2023-07-02T16:26:07,954 Created temporary directory: /tmp/pip-build-tracker-rpzkf5fk 2023-07-02T16:26:07,955 Initialized build tracking at /tmp/pip-build-tracker-rpzkf5fk 2023-07-02T16:26:07,955 Created build tracker: /tmp/pip-build-tracker-rpzkf5fk 2023-07-02T16:26:07,955 Entered build tracker: /tmp/pip-build-tracker-rpzkf5fk 2023-07-02T16:26:07,956 Created temporary directory: /tmp/pip-wheel-52y_hqte 2023-07-02T16:26:07,959 Created temporary directory: /tmp/pip-ephem-wheel-cache-ow4nlj1b 2023-07-02T16:26:07,987 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-07-02T16:26:07,990 2 location(s) to search for versions of mdtraj: 2023-07-02T16:26:07,990 * https://pypi.org/simple/mdtraj/ 2023-07-02T16:26:07,990 * https://www.piwheels.org/simple/mdtraj/ 2023-07-02T16:26:07,991 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2023-07-02T16:26:07,991 Getting page https://pypi.org/simple/mdtraj/ 2023-07-02T16:26:07,993 Found index url 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2023-07-02T16:26:08,069 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/c5/fa/7f4579a0eb11ea6eab4cf94a0b10ca9bebdeeee53e022ad7a66d7a3c5dfb/mdtraj-0.4.3.win32-py3.2.msi (from https://pypi.org/simple/mdtraj/) 2023-07-02T16:26:08,070 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/28/e5/cb27f0a2b7a3c604704fe9fa92d8b3f5e82bd3a5a50f17548d79875618d7/mdtraj-0.4.3.win32-py3.3.msi (from https://pypi.org/simple/mdtraj/) 2023-07-02T16:26:08,070 Found link https://files.pythonhosted.org/packages/e5/88/d95a7bf9ab9f170c4a765b24aef3249f8b48419eb8200c0e6e0cefb8df27/mdtraj-0.4.3.zip (from https://pypi.org/simple/mdtraj/), version: 0.4.3 2023-07-02T16:26:08,070 Found link https://files.pythonhosted.org/packages/d7/77/493f388512cb4e90e787ed60e206b053c4999f59ea8e473f182c041e7bb5/mdtraj-0.5.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.5.0 2023-07-02T16:26:08,070 Skipping link: unsupported archive format: .msi: 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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/) 2023-07-02T16:26:08,086 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/) 2023-07-02T16:26:08,086 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/) 2023-07-02T16:26:08,086 Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.6 2023-07-02T16:26:08,086 Found link https://files.pythonhosted.org/packages/2f/03/c174bfb6471f796472ce1d8695f6c0d1a20ad6516cb789b70052df45b7a6/mdtraj-1.9.7.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.7 2023-07-02T16:26:08,087 Found link https://files.pythonhosted.org/packages/53/02/a30f67a8bd3dba6d6e4ecc02bee290f425bf30c504a8a959a04e2be321ac/mdtraj-1.9.8.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.8 2023-07-02T16:26:08,087 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2023-07-02T16:26:08,087 Getting page https://www.piwheels.org/simple/mdtraj/ 2023-07-02T16:26:08,088 Found index url https://www.piwheels.org/simple/ 2023-07-02T16:26:08,282 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2023-07-02T16:26:08,284 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/) 2023-07-02T16:26:08,284 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2023-07-02T16:26:08,284 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2023-07-02T16:26:08,285 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2023-07-02T16:26:08,309 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2023-07-02T16:26:08,327 Collecting mdtraj==1.9.8 2023-07-02T16:26:08,329 Created temporary directory: /tmp/pip-unpack-a2xojvk_ 2023-07-02T16:26:08,379 Downloading mdtraj-1.9.8.tar.gz (2.2 MB) 2023-07-02T16:26:09,664 Added mdtraj==1.9.8 from https://files.pythonhosted.org/packages/53/02/a30f67a8bd3dba6d6e4ecc02bee290f425bf30c504a8a959a04e2be321ac/mdtraj-1.9.8.tar.gz to build tracker '/tmp/pip-build-tracker-rpzkf5fk' 2023-07-02T16:26:09,684 Created temporary directory: /tmp/pip-build-env-dkc13pqe 2023-07-02T16:26:09,698 Installing build dependencies: started 2023-07-02T16:26:09,699 Running command pip subprocess to install build dependencies 2023-07-02T16:26:10,897 Using pip 23.1.2 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2023-07-02T16:26:11,279 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-07-02T16:26:11,280 Ignoring numpy: markers 'python_version == "3.6"' don't match your environment 2023-07-02T16:26:11,281 Ignoring numpy: markers 'python_version == "3.7"' don't match your environment 2023-07-02T16:26:11,283 Ignoring numpy: markers 'python_version == "3.8"' don't match your environment 2023-07-02T16:26:11,284 Ignoring numpy: markers 'python_version == "3.10"' don't match your environment 2023-07-02T16:26:11,285 Ignoring numpy: markers 'python_version >= "3.11"' don't match your environment 2023-07-02T16:26:12,986 Collecting setuptools 2023-07-02T16:26:13,055 Using cached https://www.piwheels.org/simple/setuptools/setuptools-68.0.0-py3-none-any.whl (804 kB) 2023-07-02T16:26:13,307 Collecting wheel 2023-07-02T16:26:13,325 Using cached https://www.piwheels.org/simple/wheel/wheel-0.40.0-py3-none-any.whl (64 kB) 2023-07-02T16:26:14,546 Collecting numpy==1.19.5 2023-07-02T16:26:15,283 