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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/) 2023-09-26T00:22:01,339 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/) 2023-09-26T00:22:01,339 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/) 2023-09-26T00:22:01,340 Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz (from 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https://pypi.org/simple/mdtraj/) 2023-09-26T00:22:01,343 Found link https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.9 2023-09-26T00:22:01,343 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2023-09-26T00:22:01,344 Getting page https://www.piwheels.org/simple/mdtraj/ 2023-09-26T00:22:01,346 Found index url https://www.piwheels.org/simple/ 2023-09-26T00:22:01,507 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2023-09-26T00:22:01,511 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/) 2023-09-26T00:22:01,511 Skipping link: No binaries permitted for mdtraj: 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https://www.piwheels.org/simple/mdtraj/) 2023-09-26T00:22:01,514 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/) 2023-09-26T00:22:01,514 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/) 2023-09-26T00:22:01,514 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2023-09-26T00:22:01,515 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2023-09-26T00:22:01,515 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2023-09-26T00:22:01,540 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2023-09-26T00:22:01,559 Collecting mdtraj==1.9.9 2023-09-26T00:22:01,561 Created temporary directory: /tmp/pip-unpack-uxmlcs_l 2023-09-26T00:22:01,697 Downloading mdtraj-1.9.9.tar.gz (2.2 MB) 2023-09-26T00:22:03,005 Added mdtraj==1.9.9 from https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz to build tracker '/tmp/pip-build-tracker-009g3a57' 2023-09-26T00:22:03,010 Created temporary directory: /tmp/pip-build-env-esueuvwf 2023-09-26T00:22:03,015 Installing build dependencies: started 2023-09-26T00:22:03,017 Running command pip subprocess to install build dependencies 2023-09-26T00:22:04,186 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-26T00:22:04,707 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-26T00:22:06,259 Collecting setuptools 2023-09-26T00:22:06,260 Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-26T00:22:06,265 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-26T00:22:06,471 Collecting wheel 2023-09-26T00:22:06,486 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-26T00:22:06,597 Collecting oldest-supported-numpy 2023-09-26T00:22:06,619 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2023.8.3-py3-none-any.whl (4.8 kB) 2023-09-26T00:22:07,992 Collecting Cython~=0.29.36 2023-09-26T00:22:07,993 Obtaining dependency information for Cython~=0.29.36 from https://files.pythonhosted.org/packages/3f/d6/9eed523aeaca42acbaa3e6d3850edae780dc7f8da9df1bf6a2ceb851839c/Cython-0.29.36-py2.py3-none-any.whl.metadata 2023-09-26T00:22:08,001 Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-26T00:22:09,035 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) 2023-09-26T00:22:09,042 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) 2023-09-26T00:22:09,050 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) 2023-09-26T00:22:09,056 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) 2023-09-26T00:22:09,064 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) 2023-09-26T00:22:09,437 Collecting numpy==1.23.2 (from oldest-supported-numpy) 2023-09-26T00:22:10,295 Using cached https://www.piwheels.org/simple/numpy/numpy-1.23.2-cp311-cp311-linux_armv7l.whl (12.4 MB) 2023-09-26T00:22:10,678 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-26T00:22:10,716 Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB) 2023-09-26T00:22:13,351 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2023-09-26T00:22:13,571 Creating /tmp/pip-build-env-esueuvwf/overlay/local/bin 2023-09-26T00:22:13,573 changing mode of /tmp/pip-build-env-esueuvwf/overlay/local/bin/wheel to 755 2023-09-26T00:22:24,566 changing mode of /tmp/pip-build-env-esueuvwf/overlay/local/bin/f2py to 755 2023-09-26T00:22:24,568 changing mode of /tmp/pip-build-env-esueuvwf/overlay/local/bin/f2py3 to 755 2023-09-26T00:22:24,570 changing mode of /tmp/pip-build-env-esueuvwf/overlay/local/bin/f2py3.11 to 755 2023-09-26T00:22:27,075 changing mode of /tmp/pip-build-env-esueuvwf/overlay/local/bin/cygdb to 755 2023-09-26T00:22:27,077 changing mode of /tmp/pip-build-env-esueuvwf/overlay/local/bin/cython to 755 2023-09-26T00:22:27,079 changing mode of /tmp/pip-build-env-esueuvwf/overlay/local/bin/cythonize to 755 2023-09-26T00:22:27,133 Successfully installed Cython-0.29.36 numpy-1.23.2 oldest-supported-numpy-2023.8.3 setuptools-68.2.2 wheel-0.41.2 2023-09-26T00:22:27,819 Installing build dependencies: finished with status 'done' 2023-09-26T00:22:27,833 Getting requirements to build wheel: started 2023-09-26T00:22:27,834 Running command Getting requirements to build wheel 2023-09-26T00:22:28,503 Using built-in specs. 2023-09-26T00:22:28,504 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-26T00:22:28,505 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2023-09-26T00:22:28,505 Target: arm-linux-gnueabihf 2023-09-26T00:22:28,506 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 2023-09-26T00:22:28,506 Thread model: posix 2023-09-26T00:22:28,507 Supported LTO compression algorithms: zlib zstd 2023-09-26T00:22:28,508 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-26T00:22:32,343 C compiler: 2023-09-26T00:22:32,343 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-09-26T00:22:32,344 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-09-26T00:22:32,344 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-09-26T00:22:32,345 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-09-26T00:22:32,345 Attempting to autodetect NEON support... Did not detect NEON support 2023-09-26T00:22:32,346 running egg_info 2023-09-26T00:22:32,349 writing mdtraj.egg-info/PKG-INFO 2023-09-26T00:22:32,353 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2023-09-26T00:22:32,355 writing entry points to mdtraj.egg-info/entry_points.txt 2023-09-26T00:22:32,356 writing requirements to mdtraj.egg-info/requires.txt 2023-09-26T00:22:32,357 writing top-level names to mdtraj.egg-info/top_level.txt 2023-09-26T00:22:32,389 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-09-26T00:22:32,418 reading manifest template 'MANIFEST.in' 2023-09-26T00:22:33,203 no previously-included directories found matching '__pycache__' 2023-09-26T00:22:33,204 no previously-included directories found matching '*.pyc' 2023-09-26T00:22:33,205 adding license file 'LICENSE' 2023-09-26T00:22:33,218 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-09-26T00:22:33,307 Getting requirements to build wheel: finished with status 'done' 2023-09-26T00:22:33,318 Created temporary directory: /tmp/pip-modern-metadata-ko0abzrm 2023-09-26T00:22:33,320 Preparing metadata (pyproject.toml): started 2023-09-26T00:22:33,321 Running command Preparing metadata (pyproject.toml) 2023-09-26T00:22:33,928 Using built-in specs. 2023-09-26T00:22:33,929 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-26T00:22:33,929 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2023-09-26T00:22:33,930 Target: arm-linux-gnueabihf 2023-09-26T00:22:33,931 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 2023-09-26T00:22:33,931 Thread model: posix 2023-09-26T00:22:33,932 Supported LTO compression algorithms: zlib zstd 2023-09-26T00:22:33,932 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-26T00:22:37,710 /tmp/pip-wheel-sppucq18/mdtraj_4b4355f3616d46298bd275003a9c28c3/basesetup.py:451: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-ko0abzrm --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2023-09-26T00:22:37,710 warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 2023-09-26T00:22:39,929 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-26T00:22:39,930 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-26T00:22:39,931 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-26T00:23:16,054 C compiler: 2023-09-26T00:23:16,055 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-09-26T00:23:16,055 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-09-26T00:23:16,056 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-09-26T00:23:16,056 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-09-26T00:23:16,057 Attempting to autodetect NEON support... Did not detect NEON support 2023-09-26T00:23:16,058 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx 2023-09-26T00:23:16,058 [ 2/12] Cythonizing mdtraj/geometry/drid.pyx 2023-09-26T00:23:16,059 [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx 2023-09-26T00:23:16,059 [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx 2023-09-26T00:23:16,060 [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx 2023-09-26T00:23:16,060 [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2023-09-26T00:23:16,061 [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx 2023-09-26T00:23:16,061 [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx 2023-09-26T00:23:16,062 [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx 2023-09-26T00:23:16,062 [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx 2023-09-26T00:23:16,063 [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx 2023-09-26T00:23:16,064 [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx 2023-09-26T00:23:16,106 running dist_info 2023-09-26T00:23:16,128 creating /tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info 2023-09-26T00:23:16,135 writing /tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info/PKG-INFO 2023-09-26T00:23:16,138 writing dependency_links to /tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info/dependency_links.txt 2023-09-26T00:23:16,140 writing entry points to /tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info/entry_points.txt 2023-09-26T00:23:16,141 writing requirements to /tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info/requires.txt 2023-09-26T00:23:16,142 writing top-level names to /tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info/top_level.txt 2023-09-26T00:23:16,144 writing manifest file '/tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info/SOURCES.txt' 2023-09-26T00:23:16,187 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,187 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,188 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,189 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,189 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,190 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,190 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,191 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,192 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,192 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,193 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,193 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,193 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,194 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,194 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,195 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,195 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,196 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,197 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,197 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,198 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,198 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,199 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,199 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,200 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,201 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,201 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,202 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,202 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,203 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,203 