52,454 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T15:28:52,454 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-30T15:28:52,455 from mdtraj/formats/dcd/dcd.c:782: 2024-05-30T15:28:52,456 /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-30T15:28:52,457 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T15:28:52,457 | ^~~~~~~ 2024-05-30T15:29:01,530 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2024-05-30T15:29:01,531 mdtraj/formats/dcd/dcd.c:694:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:29:01,531 694 | #define PyInt_FromLong PyLong_FromLong 2024-05-30T15:29:01,532 | ^~~~~~~~~~~~~~~ 2024-05-30T15:29:01,536 mdtraj/formats/dcd/dcd.c:5458:7: note: ‘__pyx_v_i’ was declared here 2024-05-30T15:29:01,536 5458 | int __pyx_v_i; 2024-05-30T15:29:01,537 | ^~~~~~~~~ 2024-05-30T15:29:04,715 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:29:06,269 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:29:06,393 building 'mdtraj.formats.dtr' extension 2024-05-30T15:29:06,393 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr 2024-05-30T15:29:06,394 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src 2024-05-30T15:29:06,395 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:29:06,720 In file included from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-30T15:29:06,720 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T15:29:06,721 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-30T15:29:06,721 from mdtraj/formats/dtr/dtr.cpp:803: 2024-05-30T15:29:06,722 /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-30T15:29:06,723 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T15:29:06,723 | ^~~~~~~ 2024-05-30T15:29:20,961 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:29:23,324 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2024-05-30T15:29:23,325 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=] 2024-05-30T15:29:23,325 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2024-05-30T15:29:23,326 | ~~^ ~ 2024-05-30T15:29:23,327 | | | 2024-05-30T15:29:23,327 | | size_t {aka unsigned int} 2024-05-30T15:29:23,328 | long int 2024-05-30T15:29:23,328 | %d 2024-05-30T15:29:23,329 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=] 2024-05-30T15:29:23,330 487 | printf("size %d framesize %d\n\n", 2024-05-30T15:29:23,331 | ~^ 2024-05-30T15:29:23,331 | | 2024-05-30T15:29:23,332 | int 2024-05-30T15:29:23,333 | %lld 2024-05-30T15:29:23,333 488 | keys[i].size(), m_framesize); 2024-05-30T15:29:23,334 | ~~~~~~~~~~~~~~ 2024-05-30T15:29:23,335 | | 2024-05-30T15:29:23,336 | uint64_t {aka long long unsigned int} 2024-05-30T15:29:23,336 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=] 2024-05-30T15:29:23,337 487 | printf("size %d framesize %d\n\n", 2024-05-30T15:29:23,338 | ~^ 2024-05-30T15:29:23,339 | | 2024-05-30T15:29:23,339 | int 2024-05-30T15:29:23,340 | %lld 2024-05-30T15:29:23,341 488 | keys[i].size(), m_framesize); 2024-05-30T15:29:23,341 | ~~~~~~~~~~~ 2024-05-30T15:29:23,342 | | 2024-05-30T15:29:23,343 | uint64_t {aka long long unsigned int} 2024-05-30T15:29:23,343 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=] 2024-05-30T15:29:23,344 494 | "non-constant time interval at frame %ld\n", i); 2024-05-30T15:29:23,345 | ~~^ ~ 2024-05-30T15:29:23,345 | | | 2024-05-30T15:29:23,346 | | size_t {aka unsigned int} 2024-05-30T15:29:23,347 | long int 2024-05-30T15:29:23,348 | %d 2024-05-30T15:29:23,349 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=] 2024-05-30T15:29:23,349 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2024-05-30T15:29:23,350 | ~~^ ~ 2024-05-30T15:29:23,350 | | | 2024-05-30T15:29:23,351 | | size_t {aka unsigned int} 2024-05-30T15:29:23,351 | long int 2024-05-30T15:29:23,352 | %d 2024-05-30T15:29:23,491 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-30T15:29:23,492 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=] 2024-05-30T15:29:23,492 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2024-05-30T15:29:23,493 | ~~^ 2024-05-30T15:29:23,493 | | 2024-05-30T15:29:23,494 | long int 2024-05-30T15:29:23,495 | %lld 2024-05-30T15:29:23,496 1302 | 3*natoms, pos.count); 2024-05-30T15:29:23,496 | ~~~~~~~~~ 2024-05-30T15:29:23,497 | | 2024-05-30T15:29:23,498 | uint64_t {aka long long unsigned int} 2024-05-30T15:29:23,498 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=] 2024-05-30T15:29:23,499 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2024-05-30T15:29:23,500 | ~~^ 2024-05-30T15:29:23,501 | | 2024-05-30T15:29:23,501 | long int 2024-05-30T15:29:23,502 | %lld 2024-05-30T15:29:23,502 1311 | 3*natoms, vel.count); 2024-05-30T15:29:23,503 | ~~~~~~~~~ 2024-05-30T15:29:23,504 | | 2024-05-30T15:29:23,504 | uint64_t {aka long long unsigned int} 2024-05-30T15:29:23,525 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-30T15:29:23,525 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=] 