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,204 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,204 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,204 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,205 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,205 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,206 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,206 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,207 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,207 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:23:16,215 reading manifest file '/tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info/SOURCES.txt' 2023-09-26T00:23:16,217 reading manifest template 'MANIFEST.in' 2023-09-26T00:23:16,913 no previously-included directories found matching '__pycache__' 2023-09-26T00:23:16,914 no previously-included directories found matching '*.pyc' 2023-09-26T00:23:16,914 adding license file 'LICENSE' 2023-09-26T00:23:16,925 writing manifest file '/tmp/pip-modern-metadata-ko0abzrm/mdtraj.egg-info/SOURCES.txt' 2023-09-26T00:23:16,927 creating '/tmp/pip-modern-metadata-ko0abzrm/mdtraj-1.9.9.dist-info' 2023-09-26T00:23:17,589 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-26T00:23:17,594 Source in /tmp/pip-wheel-sppucq18/mdtraj_4b4355f3616d46298bd275003a9c28c3 has version 1.9.9, which satisfies requirement mdtraj==1.9.9 from https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz 2023-09-26T00:23:17,595 Removed mdtraj==1.9.9 from https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz from build tracker '/tmp/pip-build-tracker-009g3a57' 2023-09-26T00:23:17,599 Created temporary directory: /tmp/pip-unpack-e_mor4gz 2023-09-26T00:23:17,600 Created temporary directory: /tmp/pip-unpack-qoq8t_k6 2023-09-26T00:23:17,609 Building wheels for collected packages: mdtraj 2023-09-26T00:23:17,613 Created temporary directory: /tmp/pip-wheel-7cs8ctq0 2023-09-26T00:23:17,613 Destination directory: /tmp/pip-wheel-7cs8ctq0 2023-09-26T00:23:17,615 Building wheel for mdtraj (pyproject.toml): started 2023-09-26T00:23:17,616 Running command Building wheel for mdtraj (pyproject.toml) 2023-09-26T00:23:18,244 Using built-in specs. 2023-09-26T00:23:18,245 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-26T00:23:18,245 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2023-09-26T00:23:18,246 Target: arm-linux-gnueabihf 2023-09-26T00:23:18,246 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 2023-09-26T00:23:18,247 Thread model: posix 2023-09-26T00:23:18,247 Supported LTO compression algorithms: zlib zstd 2023-09-26T00:23:18,248 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-26T00:23:23,994 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-26T00:23:23,995 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-26T00:23:23,996 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-26T00:23:59,658 C compiler: 2023-09-26T00:23:59,659 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-09-26T00:23:59,660 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-09-26T00:23:59,661 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-09-26T00:23:59,661 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-09-26T00:23:59,662 Attempting to autodetect NEON support... Did not detect NEON support 2023-09-26T00:23:59,663 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx 2023-09-26T00:23:59,664 [ 2/12] Cythonizing mdtraj/geometry/drid.pyx 2023-09-26T00:23:59,664 [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx 2023-09-26T00:23:59,665 [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx 2023-09-26T00:23:59,666 [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx 2023-09-26T00:23:59,666 [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2023-09-26T00:23:59,667 [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx 2023-09-26T00:23:59,668 [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx 2023-09-26T00:23:59,668 [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx 2023-09-26T00:23:59,669 [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx 2023-09-26T00:23:59,669 [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx 2023-09-26T00:23:59,670 [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx 2023-09-26T00:23:59,748 running bdist_wheel 2023-09-26T00:23:59,784 running build 2023-09-26T00:23:59,785 running build_py 2023-09-26T00:23:59,794 creating build 2023-09-26T00:23:59,794 creating build/lib.linux-armv7l-cpython-311 2023-09-26T00:23:59,795 creating build/lib.linux-armv7l-cpython-311/mdtraj 2023-09-26T00:23:59,796 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2023-09-26T00:23:59,798 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2023-09-26T00:23:59,800 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj 2023-09-26T00:23:59,803 creating build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2023-09-26T00:23:59,804 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2023-09-26T00:23:59,806 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2023-09-26T00:23:59,808 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/scripts 2023-09-26T00:23:59,811 creating build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2023-09-26T00:23:59,812 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2023-09-26T00:23:59,814 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2023-09-26T00:23:59,816 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2023-09-26T00:23:59,818 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2023-09-26T00:23:59,820 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2023-09-26T00:23:59,822 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/reporters 2023-09-26T00:23:59,825 creating build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,825 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,828 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,830 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,832 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,834 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,837 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,839 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,841 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,843 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,845 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,847 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,849 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,851 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,854 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,855 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:23:59,858 creating build/lib.linux-armv7l-cpython-311/mdtraj/testing 2023-09-26T00:23:59,859 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2023-09-26T00:23:59,861 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2023-09-26T00:23:59,863 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2023-09-26T00:23:59,865 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/testing 2023-09-26T00:23:59,867 creating build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2023-09-26T00:23:59,868 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2023-09-26T00:23:59,870 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2023-09-26T00:23:59,873 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/nmr 2023-09-26T00:23:59,875 creating build/lib.linux-armv7l-cpython-311/mdtraj/core 2023-09-26T00:23:59,876 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2023-09-26T00:23:59,878 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2023-09-26T00:23:59,881 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2023-09-26T00:23:59,884 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2023-09-26T00:23:59,886 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2023-09-26T00:23:59,890 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/core 2023-09-26T00:23:59,892 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,893 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,896 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,897 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,899 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,901 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,903 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,906 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,907 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,910 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils 2023-09-26T00:23:59,912 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,914 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,917 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,919 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,922 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,924 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,926 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,929 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,931 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,934 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,937 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,940 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,942 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,944 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,947 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,949 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,952 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,954 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,955 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:23:59,959 creating build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,960 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,962 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,964 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,966 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,968 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,970 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,972 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,975 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,977 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,979 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,981 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,984 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,986 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit 2023-09-26T00:23:59,989 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2023-09-26T00:23:59,990 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2023-09-26T00:23:59,993 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2023-09-26T00:23:59,995 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb 2023-09-26T00:23:59,998 creating build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2023-09-26T00:23:59,999 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2023-09-26T00:24:00,002 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data 2023-09-26T00:24:00,011 running build_ext 2023-09-26T00:24:00,014 building 'mdtraj.formats.xtc' extension 2023-09-26T00:24:00,015 creating build/temp.linux-armv7l-cpython-311 2023-09-26T00:24:00,015 creating build/temp.linux-armv7l-cpython-311/mdtraj 2023-09-26T00:24:00,016 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats 2023-09-26T00:24:00,016 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc 2023-09-26T00:24:00,017 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/xtc/src 2023-09-26T00:24:00,018 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-esueuvwf/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 2023-09-26T00:24:00,140 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-esueuvwf/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 2023-09-26T00:24:00,289 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-09-26T00:24:00,289 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:00,290 788 | int smallnum, smaller, larger, i, is_smaller, run; 2023-09-26T00:24:00,290 | ^~~~~~ 2023-09-26T00:24:00,291 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:00,292 785 | int smallidx, minidx, maxidx; 2023-09-26T00:24:00,292 | ^~~~~~ 2023-09-26T00:24:00,299 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-09-26T00:24:00,299 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:00,300 1016 | int errval=1; 2023-09-26T00:24:00,301 | ^~~~~~ 2023-09-26T00:24:00,305 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2023-09-26T00:24:00,306 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:00,307 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2023-09-26T00:24:00,307 | ^~~~~~ 2023-09-26T00:24:00,308 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:00,308 1302 | int smallidx, minidx, maxidx; 2023-09-26T00:24:00,309 | ^~~~~~ 2023-09-26T00:24:00,318 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-09-26T00:24:00,319 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:00,319 1509 | int errval=1; 2023-09-26T00:24:00,320 | ^~~~~~ 2023-09-26T00:24:02,930 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-esueuvwf/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 2023-09-26T00:24:03,006 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2023-09-26T00:24:03,007 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:15: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-26T00:24:03,007 66 | int i,j,result; 2023-09-26T00:24:03,008 | ^ 2023-09-26T00:24:03,009 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:13: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-26T00:24:03,010 66 | int i,j,result; 2023-09-26T00:24:03,011 | ^ 2023-09-26T00:24:03,011 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2023-09-26T00:24:03,012 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-26T00:24:03,013 119 | if (NULL == xd) 2023-09-26T00:24:03,014 | ^~ 2023-09-26T00:24:03,014 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’ 2023-09-26T00:24:03,015 122 | do { 2023-09-26T00:24:03,015 | ^~ 2023-09-26T00:24:03,148 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-esueuvwf/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 2023-09-26T00:24:03,544 In file included from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2023-09-26T00:24:03,545 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-09-26T00:24:03,545 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-09-26T00:24:03,546 from mdtraj/formats/xtc/xtc.c:784: 2023-09-26T00:24:03,546 /tmp/pip-build-env-esueuvwf/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] 2023-09-26T00:24:03,547 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-09-26T00:24:03,547 | ^~~~~~~ 2023-09-26T00:24:11,947 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2023-09-26T00:24:11,947 mdtraj/formats/xtc/xtc.c:696:40: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:11,948 696 | #define PyInt_FromLong PyLong_FromLong 2023-09-26T00:24:11,949 | ^~~~~~~~~~~~~~~ 2023-09-26T00:24:11,957 mdtraj/formats/xtc/xtc.c:9570:7: note: ‘__pyx_v_status’ was declared here 2023-09-26T00:24:11,957 9570 | int __pyx_v_status; 2023-09-26T00:24:11,958 | ^~~~~~~~~~~~~~ 2023-09-26T00:24:22,885 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2023-09-26T00:24:22,893 mdtraj/formats/xtc/xtc.c:8089:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:22,894 8089 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2023-09-26T00:24:22,894 | ^ 2023-09-26T00:24:22,899 mdtraj/formats/xtc/xtc.c:6492:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ was declared here 2023-09-26T00:24:22,900 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2023-09-26T00:24:22,901 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:22,907 mdtraj/formats/xtc/xtc.c:8085:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:22,907 8085 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2023-09-26T00:24:22,908 | ^ 2023-09-26T00:24:22,913 mdtraj/formats/xtc/xtc.c:6492:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ was declared here 2023-09-26T00:24:22,914 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2023-09-26T00:24:22,914 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:22,921 mdtraj/formats/xtc/xtc.c:8081:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:22,921 8081 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-09-26T00:24:22,922 | ^ 2023-09-26T00:24:22,927 mdtraj/formats/xtc/xtc.c:6492:21: note: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ was declared here 2023-09-26T00:24:22,927 6492 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_stride; 2023-09-26T00:24:22,928 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:22,934 mdtraj/formats/xtc/xtc.c:8041:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:22,935 8041 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-09-26T00:24:22,935 | ^ 2023-09-26T00:24:22,941 mdtraj/formats/xtc/xtc.c:6488:21: note: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ was declared here 2023-09-26T00:24:22,941 6488 | __Pyx_LocalBuf_ND __pyx_pybuffernd_time_stride; 2023-09-26T00:24:22,942 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:22,948 mdtraj/formats/xtc/xtc.c:8023:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:22,949 8023 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-09-26T00:24:22,949 | ^ 2023-09-26T00:24:22,955 mdtraj/formats/xtc/xtc.c:6484:21: note: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ was declared here 2023-09-26T00:24:22,955 6484 | __Pyx_LocalBuf_ND __pyx_pybuffernd_step_stride; 2023-09-26T00:24:22,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:22,962 mdtraj/formats/xtc/xtc.c:8099:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:22,963 8099 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-09-26T00:24:22,963 | ^ 2023-09-26T00:24:22,968 mdtraj/formats/xtc/xtc.c:6480:21: note: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ was declared here 2023-09-26T00:24:22,969 6480 | __Pyx_LocalBuf_ND __pyx_pybuffernd_prec_stride; 2023-09-26T00:24:22,970 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:22,976 mdtraj/formats/xtc/xtc.c:8061:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:22,977 8061 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2023-09-26T00:24:22,977 | ^ 2023-09-26T00:24:22,982 mdtraj/formats/xtc/xtc.c:6474:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ was declared here 2023-09-26T00:24:22,983 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2023-09-26T00:24:22,984 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:22,990 mdtraj/formats/xtc/xtc.c:8057:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:22,991 8057 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2023-09-26T00:24:22,991 | ^ 2023-09-26T00:24:22,996 mdtraj/formats/xtc/xtc.c:6474:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ was declared here 2023-09-26T00:24:22,997 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2023-09-26T00:24:22,998 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:23,004 mdtraj/formats/xtc/xtc.c:8053:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:23,005 8053 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-09-26T00:24:23,005 | ^ 2023-09-26T00:24:23,010 mdtraj/formats/xtc/xtc.c:6474:21: note: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ was declared here 2023-09-26T00:24:23,011 6474 | __Pyx_LocalBuf_ND __pyx_pybuffernd_box_stride; 2023-09-26T00:24:23,011 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:23,018 mdtraj/formats/xtc/xtc.c:7676:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:23,018 7676 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2023-09-26T00:24:23,019 | ^ 2023-09-26T00:24:23,024 mdtraj/formats/xtc/xtc.c:6476:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ was declared here 2023-09-26T00:24:23,025 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2023-09-26T00:24:23,025 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:23,031 mdtraj/formats/xtc/xtc.c:7672:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:23,032 7672 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2023-09-26T00:24:23,032 | ^ 2023-09-26T00:24:23,038 mdtraj/formats/xtc/xtc.c:6476:21: note: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ was declared here 2023-09-26T00:24:23,038 6476 | __Pyx_LocalBuf_ND __pyx_pybuffernd_framebuffer; 2023-09-26T00:24:23,039 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:27,656 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 2023-09-26T00:24:27,809 building 'mdtraj.formats.trr' extension 2023-09-26T00:24:27,810 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-esueuvwf/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 2023-09-26T00:24:27,920 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-esueuvwf/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 2023-09-26T00:24:28,065 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-09-26T00:24:28,066 mdtraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:28,066 788 | int smallnum, smaller, larger, i, is_smaller, run; 2023-09-26T00:24:28,067 | ^~~~~~ 2023-09-26T00:24:28,068 mdtraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:28,068 785 | int smallidx, minidx, maxidx; 2023-09-26T00:24:28,069 | ^~~~~~ 2023-09-26T00:24:28,077 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-09-26T00:24:28,078 mdtraj/formats/xtc/src/xdrfile.c:1016:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:28,079 1016 | int errval=1; 2023-09-26T00:24:28,079 | ^~~~~~ 2023-09-26T00:24:28,085 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2023-09-26T00:24:28,086 mdtraj/formats/xtc/src/xdrfile.c:1305:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:28,087 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2023-09-26T00:24:28,087 | ^~~~~~ 2023-09-26T00:24:28,088 mdtraj/formats/xtc/src/xdrfile.c:1302:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:28,089 1302 | int smallidx, minidx, maxidx; 2023-09-26T00:24:28,089 | ^~~~~~ 2023-09-26T00:24:28,099 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-09-26T00:24:28,101 mdtraj/formats/xtc/src/xdrfile.c:1509:13: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-09-26T00:24:28,101 1509 | int errval=1; 2023-09-26T00:24:28,102 | ^~~~~~ 2023-09-26T00:24:30,702 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-esueuvwf/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 2023-09-26T00:24:31,493 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-esueuvwf/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 2023-09-26T00:24:31,885 In file included from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2023-09-26T00:24:31,886 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-09-26T00:24:31,887 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-09-26T00:24:31,888 from mdtraj/formats/xtc/trr.c:784: 2023-09-26T00:24:31,888 /tmp/pip-build-env-esueuvwf/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] 2023-09-26T00:24:31,889 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-09-26T00:24:31,890 | ^~~~~~~ 2023-09-26T00:24:41,069 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2023-09-26T00:24:41,070 mdtraj/formats/xtc/trr.c:696:40: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:41,070 696 | #define PyInt_FromLong PyLong_FromLong 2023-09-26T00:24:41,071 | ^~~~~~~~~~~~~~~ 2023-09-26T00:24:41,081 mdtraj/formats/xtc/trr.c:11096:7: note: ‘__pyx_v_status’ was declared here 2023-09-26T00:24:41,081 11096 | int __pyx_v_status; 2023-09-26T00:24:41,082 | ^~~~~~~~~~~~~~ 2023-09-26T00:24:52,344 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2023-09-26T00:24:52,353 mdtraj/formats/xtc/trr.c:8449:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,353 8449 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2023-09-26T00:24:52,353 | ^ 2023-09-26T00:24:52,359 mdtraj/formats/xtc/trr.c:6986:21: note: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ was declared here 2023-09-26T00:24:52,360 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2023-09-26T00:24:52,360 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,367 mdtraj/formats/xtc/trr.c:8445:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,368 8445 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2023-09-26T00:24:52,368 | ^ 2023-09-26T00:24:52,374 mdtraj/formats/xtc/trr.c:6986:21: note: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ was declared here 2023-09-26T00:24:52,375 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2023-09-26T00:24:52,375 