2024-05-30T15:29:23,526 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2024-05-30T15:29:23,527 | ~~^ 2024-05-30T15:29:23,527 | | 2024-05-30T15:29:23,528 | long int 2024-05-30T15:29:23,529 | %lld 2024-05-30T15:29:23,530 1573 | velblob.count, 3*natoms); 2024-05-30T15:29:23,531 | ~~~~~~~~~~~~~ 2024-05-30T15:29:23,531 | | 2024-05-30T15:29:23,532 | uint64_t {aka long long unsigned int} 2024-05-30T15:29:24,835 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2024-05-30T15:29:24,836 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2024-05-30T15:29:24,836 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2024-05-30T15:29:24,837 | ~~~~~~~~^~~~~ 2024-05-30T15:29:27,620 In file included from /usr/include/c++/12/map:60, 2024-05-30T15:29:27,621 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-30T15:29:27,621 /usr/include/c++/12/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-30T15:29:27,622 /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T15:29:27,623 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-30T15:29:27,623 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:27,691 /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-30T15:29:27,692 /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T15:29:27,693 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-30T15:29:27,693 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:27,752 In file included from /usr/include/c++/12/map:61: 2024-05-30T15:29:27,753 /usr/include/c++/12/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-30T15:29:27,753 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T15:29:27,754 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-30T15:29:27,755 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:27,755 531 | std::forward_as_tuple(std::move(__k)), 2024-05-30T15:29:27,756 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:27,757 532 | std::tuple<>()); 2024-05-30T15:29:27,757 | ~~~~~~~~~~~~~~~ 2024-05-30T15:29:27,845 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’, 2024-05-30T15:29:27,846 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28: 2024-05-30T15:29:27,846 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T15:29:27,847 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-30T15:29:27,848 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:27,849 531 | std::forward_as_tuple(std::move(__k)), 2024-05-30T15:29:27,849 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:27,850 532 | std::tuple<>()); 2024-05-30T15:29:27,851 | ~~~~~~~~~~~~~~~ 2024-05-30T15:29:28,694 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2024-05-30T15:29:28,695 mdtraj/formats/dtr/src/dtrplugin.cxx:706:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2024-05-30T15:29:28,696 706 | sprintf(sub, "%03x/", i); 2024-05-30T15:29:28,696 | ^~~~ 2024-05-30T15:29:28,697 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2024-05-30T15:29:28,698 706 | sprintf(sub, "%03x/", i); 2024-05-30T15:29:28,698 | ^~~~~~~ 2024-05-30T15:29:28,699 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2024-05-30T15:29:28,700 706 | sprintf(sub, "%03x/", i); 2024-05-30T15:29:28,701 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2024-05-30T15:29:28,701 mdtraj/formats/dtr/src/dtrplugin.cxx:714:30: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2024-05-30T15:29:28,702 714 | sprintf(subsub, "%03x", j); 2024-05-30T15:29:28,703 | ^~~~ 2024-05-30T15:29:28,704 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2024-05-30T15:29:28,704 714 | sprintf(subsub, "%03x", j); 2024-05-30T15:29:28,705 | ^~~~~~ 2024-05-30T15:29:28,705 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2024-05-30T15:29:28,706 714 | sprintf(subsub, "%03x", j); 2024-05-30T15:29:28,706 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:29,102 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2024-05-30T15:29:29,102 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-30T15:29:29,103 667 | sprintf(answer, "%03x/", d1); 2024-05-30T15:29:29,103 | ^ 2024-05-30T15:29:29,104 In function ‘std::string DDreldir(const std::string&, int, int)’, 2024-05-30T15:29:29,105 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2024-05-30T15:29:29,105 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2024-05-30T15:29:29,106 667 | sprintf(answer, "%03x/", d1); 2024-05-30T15:29:29,106 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:29,107 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2024-05-30T15:29:29,108 mdtraj/formats/dtr/src/dtrplugin.cxx:665:35: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 2024-05-30T15:29:29,109 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-30T15:29:29,109 | ^~~~ 2024-05-30T15:29:29,110 In function ‘std::string DDreldir(const std::string&, int, int)’, 2024-05-30T15:29:29,111 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2024-05-30T15:29:29,112 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2024-05-30T15:29:29,113 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-30T15:29:29,113 | ^~~~~~~~~~~~ 2024-05-30T15:29:29,114 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2024-05-30T15:29:29,115 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-30T15:29:29,115 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:32,269 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’, 2024-05-30T15:29:32,269 inlined from ‘int desres::molfile::DtrReader::frame_from_bytes(const void*, uint64_t, molfile_timestep_t*) const’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1735:38: 2024-05-30T15:29:32,270 /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T15:29:32,271 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-30T15:29:32,272 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:32,272 531 | std::forward_as_tuple(std::move(__k)), 2024-05-30T15:29:32,273 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T15:29:32,273 532 | std::tuple<>()); 2024-05-30T15:29:32,274 | ~~~~~~~~~~~~~~~ 2024-05-30T15:29:37,249 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:29:37,575 building 'mdtraj._rmsd' extension 2024-05-30T15:29:37,576 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd 2024-05-30T15:29:37,577 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src 2024-05-30T15:29:37,577 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:18,018 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:18,223 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:18,481 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:19,229 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:30:19,533 building 'mdtraj._lprmsd' extension 2024-05-30T15:30:19,533 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:19,797 In file included from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-30T15:30:19,798 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T15:30:19,798 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-30T15:30:19,799 from mdtraj/rmsd/_lprmsd.cpp:812: 2024-05-30T15:30:19,799 /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-30T15:30:19,800 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T15:30:19,800 | ^~~~~~~ 2024-05-30T15:30:43,844 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:46,645 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:46,847 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:48,104 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:48,405 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:48,663 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:49,443 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:30:49,734 building 'mdtraj.core.lib.libtheobald' extension 2024-05-30T15:30:49,735 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2024-05-30T15:30:50,477 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2024-05-30T15:30:50,678 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src/center.o 2024-05-30T15:30:50,704 building 'mdtraj.geometry._geometry' extension 2024-05-30T15:30:50,705 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry 2024-05-30T15:30:50,706 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src 2024-05-30T15:30:50,707 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:30:50,983 In file included from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2024-05-30T15:30:50,984 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T15:30:50,985 from /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-30T15:30:50,985 from mdtraj/geometry/src/_geometry.cpp:814: 2024-05-30T15:30:50,986 /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-05-30T15:30:50,987 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T15:30:50,988 | ^~~~~~~ 2024-05-30T15:31:25,266 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:31:39,533 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:31:43,549 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:31:44,692 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/sasa.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:31:45,039 building 'mdtraj.geometry.drid' extension 2024-05-30T15:31:45,040 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:32:14,333 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:32:14,971 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:32:15,079 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/moments.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:32:15,369 building 'mdtraj.geometry.neighbors' extension 2024-05-30T15:32:15,370 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:32:42,836 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:32:44,137 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighbors.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:32:44,418 building 'mdtraj.geometry.neighborlist' extension 2024-05-30T15:32:44,418 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:33:09,158 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T15:33:13,582 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2024-05-30T15:33:13,583 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2024-05-30T15:33:13,583 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:33:13,584 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2024-05-30T15:33:13,585 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-30T15:33:13,586 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-30T15:33:13,586 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-30T15:33:13,587 341 | float periodicBoxVectors[3][3]; 2024-05-30T15:33:13,588 | ^~~~~~~~~~~~~~~~~~ 2024-05-30T15:33:13,589 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2024-05-30T15:33:13,589 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2024-05-30T15:33:13,590 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:33:13,591 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2024-05-30T15:33:13,591 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-30T15:33:13,592 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-30T15:33:13,593 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-30T15:33:13,593 341 | float periodicBoxVectors[3][3]; 2024-05-30T15:33:13,594 | ^~~~~~~~~~~~~~~~~~ 2024-05-30T15:33:13,594 mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:33:13,595 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); 2024-05-30T15:33:13,595 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-30T15:33:13,596 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-30T15:33:13,596 341 | float periodicBoxVectors[3][3]; 2024-05-30T15:33:13,597 | ^~~~~~~~~~~~~~~~~~ 2024-05-30T15:33:13,597 mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-30T15:33:13,598 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); 2024-05-30T15:33:13,599 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-30T15:33:13,599 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2024-05-30T15:33:13,600 341 | float periodicBoxVectors[3][3]; 2024-05-30T15:33:13,601 | ^~~~~~~~~~~~~~~~~~ 2024-05-30T15:33:14,420 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src/neighborlist.o -L/usr/lib/arm-linux-gnueabihf -lgomp -o build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so 2024-05-30T15:33:14,737 installing to build/bdist.linux-armv7l/wheel 2024-05-30T15:33:14,738 running install 2024-05-30T15:33:14,762 running install_lib 2024-05-30T15:33:14,771 creating build/bdist.linux-armv7l 2024-05-30T15:33:14,772 creating build/bdist.linux-armv7l/wheel 2024-05-30T15:33:14,774 creating build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T15:33:14,775 copying build/lib.linux-armv7l-cpython-311/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T15:33:14,778 copying build/lib.linux-armv7l-cpython-311/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T15:33:14,780 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,781 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,784 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,786 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,816 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,819 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,821 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,823 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,826 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,875 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,877 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,879 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,881 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,883 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,886 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,907 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,909 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,911 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,936 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,939 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T15:33:14,941 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,942 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,944 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,947 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,948 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,950 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,952 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,955 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,957 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,989 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:14,991 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,011 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,013 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,015 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,018 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,029 