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,376 mdtraj/formats/xtc/trr.c:1935:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,376 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2023-09-26T00:24:52,377 | ^ 2023-09-26T00:24:52,382 mdtraj/formats/xtc/trr.c:6986:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2023-09-26T00:24:52,383 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2023-09-26T00:24:52,384 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,390 mdtraj/formats/xtc/trr.c:8439:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,391 8439 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2023-09-26T00:24:52,392 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-09-26T00:24:52,397 mdtraj/formats/xtc/trr.c:6986:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ was declared here 2023-09-26T00:24:52,398 6986 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2023-09-26T00:24:52,399 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,405 mdtraj/formats/xtc/trr.c:8392:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,405 8392 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2023-09-26T00:24:52,406 | ^ 2023-09-26T00:24:52,412 mdtraj/formats/xtc/trr.c:7002:21: note: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ was declared here 2023-09-26T00:24:52,412 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2023-09-26T00:24:52,413 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,420 mdtraj/formats/xtc/trr.c:8388:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,420 8388 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2023-09-26T00:24:52,421 | ^ 2023-09-26T00:24:52,426 mdtraj/formats/xtc/trr.c:7002:21: note: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ was declared here 2023-09-26T00:24:52,427 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2023-09-26T00:24:52,428 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,429 mdtraj/formats/xtc/trr.c:1935:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,429 1935 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2023-09-26T00:24:52,429 | ^ 2023-09-26T00:24:52,435 mdtraj/formats/xtc/trr.c:7002:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2023-09-26T00:24:52,435 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2023-09-26T00:24:52,436 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,443 mdtraj/formats/xtc/trr.c:8382:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,443 8382 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2023-09-26T00:24:52,444 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-09-26T00:24:52,449 mdtraj/formats/xtc/trr.c:7002:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ was declared here 2023-09-26T00:24:52,450 7002 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2023-09-26T00:24:52,450 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,458 mdtraj/formats/xtc/trr.c:8782:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,458 8782 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-09-26T00:24:52,459 | ^ 2023-09-26T00:24:52,464 mdtraj/formats/xtc/trr.c:7008:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ was declared here 2023-09-26T00:24:52,465 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2023-09-26T00:24:52,465 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,473 mdtraj/formats/xtc/trr.c:8778:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,473 8778 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-09-26T00:24:52,474 | ^ 2023-09-26T00:24:52,479 mdtraj/formats/xtc/trr.c:7008:21: note: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ was declared here 2023-09-26T00:24:52,480 7008 | __Pyx_LocalBuf_ND __pyx_pybuffernd_xyz_buffer; 2023-09-26T00:24:52,481 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,487 mdtraj/formats/xtc/trr.c:8623:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,488 8623 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-09-26T00:24:52,489 | ^ 2023-09-26T00:24:52,494 mdtraj/formats/xtc/trr.c:7004:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ was declared here 2023-09-26T00:24:52,495 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2023-09-26T00:24:52,495 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,502 mdtraj/formats/xtc/trr.c:8619:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,503 8619 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-09-26T00:24:52,503 | ^ 2023-09-26T00:24:52,509 mdtraj/formats/xtc/trr.c:7004:21: note: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ was declared here 2023-09-26T00:24:52,510 7004 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel_buffer; 2023-09-26T00:24:52,510 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,517 mdtraj/formats/xtc/trr.c:8675:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,518 8675 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-09-26T00:24:52,519 | ^ 2023-09-26T00:24:52,524 mdtraj/formats/xtc/trr.c:6988:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ was declared here 2023-09-26T00:24:52,525 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2023-09-26T00:24:52,525 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:52,532 mdtraj/formats/xtc/trr.c:8671:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:24:52,533 8671 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-09-26T00:24:52,533 | ^ 2023-09-26T00:24:52,539 mdtraj/formats/xtc/trr.c:6988:21: note: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ was declared here 2023-09-26T00:24:52,540 6988 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces_buffer; 2023-09-26T00:24:52,540 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:24:59,099 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 2023-09-26T00:24:59,244 building 'mdtraj.formats.tng' extension 2023-09-26T00:24:59,245 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng 2023-09-26T00:24:59,246 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src 2023-09-26T00:24:59,246 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression 2023-09-26T00:24:59,248 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/lib 2023-09-26T00:24:59,249 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o 2023-09-26T00:25:00,047 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/bwt.o 2023-09-26T00:25:00,486 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/coder.o 2023-09-26T00:25:01,295 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/dict.o 2023-09-26T00:25:01,419 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o 2023-09-26T00:25:01,611 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/huffman.o 2023-09-26T00:25:02,388 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o 2023-09-26T00:25:02,882 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/lz77.o 2023-09-26T00:25:03,228 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o 2023-09-26T00:25:03,404 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/mtf.o 2023-09-26T00:25:03,491 mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: 2023-09-26T00:25:03,491 mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-26T00:25:03,492 196 | while (dict[ptr]!=v) 2023-09-26T00:25:03,493 | ^~ 2023-09-26T00:25:03,849 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/rle.o 2023-09-26T00:25:03,892 mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: 2023-09-26T00:25:03,892 mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-09-26T00:25:03,894 56 | if (v==vals[i]) 2023-09-26T00:25:03,894 | ^~ 2023-09-26T00:25:04,020 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o 2023-09-26T00:25:06,682 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/vals16.o 2023-09-26T00:25:06,812 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o 2023-09-26T00:25:06,945 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o 2023-09-26T00:25:07,198 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o 2023-09-26T00:25:08,844 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o 2023-09-26T00:25:11,574 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/lib/md5.o 2023-09-26T00:25:12,051 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o 2023-09-26T00:25:12,240 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: 2023-09-26T00:25:12,243 mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-09-26T00:25:12,244 1064 | tng_data->input_endianness_swap_func_32 = 2023-09-26T00:25:12,244 | ^ 2023-09-26T00:25:12,245 mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-09-26T00:25:12,245 1073 | tng_data->input_endianness_swap_func_64 = 2023-09-26T00:25:12,246 | ^ 2023-09-26T00:25:12,246 mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-09-26T00:25:12,247 1089 | tng_data->input_endianness_swap_func_32 = 2023-09-26T00:25:12,248 | ^ 2023-09-26T00:25:12,248 mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-09-26T00:25:12,249 1098 | tng_data->input_endianness_swap_func_64 = 2023-09-26T00:25:12,249 | ^ 2023-09-26T00:25:12,357 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: 2023-09-26T00:25:12,365 mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 2023-09-26T00:25:12,365 9565 | if(tng_data->output_endianness_swap_func_32 == 2023-09-26T00:25:12,366 | ^~ 2023-09-26T00:25:12,372 mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 2023-09-26T00:25:12,373 9570 | else if(tng_data->output_endianness_swap_func_32 == 2023-09-26T00:25:12,373 | ^~ 2023-09-26T00:25:12,379 mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 2023-09-26T00:25:12,380 9588 | if(tng_data->output_endianness_swap_func_64 == 2023-09-26T00:25:12,381 | ^~ 2023-09-26T00:25:12,386 mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 2023-09-26T00:25:12,387 9593 | else if(tng_data->output_endianness_swap_func_64 == 2023-09-26T00:25:12,388 | ^~ 2023-09-26T00:25:12,389 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: 2023-09-26T00:25:12,396 mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-09-26T00:25:12,397 9651 | tng_data->output_endianness_swap_func_32 = 2023-09-26T00:25:12,397 | ^ 2023-09-26T00:25:12,404 mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-09-26T00:25:12,404 9660 | tng_data->output_endianness_swap_func_64 = 2023-09-26T00:25:12,405 | ^ 2023-09-26T00:25:12,412 mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-09-26T00:25:12,412 9673 | tng_data->output_endianness_swap_func_32 = 2023-09-26T00:25:12,413 | ^ 2023-09-26T00:25:12,419 mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-09-26T00:25:12,420 9682 | tng_data->output_endianness_swap_func_64 = 2023-09-26T00:25:12,421 | ^ 2023-09-26T00:25:14,814 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: 2023-09-26T00:25:14,825 mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2023-09-26T00:25:14,825 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2023-09-26T00:25:14,826 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:25:14,835 mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 2023-09-26T00:25:14,836 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2023-09-26T00:25:14,837 | ^~~~~~~~~~~~~~~~~~ 2023-09-26T00:25:16,046 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: 2023-09-26T00:25:16,192 mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:25:16,193 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; 2023-09-26T00:25:16,194 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2023-09-26T00:25:16,194 mdtraj/formats/tng/src/lib/tng_io.c:5684:26: note: ‘num_first_particle’ was declared here 2023-09-26T00:25:16,195 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; 2023-09-26T00:25:16,196 | ^~~~~~~~~~~~~~~~~~ 2023-09-26T00:25:16,197 mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘n_particles’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:25:16,198 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; 2023-09-26T00:25:16,198 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2023-09-26T00:25:16,199 mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 2023-09-26T00:25:16,199 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; 2023-09-26T00:25:16,200 | ^~~~~~~~~~~ 2023-09-26T00:25:28,126 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/tng/tng.