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,053 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-30T15:33:15,054 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-30T15:33:15,056 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-30T15:33:15,057 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-30T15:33:15,059 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-30T15:33:15,062 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-30T15:33:15,065 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-30T15:33:15,068 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,070 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,073 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,076 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,079 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,081 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,083 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T15:33:15,087 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,087 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,090 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,092 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,093 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,095 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,097 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,100 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,102 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,104 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,107 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,109 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,111 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,113 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,116 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,117 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,119 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T15:33:15,122 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,124 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,125 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,127 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,129 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,131 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T15:33:15,134 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-30T15:33:15,134 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-30T15:33:15,136 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-30T15:33:15,139 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-30T15:33:15,141 copying build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T15:33:15,162 copying build/lib.linux-armv7l-cpython-311/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T15:33:15,165 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T15:33:15,165 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T15:33:15,168 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T15:33:15,169 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T15:33:15,173 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T15:33:15,175 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-30T15:33:15,176 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-30T15:33:15,178 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-30T15:33:15,180 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-30T15:33:15,183 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T15:33:15,186 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T15:33:15,189 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T15:33:15,190 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T15:33:15,192 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T15:33:15,194 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T15:33:15,196 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T15:33:15,198 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T15:33:15,200 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T15:33:15,202 copying build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T15:33:15,241 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T15:33:15,241 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T15:33:15,243 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T15:33:15,246 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T15:33:15,248 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T15:33:15,251 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-30T15:33:15,252 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-30T15:33:15,253 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-30T15:33:15,256 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-30T15:33:15,258 running install_egg_info 2024-05-30T15:33:15,271 running egg_info 2024-05-30T15:33:15,276 writing mdtraj.egg-info/PKG-INFO 2024-05-30T15:33:15,279 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-30T15:33:15,280 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-30T15:33:15,282 writing requirements to mdtraj.egg-info/requires.txt 2024-05-30T15:33:15,283 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-30T15:33:15,316 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,316 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,317 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,318 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,318 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,319 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,319 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,320 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,321 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,321 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,322 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,322 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,322 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,323 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,323 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,324 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,325 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,325 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,326 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,326 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,327 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,328 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,328 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,329 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,329 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,330 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,330 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,331 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,331 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,332 dependency /tmp/pip-build-env-dj600ech/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-05-30T15:33:15,339 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-30T15:33:15,356 reading manifest template 'MANIFEST.in' 2024-05-30T15:33:15,950 no previously-included directories found matching '__pycache__' 2024-05-30T15:33:15,951 no previously-included directories found matching '*.pyc' 2024-05-30T15:33:15,952 adding license file 'LICENSE' 2024-05-30T15:33:15,964 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-30T15:33:15,966 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.10.0-py3.11.egg-info 2024-05-30T15:33:15,979 running install_scripts 2024-05-30T15:33:16,034 creating build/bdist.linux-armv7l/wheel/mdtraj-1.10.0.dist-info/WHEEL 2024-05-30T15:33:16,037 creating '/tmp/pip-wheel-alrjb9wl/.tmp-y2keufru/mdtraj-1.10.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-30T15:33:16,039 adding 'mdtraj/__init__.py' 2024-05-30T15:33:16,268 adding 'mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:16,640 adding 'mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:16,654 adding 'mdtraj/io.py' 2024-05-30T15:33:16,656 adding 'mdtraj/version.py' 2024-05-30T15:33:16,657 adding 'mdtraj/core/__init__.py' 2024-05-30T15:33:16,660 adding 'mdtraj/core/element.py' 2024-05-30T15:33:16,663 adding 'mdtraj/core/residue_names.py' 2024-05-30T15:33:16,665 adding 'mdtraj/core/selection.py' 2024-05-30T15:33:16,673 adding 'mdtraj/core/topology.py' 2024-05-30T15:33:16,682 adding 'mdtraj/core/trajectory.py' 2024-05-30T15:33:16,684 adding 'mdtraj/core/lib/center.h' 2024-05-30T15:33:16,692 adding 'mdtraj/core/lib/libtheobald.a' 2024-05-30T15:33:16,693 adding 'mdtraj/core/lib/theobald_rmsd.h' 2024-05-30T15:33:16,695 adding 'mdtraj/formats/__init__.py' 2024-05-30T15:33:16,698 adding 'mdtraj/formats/amberrst.py' 2024-05-30T15:33:16,701 adding 'mdtraj/formats/arc.py' 2024-05-30T15:33:16,847 adding 'mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:17,249 adding 'mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:17,264 adding 'mdtraj/formats/gro.py' 2024-05-30T15:33:17,266 adding 'mdtraj/formats/gsd.py' 2024-05-30T15:33:17,271 adding 'mdtraj/formats/hdf5.py' 2024-05-30T15:33:17,273 adding 'mdtraj/formats/hoomdxml.py' 2024-05-30T15:33:17,276 adding 'mdtraj/formats/lammpstrj.py' 2024-05-30T15:33:17,278 adding 'mdtraj/formats/lh5.py' 2024-05-30T15:33:17,281 adding 'mdtraj/formats/mdcrd.py' 2024-05-30T15:33:17,283 adding 'mdtraj/formats/mol2.py' 2024-05-30T15:33:17,286 adding 'mdtraj/formats/netcdf.py' 2024-05-30T15:33:17,287 adding 'mdtraj/formats/openmmxml.py' 2024-05-30T15:33:17,290 adding 'mdtraj/formats/pdbx.py' 2024-05-30T15:33:17,292 adding 'mdtraj/formats/prmtop.py' 2024-05-30T15:33:17,293 adding 'mdtraj/formats/psf.py' 2024-05-30T15:33:17,295 adding 'mdtraj/formats/registry.py' 2024-05-30T15:33:17,559 adding 'mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:17,821 adding 'mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:17,830 adding 