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/tng.o 2023-09-26T00:25:28,514 In file included from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2023-09-26T00:25:28,514 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-09-26T00:25:28,515 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-09-26T00:25:28,515 from mdtraj/formats/tng/tng.c:810: 2023-09-26T00:25:28,516 /tmp/pip-build-env-esueuvwf/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] 2023-09-26T00:25:28,517 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-09-26T00:25:28,517 | ^~~~~~~ 2023-09-26T00:25:28,612 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’: 2023-09-26T00:25:28,615 mdtraj/formats/tng/tng.c:3706:104: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,616 3706 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,616 | ^~ 2023-09-26T00:25:28,619 mdtraj/formats/tng/tng.c:3761:88: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,620 3761 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,620 | ^~ 2023-09-26T00:25:28,623 mdtraj/formats/tng/tng.c:3793:90: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,624 3793 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,625 | ^~ 2023-09-26T00:25:28,628 mdtraj/formats/tng/tng.c:3825:95: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,629 3825 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,630 | ^~ 2023-09-26T00:25:28,632 mdtraj/formats/tng/tng.c:3895:113: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,633 3895 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,634 | ^~ 2023-09-26T00:25:28,638 mdtraj/formats/tng/tng.c:3939:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,639 3939 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,639 | ^~ 2023-09-26T00:25:28,661 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’: 2023-09-26T00:25:28,665 mdtraj/formats/tng/tng.c:4735:106: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,665 4735 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,666 | ^~ 2023-09-26T00:25:28,670 mdtraj/formats/tng/tng.c:4780:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,671 4780 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,672 | ^~ 2023-09-26T00:25:28,679 mdtraj/formats/tng/tng.c:4887:115: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,679 4887 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,680 | ^~ 2023-09-26T00:25:28,683 mdtraj/formats/tng/tng.c:4917:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,684 4917 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,685 | ^~ 2023-09-26T00:25:28,693 mdtraj/formats/tng/tng.c:5045:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,694 5045 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,694 | ^~ 2023-09-26T00:25:28,716 mdtraj/formats/tng/tng.c:5646:126: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,717 5646 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,717 | ^~ 2023-09-26T00:25:28,728 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’: 2023-09-26T00:25:28,733 mdtraj/formats/tng/tng.c:6056:152: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,734 6056 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,735 | ^~ 2023-09-26T00:25:28,754 mdtraj/formats/tng/tng.c:6324:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,756 6324 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,756 | ^~ 2023-09-26T00:25:28,764 mdtraj/formats/tng/tng.c:6426:304: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,765 6426 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,766 | ^~ 2023-09-26T00:25:28,866 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’: 2023-09-26T00:25:28,874 mdtraj/formats/tng/tng.c:8918:94: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,875 8918 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,876 | ^~ 2023-09-26T00:25:28,884 mdtraj/formats/tng/tng.c:8950:75: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,884 8950 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,885 | ^~ 2023-09-26T00:25:28,893 mdtraj/formats/tng/tng.c:8982:81: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,893 8982 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,894 | ^~ 2023-09-26T00:25:28,914 mdtraj/formats/tng/tng.c:9305:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,914 9305 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,915 | ^~ 2023-09-26T00:25:28,941 mdtraj/formats/tng/tng.c:9496:372: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,942 9496 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,942 | ^~ 2023-09-26T00:25:28,965 mdtraj/formats/tng/tng.c:9548:378: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,966 9548 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,966 | ^~ 2023-09-26T00:25:28,976 mdtraj/formats/tng/tng.c:9610:89: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-09-26T00:25:28,977 9610 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-09-26T00:25:28,978 | ^~ 2023-09-26T00:25:47,254 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/tng.cpython-311-arm-linux-gnueabihf.so 2023-09-26T00:25:47,470 building 'mdtraj.formats.dcd' extension 2023-09-26T00:25:47,471 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd 2023-09-26T00:25:47,472 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dcd/src 2023-09-26T00:25:47,473 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-esueuvwf/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 2023-09-26T00:25:47,861 In file included from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2023-09-26T00:25:47,861 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-09-26T00:25:47,862 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-09-26T00:25:47,862 from mdtraj/formats/dcd/dcd.c:782: 2023-09-26T00:25:47,863 /tmp/pip-build-env-esueuvwf/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] 2023-09-26T00:25:47,863 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-09-26T00:25:47,864 | ^~~~~~~ 2023-09-26T00:25:56,866 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2023-09-26T00:25:56,866 mdtraj/formats/dcd/dcd.c:694:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:25:56,867 694 | #define PyInt_FromLong PyLong_FromLong 2023-09-26T00:25:56,867 | ^~~~~~~~~~~~~~~ 2023-09-26T00:25:56,873 mdtraj/formats/dcd/dcd.c:5465:7: note: ‘__pyx_v_i’ was declared here 2023-09-26T00:25:56,873 5465 | int __pyx_v_i; 2023-09-26T00:25:56,874 | ^~~~~~~~~ 2023-09-26T00:26:00,086 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-esueuvwf/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 2023-09-26T00:26:01,647 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 2023-09-26T00:26:01,770 building 'mdtraj.formats.binpos' extension 2023-09-26T00:26:01,770 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/binpos 2023-09-26T00:26:01,771 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/binpos/src 2023-09-26T00:26:01,773 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/binpos/include/ -Imdtraj/formats/binpos/ -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-09-26T00:26:02,160 In file included from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2023-09-26T00:26:02,161 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-09-26T00:26:02,162 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-09-26T00:26:02,162 from mdtraj/formats/binpos/binpos.c:782: 2023-09-26T00:26:02,163 /tmp/pip-build-env-esueuvwf/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] 2023-09-26T00:26:02,163 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-09-26T00:26:02,164 | ^~~~~~~ 2023-09-26T00:26:12,351 In function ‘__pyx_pf_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_8_read’, 2023-09-26T00:26:12,351 inlined from ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’ at mdtraj/formats/binpos/binpos.c:4994:13: 2023-09-26T00:26:12,356 mdtraj/formats/binpos/binpos.c:5526:6: warning: ‘__pyx_v_status’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:26:12,357 5526 | if (__pyx_t_2) { 2023-09-26T00:26:12,357 | ^ 2023-09-26T00:26:12,358 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2023-09-26T00:26:12,361 mdtraj/formats/binpos/binpos.c:5006:7: note: ‘__pyx_v_status’ was declared here 2023-09-26T00:26:12,361 5006 | int __pyx_v_status; 2023-09-26T00:26:12,362 | ^~~~~~~~~~~~~~ 2023-09-26T00:26:12,363 mdtraj/formats/binpos/binpos.c:694:40: warning: ‘__pyx_v_i’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:26:12,363 694 | #define PyInt_FromLong PyLong_FromLong 2023-09-26T00:26:12,364 | ^~~~~~~~~~~~~~~ 2023-09-26T00:26:12,367 mdtraj/formats/binpos/binpos.c:5003:7: note: ‘__pyx_v_i’ was declared here 2023-09-26T00:26:12,367 5003 | int __pyx_v_i; 2023-09-26T00:26:12,368 | ^~~~~~~~~ 2023-09-26T00:26:14,007 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/binpos/include/ -Imdtraj/formats/binpos/ -I/tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-09-26T00:26:14,340 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/mdtraj/formats/binpos/binpos.o build/temp.linux-armv7l-cpython-311/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/mdtraj/formats/binpos.cpython-311-arm-linux-gnueabihf.so 2023-09-26T00:26:14,493 building 'mdtraj.formats.dtr' extension 2023-09-26T00:26:14,493 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr 2023-09-26T00:26:14,495 creating build/temp.linux-armv7l-cpython-311/mdtraj/formats/dtr/src 2023-09-26T00:26:14,496 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-esueuvwf/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 2023-09-26T00:26:14,809 In file included from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2023-09-26T00:26:14,810 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-09-26T00:26:14,810 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-09-26T00:26:14,811 from mdtraj/formats/dtr/dtr.cpp:803: 2023-09-26T00:26:14,811 /tmp/pip-build-env-esueuvwf/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] 2023-09-26T00:26:14,812 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-09-26T00:26:14,812 | ^~~~~~~ 2023-09-26T00:26:29,120 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-esueuvwf/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 2023-09-26T00:26:31,522 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’: 2023-09-26T00:26:31,523 mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2023-09-26T00:26:31,524 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2023-09-26T00:26:31,524 | ~~^ ~ 2023-09-26T00:26:31,525 | | | 2023-09-26T00:26:31,526 | | size_t {aka unsigned int} 2023-09-26T00:26:31,526 | long int 2023-09-26T00:26:31,527 | %d 2023-09-26T00:26:31,528 mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-09-26T00:26:31,528 487 | printf("size %d framesize %d\n\n", 2023-09-26T00:26:31,529 | ~^ 2023-09-26T00:26:31,530 | | 2023-09-26T00:26:31,531 | int 2023-09-26T00:26:31,532 | %lld 2023-09-26T00:26:31,532 488 | keys[i].size(), m_framesize); 2023-09-26T00:26:31,533 | ~~~~~~~~~~~~~~ 2023-09-26T00:26:31,533 | | 2023-09-26T00:26:31,534 | uint64_t {aka long long unsigned int} 2023-09-26T00:26:31,534 mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-09-26T00:26:31,535 487 | printf("size %d framesize %d\n\n", 2023-09-26T00:26:31,536 | ~^ 2023-09-26T00:26:31,536 | | 2023-09-26T00:26:31,537 | int 2023-09-26T00:26:31,537 | %lld 2023-09-26T00:26:31,538 488 | keys[i].size(), m_framesize); 2023-09-26T00:26:31,538 | ~~~~~~~~~~~ 2023-09-26T00:26:31,539 | | 2023-09-26T00:26:31,539 | uint64_t {aka long long unsigned int} 2023-09-26T00:26:31,540 mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2023-09-26T00:26:31,540 494 | "non-constant time interval at frame %ld\n", i); 2023-09-26T00:26:31,541 | ~~^ ~ 2023-09-26T00:26:31,542 | | | 2023-09-26T00:26:31,542 | | size_t {aka unsigned int} 2023-09-26T00:26:31,543 | long int 2023-09-26T00:26:31,543 | %d 2023-09-26T00:26:31,544 mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2023-09-26T00:26:31,545 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2023-09-26T00:26:31,545 | ~~^ ~ 2023-09-26T00:26:31,546 | | | 2023-09-26T00:26:31,547 | | size_t {aka unsigned int} 2023-09-26T00:26:31,548 | long int 2023-09-26T00:26:31,548 | %d 2023-09-26T00:26:31,695 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2023-09-26T00:26:31,695 mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-09-26T00:26:31,696 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2023-09-26T00:26:31,697 | ~~^ 2023-09-26T00:26:31,697 | | 2023-09-26T00:26:31,698 | long int 2023-09-26T00:26:31,699 | %lld 2023-09-26T00:26:31,700 1302 | 3*natoms, pos.count); 2023-09-26T00:26:31,700 | ~~~~~~~~~ 2023-09-26T00:26:31,701 | | 2023-09-26T00:26:31,702 | uint64_t {aka long long unsigned int} 2023-09-26T00:26:31,703 mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-09-26T00:26:31,703 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2023-09-26T00:26:31,704 | ~~^ 2023-09-26T00:26:31,704 | | 2023-09-26T00:26:31,705 | long int 2023-09-26T00:26:31,705 | %lld 2023-09-26T00:26:31,706 1311 | 3*natoms, vel.count); 2023-09-26T00:26:31,706 | ~~~~~~~~~ 2023-09-26T00:26:31,707 | | 2023-09-26T00:26:31,707 | uint64_t {aka long long unsigned int} 2023-09-26T00:26:31,732 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2023-09-26T00:26:31,732 mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-09-26T00:26:31,733 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2023-09-26T00:26:31,733 | ~~^ 2023-09-26T00:26:31,734 | | 2023-09-26T00:26:31,735 | long int 2023-09-26T00:26:31,735 | %lld 2023-09-26T00:26:31,736 1573 | velblob.count, 3*natoms); 2023-09-26T00:26:31,737 | ~~~~~~~~~~~~~ 2023-09-26T00:26:31,737 | | 2023-09-26T00:26:31,738 | uint64_t {aka long long unsigned int} 2023-09-26T00:26:33,040 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const std::string&, int)’: 2023-09-26T00:26:33,041 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*this.{anonymous}::DDException::eno’ is used uninitialized [-Wuninitialized] 2023-09-26T00:26:33,042 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2023-09-26T00:26:33,042 | ~~~~~~~~^~~~~ 2023-09-26T00:26:35,813 In file included from /usr/include/c++/12/map:60, 2023-09-26T00:26:35,813 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2023-09-26T00:26:35,814 /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> >]’: 2023-09-26T00:26:35,815 /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 2023-09-26T00:26:35,815 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-26T00:26:35,817 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:35,885 /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> >]’: 2023-09-26T00:26:35,886 /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 2023-09-26T00:26:35,886 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-09-26T00:26:35,887 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:35,946 In file included from /usr/include/c++/12/map:61: 2023-09-26T00:26:35,947 /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> >]’: 2023-09-26T00:26:35,947 /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 2023-09-26T00:26:35,948 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-26T00:26:35,949 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:35,950 531 | std::forward_as_tuple(std::move(__k)), 2023-09-26T00:26:35,950 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:35,951 532 | std::tuple<>()); 2023-09-26T00:26:35,951 | ~~~~~~~~~~~~~~~ 2023-09-26T00:26:36,040 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> >]’, 2023-09-26T00:26:36,041 inlined from ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:1299:28: 2023-09-26T00:26:36,042 /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 2023-09-26T00:26:36,042 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-26T00:26:36,043 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:36,044 531 | std::forward_as_tuple(std::move(__k)), 2023-09-26T00:26:36,044 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:36,045 532 | std::tuple<>()); 2023-09-26T00:26:36,045 | ~~~~~~~~~~~~~~~ 2023-09-26T00:26:36,889 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const std::string&, mode_t, int, int)’: 2023-09-26T00:26:36,890 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=] 2023-09-26T00:26:36,890 706 | sprintf(sub, "%03x/", i); 2023-09-26T00:26:36,891 | ^~~~ 2023-09-26T00:26:36,892 mdtraj/formats/dtr/src/dtrplugin.cxx:706:22: note: directive argument in the range [0, 2147483646] 2023-09-26T00:26:36,892 706 | sprintf(sub, "%03x/", i); 2023-09-26T00:26:36,893 | ^~~~~~~ 2023-09-26T00:26:36,893 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2023-09-26T00:26:36,894 706 | sprintf(sub, "%03x/", i); 2023-09-26T00:26:36,894 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-26T00:26:36,895 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=] 2023-09-26T00:26:36,896 714 | sprintf(subsub, "%03x", j); 2023-09-26T00:26:36,896 | ^~~~ 2023-09-26T00:26:36,897 mdtraj/formats/dtr/src/dtrplugin.cxx:714:29: note: directive argument in the range [0, 2147483646] 2023-09-26T00:26:36,898 714 | sprintf(subsub, "%03x", j); 2023-09-26T00:26:36,899 | ^~~~~~ 2023-09-26T00:26:36,899 mdtraj/formats/dtr/src/dtrplugin.cxx:714:20: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2023-09-26T00:26:36,900 714 | sprintf(subsub, "%03x", j); 2023-09-26T00:26:36,901 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:37,297 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2023-09-26T00:26:37,298 mdtraj/formats/dtr/src/dtrplugin.cxx:667:35: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2023-09-26T00:26:37,299 667 | sprintf(answer, "%03x/", d1); 2023-09-26T00:26:37,299 | ^ 2023-09-26T00:26:37,300 In function ‘std::string DDreldir(const std::string&, int, int)’, 2023-09-26T00:26:37,301 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2023-09-26T00:26:37,301 mdtraj/formats/dtr/src/dtrplugin.cxx:667:20: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2023-09-26T00:26:37,302 667 | sprintf(answer, "%03x/", d1); 2023-09-26T00:26:37,303 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:37,304 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const std::string&, size_t, size_t, int, int)’: 2023-09-26T00:26:37,304 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=] 2023-09-26T00:26:37,305 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-09-26T00:26:37,306 | ^~~~ 2023-09-26T00:26:37,307 In function ‘std::string DDreldir(const std::string&, int, int)’, 2023-09-26T00:26:37,307 inlined from ‘std::string framefile(const std::string&, size_t, size_t, int, int)’ at mdtraj/formats/dtr/src/dtrplugin.cxx:771:23: 2023-09-26T00:26:37,308 mdtraj/formats/dtr/src/dtrplugin.cxx:665:29: note: directive argument in the range [0, 2147483646] 2023-09-26T00:26:37,308 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-09-26T00:26:37,309 | ^~~~~~~~~~~~ 2023-09-26T00:26:37,310 mdtraj/formats/dtr/src/dtrplugin.cxx:665:20: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2023-09-26T00:26:37,310 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-09-26T00:26:37,311 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:40,453 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> >]’, 2023-09-26T00:26:40,454 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: 2023-09-26T00:26:40,454 /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 2023-09-26T00:26:40,455 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-09-26T00:26:40,456 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:40,456 531 | std::forward_as_tuple(std::move(__k)), 2023-09-26T00:26:40,457 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:26:40,458 532 | std::tuple<>()); 2023-09-26T00:26:40,458 | ~~~~~~~~~~~~~~~ 2023-09-26T00:26:45,416 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 2023-09-26T00:26:45,740 building 'mdtraj._rmsd' extension 2023-09-26T00:26:45,741 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd 2023-09-26T00:26:45,742 creating build/temp.linux-armv7l-cpython-311/mdtraj/rmsd/src 2023-09-26T00:26:45,743 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-esueuvwf/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 2023-09-26T00:27:26,259 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-esueuvwf/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 2023-09-26T00:27:26,466 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-esueuvwf/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 2023-09-26T00:27:26,727 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-esueuvwf/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 2023-09-26T00:27:27,504 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 2023-09-26T00:27:27,809 building 'mdtraj._lprmsd' extension 2023-09-26T00:27:27,810 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-esueuvwf/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 2023-09-26T00:27:28,071 In file included from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2023-09-26T00:27:28,071 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-09-26T00:27:28,072 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-09-26T00:27:28,073 from mdtraj/rmsd/_lprmsd.cpp:812: 2023-09-26T00:27:28,073 /tmp/pip-build-env-esueuvwf/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] 2023-09-26T00:27:28,074 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-09-26T00:27:28,074 | ^~~~~~~ 2023-09-26T00:27:51,949 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-esueuvwf/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 2023-09-26T00:27:54,748 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-esueuvwf/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 2023-09-26T00:27:54,949 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-esueuvwf/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 2023-09-26T00:27:56,189 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-esueuvwf/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 2023-09-26T00:27:56,491 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-esueuvwf/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 2023-09-26T00:27:56,752 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-esueuvwf/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 2023-09-26T00:27:57,538 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 2023-09-26T00:27:57,829 building 'mdtraj.core.lib.libtheobald' extension 2023-09-26T00:27:57,830 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-esueuvwf/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 2023-09-26T00:27:59,422 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-esueuvwf/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 2023-09-26T00:27:59,674 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 2023-09-26T00:27:59,699 building 'mdtraj.geometry._geometry' extension 2023-09-26T00:27:59,700 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry 2023-09-26T00:27:59,700 creating build/temp.linux-armv7l-cpython-311/mdtraj/geometry/src 2023-09-26T00:27:59,702 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-esueuvwf/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 2023-09-26T00:27:59,972 In file included from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1948, 2023-09-26T00:27:59,972 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-09-26T00:27:59,973 from /tmp/pip-build-env-esueuvwf/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-09-26T00:27:59,973 from mdtraj/geometry/src/_geometry.cpp:814: 2023-09-26T00:27:59,974 /tmp/pip-build-env-esueuvwf/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] 2023-09-26T00:27:59,974 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-09-26T00:27:59,975 | ^~~~~~~ 2023-09-26T00:28:06,396 mdtraj/geometry/src/_geometry.cpp: In function ‘void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’: 2023-09-26T00:28:06,396 mdtraj/geometry/src/_geometry.cpp:6115:224: warning: ‘__pyx_v_delta[2]’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:28:06,397 6115 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); 2023-09-26T00:28:06,398 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:28:06,398 mdtraj/geometry/src/_geometry.cpp:6036:9: note: ‘__pyx_v_delta[2]’ was declared here 2023-09-26T00:28:06,399 6036 | float __pyx_v_delta[3]; 2023-09-26T00:28:06,400 | ^~~~~~~~~~~~~ 2023-09-26T00:28:06,400 mdtraj/geometry/src/_geometry.cpp:6129:277: warning: ‘__pyx_v_delta[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:28:06,401 6129 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); 2023-09-26T00:28:06,402 