'mdtraj/formats/xyzfile.py' 2024-05-30T15:33:17,832 adding 'mdtraj/formats/pdb/__init__.py' 2024-05-30T15:33:17,836 adding 'mdtraj/formats/pdb/pdbfile.py' 2024-05-30T15:33:17,841 adding 'mdtraj/formats/pdb/pdbstructure.py' 2024-05-30T15:33:17,843 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2024-05-30T15:33:17,845 adding 'mdtraj/formats/pdb/data/residues.xml' 2024-05-30T15:33:17,847 adding 'mdtraj/geometry/__init__.py' 2024-05-30T15:33:18,327 adding 'mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:18,345 adding 'mdtraj/geometry/alignment.py' 2024-05-30T15:33:18,346 adding 'mdtraj/geometry/angle.py' 2024-05-30T15:33:18,348 adding 'mdtraj/geometry/contact.py' 2024-05-30T15:33:18,351 adding 'mdtraj/geometry/dihedral.py' 2024-05-30T15:33:18,353 adding 'mdtraj/geometry/distance.py' 2024-05-30T15:33:18,630 adding 'mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:18,639 adding 'mdtraj/geometry/dssp.py' 2024-05-30T15:33:18,642 adding 'mdtraj/geometry/hbond.py' 2024-05-30T15:33:18,644 adding 'mdtraj/geometry/internal.py' 2024-05-30T15:33:18,929 adding 'mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:19,203 adding 'mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so' 2024-05-30T15:33:19,213 adding 'mdtraj/geometry/order.py' 2024-05-30T15:33:19,214 adding 'mdtraj/geometry/rdf.py' 2024-05-30T15:33:19,216 adding 'mdtraj/geometry/rg.py' 2024-05-30T15:33:19,218 adding 'mdtraj/geometry/sasa.py' 2024-05-30T15:33:19,219 adding 'mdtraj/geometry/shape.py' 2024-05-30T15:33:19,221 adding 'mdtraj/geometry/thermodynamic_properties.py' 2024-05-30T15:33:19,222 adding 'mdtraj/nmr/__init__.py' 2024-05-30T15:33:19,224 adding 'mdtraj/nmr/scalar_couplings.py' 2024-05-30T15:33:19,226 adding 'mdtraj/nmr/shift_wrappers.py' 2024-05-30T15:33:19,228 adding 'mdtraj/reporters/__init__.py' 2024-05-30T15:33:19,230 adding 'mdtraj/reporters/basereporter.py' 2024-05-30T15:33:19,231 adding 'mdtraj/reporters/dcdreporter.py' 2024-05-30T15:33:19,232 adding 'mdtraj/reporters/hdf5reporter.py' 2024-05-30T15:33:19,234 adding 'mdtraj/reporters/netcdfreporter.py' 2024-05-30T15:33:19,235 adding 'mdtraj/reporters/xtcreporter.py' 2024-05-30T15:33:19,237 adding 'mdtraj/scripts/__init__.py' 2024-05-30T15:33:19,240 adding 'mdtraj/scripts/mdconvert.py' 2024-05-30T15:33:19,241 adding 'mdtraj/scripts/mdinspect.py' 2024-05-30T15:33:19,243 adding 'mdtraj/testing/__init__.py' 2024-05-30T15:33:19,246 adding 'mdtraj/testing/docscrape.py' 2024-05-30T15:33:19,248 adding 'mdtraj/testing/docstrings.py' 2024-05-30T15:33:19,249 adding 'mdtraj/testing/testing.py' 2024-05-30T15:33:19,251 adding 'mdtraj/utils/__init__.py' 2024-05-30T15:33:19,252 adding 'mdtraj/utils/contextmanagers.py' 2024-05-30T15:33:19,254 adding 'mdtraj/utils/delay_import.py' 2024-05-30T15:33:19,256 adding 'mdtraj/utils/rotation.py' 2024-05-30T15:33:19,257 adding 'mdtraj/utils/singleton.py' 2024-05-30T15:33:19,259 adding 'mdtraj/utils/unitcell.py' 2024-05-30T15:33:19,260 adding 'mdtraj/utils/validation.py' 2024-05-30T15:33:19,262 adding 'mdtraj/utils/zipped.py' 2024-05-30T15:33:19,264 adding 'mdtraj/utils/unit/__init__.py' 2024-05-30T15:33:19,266 adding 'mdtraj/utils/unit/basedimension.py' 2024-05-30T15:33:19,267 adding 'mdtraj/utils/unit/baseunit.py' 2024-05-30T15:33:19,269 adding 'mdtraj/utils/unit/constants.py' 2024-05-30T15:33:19,271 adding 'mdtraj/utils/unit/doctests.py' 2024-05-30T15:33:19,274 adding 'mdtraj/utils/unit/mymatrix.py' 2024-05-30T15:33:19,275 adding 'mdtraj/utils/unit/prefix.py' 2024-05-30T15:33:19,279 adding 'mdtraj/utils/unit/quantity.py' 2024-05-30T15:33:19,281 adding 'mdtraj/utils/unit/standard_dimensions.py' 2024-05-30T15:33:19,284 adding 'mdtraj/utils/unit/unit.py' 2024-05-30T15:33:19,286 adding 'mdtraj/utils/unit/unit_definitions.py' 2024-05-30T15:33:19,288 adding 'mdtraj/utils/unit/unit_math.py' 2024-05-30T15:33:19,290 adding 'mdtraj/utils/unit/unit_operators.py' 2024-05-30T15:33:19,295 adding 'mdtraj-1.10.0.dist-info/LICENSE' 2024-05-30T15:33:19,296 adding 'mdtraj-1.10.0.dist-info/METADATA' 2024-05-30T15:33:19,297 adding 'mdtraj-1.10.0.dist-info/WHEEL' 2024-05-30T15:33:19,298 adding 'mdtraj-1.10.0.dist-info/entry_points.txt' 2024-05-30T15:33:19,299 adding 'mdtraj-1.10.0.dist-info/top_level.txt' 2024-05-30T15:33:19,301 adding 'mdtraj-1.10.0.dist-info/RECORD' 2024-05-30T15:33:19,372 removing build/bdist.linux-armv7l/wheel 2024-05-30T15:33:20,215 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2024-05-30T15:33:20,352 Created wheel for mdtraj: filename=mdtraj-1.10.0-cp311-cp311-linux_armv7l.whl size=6326229 sha256=b303bd85a6fe8b1a38c95c47fe66624944c9783bcccb08afdc041d048d4a489b 2024-05-30T15:33:20,353 Stored in directory: /tmp/pip-ephem-wheel-cache-kcow35va/wheels/44/26/87/76e59d0b553300625c4afe8af0878ab05a8f8290ecb006f6c2 2024-05-30T15:33:20,369 Successfully built mdtraj 2024-05-30T15:33:20,523 Removed build tracker: '/tmp/pip-build-tracker-28yh7p3q'