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:28:06,403 mdtraj/geometry/src/_geometry.cpp:6036:9: note: ‘__pyx_v_delta[1]’ was declared here 2023-09-26T00:28:06,403 6036 | float __pyx_v_delta[3]; 2023-09-26T00:28:06,404 | ^~~~~~~~~~~~~ 2023-09-26T00:28:06,404 mdtraj/geometry/src/_geometry.cpp:6129:277: warning: ‘__pyx_v_offset[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:28:06,405 6129 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); 2023-09-26T00:28:06,405 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-09-26T00:28:06,405 mdtraj/geometry/src/_geometry.cpp:6035:9: note: ‘__pyx_v_offset[1]’ was declared here 2023-09-26T00:28:06,406 6035 | float __pyx_v_offset[3]; 2023-09-26T00:28:06,407 | ^~~~~~~~~~~~~~ 2023-09-26T00:28:33,779 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-esueuvwf/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 2023-09-26T00:28:47,929 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-esueuvwf/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 2023-09-26T00:28:51,910 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-esueuvwf/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 2023-09-26T00:28:53,013 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 2023-09-26T00:28:53,364 building 'mdtraj.geometry.drid' extension 2023-09-26T00:28:53,365 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-esueuvwf/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 2023-09-26T00:29:22,490 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-esueuvwf/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 2023-09-26T00:29:23,126 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-esueuvwf/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 2023-09-26T00:29:23,233 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 2023-09-26T00:29:23,531 building 'mdtraj.geometry.neighbors' extension 2023-09-26T00:29:23,531 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-esueuvwf/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 2023-09-26T00:29:50,727 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-esueuvwf/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 2023-09-26T00:29:52,018 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 2023-09-26T00:29:52,295 building 'mdtraj.geometry.neighborlist' extension 2023-09-26T00:29:52,296 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-esueuvwf/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 2023-09-26T00:30:16,953 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-esueuvwf/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 2023-09-26T00:30:21,384 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2023-09-26T00:30:21,385 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2023-09-26T00:30:21,385 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:30:21,386 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2023-09-26T00:30:21,386 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-09-26T00:30:21,387 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2023-09-26T00:30:21,387 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2023-09-26T00:30:21,388 341 | float periodicBoxVectors[3][3]; 2023-09-26T00:30:21,388 | ^~~~~~~~~~~~~~~~~~ 2023-09-26T00:30:21,389 In constructor ‘Voxels::Voxels(float, float, float, float, float, float, const float (&)[3][3], bool)’, 2023-09-26T00:30:21,389 inlined from ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’ at mdtraj/geometry/src/neighborlist.cpp:377:116: 2023-09-26T00:30:21,390 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:30:21,391 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2023-09-26T00:30:21,391 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-09-26T00:30:21,392 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2023-09-26T00:30:21,393 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2023-09-26T00:30:21,393 341 | float periodicBoxVectors[3][3]; 2023-09-26T00:30:21,394 | ^~~~~~~~~~~~~~~~~~ 2023-09-26T00:30:21,395 mdtraj/geometry/src/neighborlist.cpp:374:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:30:21,396 374 | edgeSizeY = 0.6f*periodicBoxVectors[1][1]/floorf(periodicBoxVectors[1][1]/maxDistance); 2023-09-26T00:30:21,396 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-09-26T00:30:21,397 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2023-09-26T00:30:21,397 341 | float periodicBoxVectors[3][3]; 2023-09-26T00:30:21,398 | ^~~~~~~~~~~~~~~~~~ 2023-09-26T00:30:21,399 mdtraj/geometry/src/neighborlist.cpp:375:49: warning: ‘periodicBoxVectors’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-26T00:30:21,399 375 | edgeSizeZ = 0.6f*periodicBoxVectors[2][2]/floorf(periodicBoxVectors[2][2]/maxDistance); 2023-09-26T00:30:21,400 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-09-26T00:30:21,401 mdtraj/geometry/src/neighborlist.cpp:341:11: note: ‘periodicBoxVectors’ declared here 2023-09-26T00:30:21,401 341 | float periodicBoxVectors[3][3]; 2023-09-26T00:30:21,402 | ^~~~~~~~~~~~~~~~~~ 2023-09-26T00:30:22,222 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 2023-09-26T00:30:22,532 installing to build/bdist.linux-armv7l/wheel 2023-09-26T00:30:22,532 running install 2023-09-26T00:30:22,556 running install_lib 2023-09-26T00:30:22,565 creating build/bdist.linux-armv7l 2023-09-26T00:30:22,565 creating build/bdist.linux-armv7l/wheel 2023-09-26T00:30:22,568 creating build/bdist.linux-armv7l/wheel/mdtraj 2023-09-26T00:30:22,569 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-09-26T00:30:22,571 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-09-26T00:30:22,573 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-09-26T00:30:22,576 copying build/lib.linux-armv7l-cpython-311/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-09-26T00:30:22,578 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-09-26T00:30:22,579 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-09-26T00:30:22,581 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-09-26T00:30:22,584 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-09-26T00:30:22,586 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-09-26T00:30:22,589 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-09-26T00:30:22,591 copying build/lib.linux-armv7l-cpython-311/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-09-26T00:30:22,593 copying build/lib.linux-armv7l-cpython-311/mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2023-09-26T00:30:22,623 copying build/lib.linux-armv7l-cpython-311/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-09-26T00:30:22,625 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,626 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,648 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,650 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,652 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,655 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,657 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,660 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,662 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,664 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,696 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,717 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,720 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,721 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,764 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,767 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,769 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,771 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,773 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,775 copying build/lib.linux-armv7l-cpython-311/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-09-26T00:30:22,777 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-09-26T00:30:22,778 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-09-26T00:30:22,780 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-09-26T00:30:22,783 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-09-26T00:30:22,785 copying build/lib.linux-armv7l-cpython-311/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-09-26T00:30:22,787 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-09-26T00:30:22,788 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-09-26T00:30:22,790 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-09-26T00:30:22,793 copying build/lib.linux-armv7l-cpython-311/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-09-26T00:30:22,795 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2023-09-26T00:30:22,796 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-09-26T00:30:22,799 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-09-26T00:30:22,802 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-09-26T00:30:22,805 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-09-26T00:30:22,808 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-09-26T00:30:22,809 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-09-26T00:30:22,812 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-09-26T00:30:22,814 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-09-26T00:30:22,815 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-09-26T00:30:22,819 copying build/lib.linux-armv7l-cpython-311/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-09-26T00:30:22,821 copying build/lib.linux-armv7l-cpython-311/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-09-26T00:30:22,824 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,825 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,828 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,829 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,832 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,834 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,837 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,838 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,841 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,843 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,846 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,848 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,850 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,853 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,856 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,859 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-09-26T00:30:22,861 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,863 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,865 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,867 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,870 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,872 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,874 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/six.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,877 copying build/lib.linux-armv7l-cpython-311/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-09-26T00:30:22,879 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,881 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,897 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,901 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,904 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,906 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,909 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,911 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,914 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-09-26T00:30:22,915 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-09-26T00:30:22,918 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-09-26T00:30:22,921 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-09-26T00:30:22,923 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-09-26T00:30:22,925 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-09-26T00:30:22,928 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-09-26T00:30:22,930 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,958 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,995 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:22,998 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,000 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,003 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,005 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,029 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,031 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,033 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/binpos.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,046 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,048 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,051 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,053 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,056 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/tng.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,089 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,091 copying build/lib.linux-armv7l-cpython-311/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-09-26T00:30:23,093 copying build/lib.linux-armv7l-cpython-311/mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2023-09-26T00:30:23,121 copying build/lib.linux-armv7l-cpython-311/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-09-26T00:30:23,123 running install_egg_info 2023-09-26T00:30:23,139 running egg_info 2023-09-26T00:30:23,146 writing mdtraj.egg-info/PKG-INFO 2023-09-26T00:30:23,150 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2023-09-26T00:30:23,151 writing entry points to mdtraj.egg-info/entry_points.txt 2023-09-26T00:30:23,153 writing requirements to mdtraj.egg-info/requires.txt 2023-09-26T00:30:23,154 writing top-level names to mdtraj.egg-info/top_level.txt 2023-09-26T00:30:23,192 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,192 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,193 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,194 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,194 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,195 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,195 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,196 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,197 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,197 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,198 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,199 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,199 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,200 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,201 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,202 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,202 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,203 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,203 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,204 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,204 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,205 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,205 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,206 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,206 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,207 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,207 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,208 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,208 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,209 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,209 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,209 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,210 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,211 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,211 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,212 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,212 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,213 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,213 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,213 dependency /tmp/pip-build-env-esueuvwf/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 2023-09-26T00:30:23,227 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-09-26T00:30:23,250 reading manifest template 'MANIFEST.in' 2023-09-26T00:30:24,030 no previously-included directories found matching '__pycache__' 2023-09-26T00:30:24,031 no previously-included directories found matching '*.pyc' 2023-09-26T00:30:24,032 adding license file 'LICENSE' 2023-09-26T00:30:24,046 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-09-26T00:30:24,048 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.9.9-py3.11.egg-info 2023-09-26T00:30:24,061 running install_scripts 2023-09-26T00:30:24,116 creating build/bdist.linux-armv7l/wheel/mdtraj-1.9.9.dist-info/WHEEL 2023-09-26T00:30:24,119 creating '/tmp/pip-wheel-7cs8ctq0/.tmp-n2zhb7jb/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-26T00:30:24,121 adding 'mdtraj/__init__.py' 2023-09-26T00:30:24,345 adding 'mdtraj/_lprmsd.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:24,710 adding 'mdtraj/_rmsd.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:24,727 adding 'mdtraj/io.py' 2023-09-26T00:30:24,728 adding 'mdtraj/version.py' 2023-09-26T00:30:24,730 adding 'mdtraj/core/__init__.py' 2023-09-26T00:30:24,733 adding 'mdtraj/core/element.py' 2023-09-26T00:30:24,736 adding 'mdtraj/core/residue_names.py' 2023-09-26T00:30:24,738 adding 'mdtraj/core/selection.py' 2023-09-26T00:30:24,746 adding 'mdtraj/core/topology.py' 2023-09-26T00:30:24,755 adding 'mdtraj/core/trajectory.py' 2023-09-26T00:30:24,757 adding 'mdtraj/core/lib/center.h' 2023-09-26T00:30:24,765 adding 'mdtraj/core/lib/libtheobald.a' 2023-09-26T00:30:24,767 adding 'mdtraj/core/lib/theobald_rmsd.h' 2023-09-26T00:30:24,770 adding 'mdtraj/formats/__init__.py' 2023-09-26T00:30:24,773 adding 'mdtraj/formats/amberrst.py' 2023-09-26T00:30:24,775 adding 'mdtraj/formats/arc.py' 2023-09-26T00:30:24,913 adding 'mdtraj/formats/binpos.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:25,061 adding 'mdtraj/formats/dcd.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:25,456 adding 'mdtraj/formats/dtr.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:25,475 adding 'mdtraj/formats/gro.py' 2023-09-26T00:30:25,477 adding 'mdtraj/formats/gsd.py' 2023-09-26T00:30:25,481 adding 'mdtraj/formats/hdf5.py' 2023-09-26T00:30:25,483 adding 'mdtraj/formats/hoomdxml.py' 2023-09-26T00:30:25,486 adding 'mdtraj/formats/lammpstrj.py' 2023-09-26T00:30:25,489 adding 'mdtraj/formats/lh5.py' 2023-09-26T00:30:25,491 adding 'mdtraj/formats/mdcrd.py' 2023-09-26T00:30:25,494 adding 'mdtraj/formats/mol2.py' 2023-09-26T00:30:25,497 adding 'mdtraj/formats/netcdf.py' 2023-09-26T00:30:25,498 adding 'mdtraj/formats/openmmxml.py' 2023-09-26T00:30:25,501 adding 'mdtraj/formats/pdbx.py' 2023-09-26T00:30:25,502 adding 'mdtraj/formats/prmtop.py' 2023-09-26T00:30:25,504 adding 'mdtraj/formats/psf.py' 2023-09-26T00:30:25,506 adding 'mdtraj/formats/registry.py' 2023-09-26T00:30:25,875 adding 'mdtraj/formats/tng.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:26,147 adding 'mdtraj/formats/trr.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:26,404 adding 'mdtraj/formats/xtc.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:26,416 adding 'mdtraj/formats/xyzfile.py' 2023-09-26T00:30:26,418 adding 'mdtraj/formats/pdb/__init__.py' 2023-09-26T00:30:26,422 adding 'mdtraj/formats/pdb/pdbfile.py' 2023-09-26T00:30:26,426 adding 'mdtraj/formats/pdb/pdbstructure.py' 2023-09-26T00:30:26,429 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2023-09-26T00:30:26,431 adding 'mdtraj/formats/pdb/data/residues.xml' 2023-09-26T00:30:26,433 adding 'mdtraj/geometry/__init__.py' 2023-09-26T00:30:26,899 adding 'mdtraj/geometry/_geometry.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:26,921 adding 'mdtraj/geometry/alignment.py' 2023-09-26T00:30:26,923 adding 'mdtraj/geometry/angle.py' 2023-09-26T00:30:26,925 adding 'mdtraj/geometry/contact.py' 2023-09-26T00:30:26,928 adding 'mdtraj/geometry/dihedral.py' 2023-09-26T00:30:26,930 adding 'mdtraj/geometry/distance.py' 2023-09-26T00:30:27,201 adding 'mdtraj/geometry/drid.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:27,213 adding 'mdtraj/geometry/dssp.py' 2023-09-26T00:30:27,215 adding 'mdtraj/geometry/hbond.py' 2023-09-26T00:30:27,218 adding 'mdtraj/geometry/internal.py' 2023-09-26T00:30:27,497 adding 'mdtraj/geometry/neighborlist.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:27,765 adding 'mdtraj/geometry/neighbors.cpython-311-arm-linux-gnueabihf.so' 2023-09-26T00:30:27,777 adding 'mdtraj/geometry/order.py' 2023-09-26T00:30:27,779 adding 'mdtraj/geometry/rdf.py' 2023-09-26T00:30:27,780 adding 'mdtraj/geometry/rg.py' 2023-09-26T00:30:27,782 adding 'mdtraj/geometry/sasa.py' 2023-09-26T00:30:27,784 adding 'mdtraj/geometry/shape.py' 2023-09-26T00:30:27,785 adding 'mdtraj/geometry/thermodynamic_properties.py' 2023-09-26T00:30:27,787 adding 'mdtraj/nmr/__init__.py' 2023-09-26T00:30:27,789 adding 'mdtraj/nmr/scalar_couplings.py' 2023-09-26T00:30:27,791 adding 'mdtraj/nmr/shift_wrappers.py' 2023-09-26T00:30:27,792 adding 'mdtraj/reporters/__init__.py' 2023-09-26T00:30:27,794 adding 'mdtraj/reporters/basereporter.py' 2023-09-26T00:30:27,796 adding 'mdtraj/reporters/dcdreporter.py' 2023-09-26T00:30:27,797 adding 'mdtraj/reporters/hdf5reporter.py' 2023-09-26T00:30:27,798 adding 'mdtraj/reporters/netcdfreporter.py' 2023-09-26T00:30:27,800 adding 'mdtraj/reporters/xtcreporter.py' 2023-09-26T00:30:27,802 adding 'mdtraj/scripts/__init__.py' 2023-09-26T00:30:27,804 adding 'mdtraj/scripts/mdconvert.py' 2023-09-26T00:30:27,806 adding 'mdtraj/scripts/mdinspect.py' 2023-09-26T00:30:27,808 adding 'mdtraj/testing/__init__.py' 2023-09-26T00:30:27,810 adding 'mdtraj/testing/docscrape.py' 2023-09-26T00:30:27,812 adding 'mdtraj/testing/docstrings.py' 2023-09-26T00:30:27,814 adding 'mdtraj/testing/testing.py' 2023-09-26T00:30:27,816 adding 'mdtraj/utils/__init__.py' 2023-09-26T00:30:27,817 adding 'mdtraj/utils/contextmanagers.py' 2023-09-26T00:30:27,819 adding 'mdtraj/utils/delay_import.py' 2023-09-26T00:30:27,821 adding 'mdtraj/utils/rotation.py' 2023-09-26T00:30:27,822 adding 'mdtraj/utils/singleton.py' 2023-09-26T00:30:27,825 adding 'mdtraj/utils/six.py' 2023-09-26T00:30:27,826 adding 'mdtraj/utils/unitcell.py' 2023-09-26T00:30:27,828 adding 'mdtraj/utils/validation.py' 2023-09-26T00:30:27,830 adding 'mdtraj/utils/zipped.py' 2023-09-26T00:30:27,832 adding 'mdtraj/utils/unit/__init__.py' 2023-09-26T00:30:27,834 adding 'mdtraj/utils/unit/basedimension.py' 2023-09-26T00:30:27,835 adding 'mdtraj/utils/unit/baseunit.py' 2023-09-26T00:30:27,837 adding 'mdtraj/utils/unit/constants.py' 2023-09-26T00:30:27,839 adding 'mdtraj/utils/unit/doctests.py' 2023-09-26T00:30:27,842 adding 'mdtraj/utils/unit/mymatrix.py' 2023-09-26T00:30:27,843 adding 'mdtraj/utils/unit/prefix.py' 2023-09-26T00:30:27,847 adding 'mdtraj/utils/unit/quantity.py' 2023-09-26T00:30:27,849 adding 'mdtraj/utils/unit/standard_dimensions.py' 2023-09-26T00:30:27,852 adding 'mdtraj/utils/unit/unit.py' 2023-09-26T00:30:27,854 adding 'mdtraj/utils/unit/unit_definitions.py' 2023-09-26T00:30:27,855 adding 'mdtraj/utils/unit/unit_math.py' 2023-09-26T00:30:27,857 adding 'mdtraj/utils/unit/unit_operators.py' 2023-09-26T00:30:27,862 adding 'mdtraj-1.9.9.dist-info/LICENSE' 2023-09-26T00:30:27,863 adding 'mdtraj-1.9.9.dist-info/METADATA' 2023-09-26T00:30:27,864 adding 'mdtraj-1.9.9.dist-info/WHEEL' 2023-09-26T00:30:27,865 adding 'mdtraj-1.9.9.dist-info/entry_points.txt' 2023-09-26T00:30:27,866 adding 'mdtraj-1.9.9.dist-info/top_level.txt' 2023-09-26T00:30:27,868 adding 'mdtraj-1.9.9.dist-info/RECORD' 2023-09-26T00:30:27,948 removing build/bdist.linux-armv7l/wheel 2023-09-26T00:30:28,545 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2023-09-26T00:30:28,724 Created wheel for mdtraj: filename=mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl size=7383166 sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b 2023-09-26T00:30:28,725 Stored in directory: /tmp/pip-ephem-wheel-cache-ckoc5nvm/wheels/b3/bd/6b/b0c9757b8d78eee2297ac5433f5a3ccf677552ee461c208117 2023-09-26T00:30:28,742 Successfully built mdtraj 2023-09-26T00:30:28,925 Removed build tracker: '/tmp/pip-build-tracker-009g3a57'