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.5-cp39-cp39-linux_armv7l.whl (10.5 MB) 2023-07-02T16:26:17,002 Collecting Cython>0.28 2023-07-02T16:26:17,393 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.35-cp39-cp39-linux_armv7l.whl (5.0 MB) 2023-07-02T16:26:19,360 Installing collected packages: wheel, setuptools, numpy, Cython 2023-07-02T16:26:19,587 Creating /tmp/pip-build-env-dkc13pqe/overlay/bin 2023-07-02T16:26:19,589 changing mode of /tmp/pip-build-env-dkc13pqe/overlay/bin/wheel to 755 2023-07-02T16:26:28,087 changing mode of /tmp/pip-build-env-dkc13pqe/overlay/bin/f2py to 755 2023-07-02T16:26:28,090 changing mode of /tmp/pip-build-env-dkc13pqe/overlay/bin/f2py3 to 755 2023-07-02T16:26:28,092 changing mode of /tmp/pip-build-env-dkc13pqe/overlay/bin/f2py3.9 to 755 2023-07-02T16:26:30,798 changing mode of /tmp/pip-build-env-dkc13pqe/overlay/bin/cygdb to 755 2023-07-02T16:26:30,800 changing mode of /tmp/pip-build-env-dkc13pqe/overlay/bin/cython to 755 2023-07-02T16:26:30,803 changing mode of /tmp/pip-build-env-dkc13pqe/overlay/bin/cythonize to 755 2023-07-02T16:26:30,826 Successfully installed Cython-0.29.35 numpy-1.19.5 setuptools-68.0.0 wheel-0.40.0 2023-07-02T16:26:31,210 Installing build dependencies: finished with status 'done' 2023-07-02T16:26:31,220 Getting requirements to build wheel: started 2023-07-02T16:26:31,221 Running command Getting requirements to build wheel 2023-07-02T16:26:31,915 Using built-in specs. 2023-07-02T16:26:31,916 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-07-02T16:26:31,916 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2023-07-02T16:26:31,916 Target: arm-linux-gnueabihf 2023-07-02T16:26:31,916 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-07-02T16:26:31,916 Thread model: posix 2023-07-02T16:26:31,916 Supported LTO compression algorithms: zlib zstd 2023-07-02T16:26:31,917 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2023-07-02T16:26:35,758 C compiler: 2023-07-02T16:26:35,758 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-07-02T16:26:35,758 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-07-02T16:26:35,758 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-07-02T16:26:35,758 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-07-02T16:26:35,759 Attempting to autodetect NEON support... Did not detect NEON support 2023-07-02T16:26:35,759 running egg_info 2023-07-02T16:26:35,764 writing mdtraj.egg-info/PKG-INFO 2023-07-02T16:26:35,766 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2023-07-02T16:26:35,768 writing entry points to mdtraj.egg-info/entry_points.txt 2023-07-02T16:26:35,769 writing requirements to mdtraj.egg-info/requires.txt 2023-07-02T16:26:35,771 writing top-level names to mdtraj.egg-info/top_level.txt 2023-07-02T16:26:35,808 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-07-02T16:26:35,837 reading manifest template 'MANIFEST.in' 2023-07-02T16:26:36,577 no previously-included directories found matching '__pycache__' 2023-07-02T16:26:36,578 no previously-included directories found matching '*.pyc' 2023-07-02T16:26:36,578 adding license file 'LICENSE' 2023-07-02T16:26:36,602 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-07-02T16:26:36,695 Getting requirements to build wheel: finished with status 'done' 2023-07-02T16:26:36,704 Created temporary directory: /tmp/pip-modern-metadata-cyci3neu 2023-07-02T16:26:36,707 Preparing metadata (pyproject.toml): started 2023-07-02T16:26:36,708 Running command Preparing metadata (pyproject.toml) 2023-07-02T16:26:37,345 Using built-in specs. 2023-07-02T16:26:37,346 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-07-02T16:26:37,346 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2023-07-02T16:26:37,346 Target: arm-linux-gnueabihf 2023-07-02T16:26:37,346 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-07-02T16:26:37,346 Thread model: posix 2023-07-02T16:26:37,346 Supported LTO compression algorithms: zlib zstd 2023-07-02T16:26:37,346 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2023-07-02T16:26:41,029 ./basesetup.py:451: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-cyci3neu --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2023-07-02T16:26:41,030 warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 2023-07-02T16:26:43,009 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-07-02T16:26:43,010 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-07-02T16:26:43,010 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-07-02T16:27:09,547 C compiler: 2023-07-02T16:27:09,547 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-07-02T16:27:09,547 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-07-02T16:27:09,548 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-07-02T16:27:09,548 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-07-02T16:27:09,548 Attempting to autodetect NEON support... Did not detect NEON support 2023-07-02T16:27:09,548 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx 2023-07-02T16:27:09,548 [ 2/12] Cythonizing mdtraj/geometry/drid.pyx 2023-07-02T16:27:09,549 [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx 2023-07-02T16:27:09,549 [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx 2023-07-02T16:27:09,549 [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx 2023-07-02T16:27:09,549 [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2023-07-02T16:27:09,549 [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx 2023-07-02T16:27:09,549 [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx 2023-07-02T16:27:09,549 [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx 2023-07-02T16:27:09,550 [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx 2023-07-02T16:27:09,550 [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx 2023-07-02T16:27:09,550 [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx 2023-07-02T16:27:09,605 running dist_info 2023-07-02T16:27:09,626 creating /tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info 2023-07-02T16:27:09,632 writing /tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info/PKG-INFO 2023-07-02T16:27:09,635 writing dependency_links to /tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info/dependency_links.txt 2023-07-02T16:27:09,637 writing entry points to /tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info/entry_points.txt 2023-07-02T16:27:09,638 writing requirements to /tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info/requires.txt 2023-07-02T16:27:09,639 writing top-level names to /tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info/top_level.txt 2023-07-02T16:27:09,641 writing manifest file '/tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info/SOURCES.txt' 2023-07-02T16:27:09,703 reading manifest file '/tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info/SOURCES.txt' 2023-07-02T16:27:09,705 reading manifest template 'MANIFEST.in' 2023-07-02T16:27:10,521 no previously-included directories found matching '__pycache__' 2023-07-02T16:27:10,522 no previously-included directories found matching '*.pyc' 2023-07-02T16:27:10,522 adding license file 'LICENSE' 2023-07-02T16:27:10,536 writing manifest file '/tmp/pip-modern-metadata-cyci3neu/mdtraj.egg-info/SOURCES.txt' 2023-07-02T16:27:10,537 creating '/tmp/pip-modern-metadata-cyci3neu/mdtraj-1.9.8.dist-info' 2023-07-02T16:27:11,350 Preparing metadata (pyproject.toml): finished with status 'done' 2023-07-02T16:27:11,357 Source in /tmp/pip-wheel-52y_hqte/mdtraj_a10b2cdd60cf412eaf105c2fde65d5d6 has version 1.9.8, which satisfies requirement mdtraj==1.9.8 from https://files.pythonhosted.org/packages/53/02/a30f67a8bd3dba6d6e4ecc02bee290f425bf30c504a8a959a04e2be321ac/mdtraj-1.9.8.tar.gz 2023-07-02T16:27:11,358 Removed mdtraj==1.9.8 from https://files.pythonhosted.org/packages/53/02/a30f67a8bd3dba6d6e4ecc02bee290f425bf30c504a8a959a04e2be321ac/mdtraj-1.9.8.tar.gz from build tracker '/tmp/pip-build-tracker-rpzkf5fk' 2023-07-02T16:27:11,362 Created temporary directory: /tmp/pip-unpack-0cb4qgof 2023-07-02T16:27:11,363 Building wheels for collected packages: mdtraj 2023-07-02T16:27:11,367 Created temporary directory: /tmp/pip-wheel-d7930_73 2023-07-02T16:27:11,368 Destination directory: /tmp/pip-wheel-d7930_73 2023-07-02T16:27:11,370 Building wheel for mdtraj (pyproject.toml): started 2023-07-02T16:27:11,371 Running command Building wheel for mdtraj (pyproject.toml) 2023-07-02T16:27:12,050 Using built-in specs. 2023-07-02T16:27:12,050 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-07-02T16:27:12,051 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2023-07-02T16:27:12,051 Target: arm-linux-gnueabihf 2023-07-02T16:27:12,051 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-07-02T16:27:12,051 Thread model: posix 2023-07-02T16:27:12,051 Supported LTO compression algorithms: zlib zstd 2023-07-02T16:27:12,051 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2023-07-02T16:27:17,770 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-07-02T16:27:17,771 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-07-02T16:27:17,771 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-07-02T16:27:44,285 C compiler: 2023-07-02T16:27:44,286 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-07-02T16:27:44,286 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-07-02T16:27:44,286 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-07-02T16:27:44,286 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-07-02T16:27:44,286 Attempting to autodetect NEON support... Did not detect NEON support 2023-07-02T16:27:44,286 [ 1/12] Cythonizing mdtraj/formats/dcd/dcd.pyx 2023-07-02T16:27:44,287 [ 2/12] Cythonizing mdtraj/geometry/drid.pyx 2023-07-02T16:27:44,287 [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx 2023-07-02T16:27:44,287 [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx 2023-07-02T16:27:44,287 [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx 2023-07-02T16:27:44,287 [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2023-07-02T16:27:44,287 [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx 2023-07-02T16:27:44,287 [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx 2023-07-02T16:27:44,288 [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx 2023-07-02T16:27:44,288 [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx 2023-07-02T16:27:44,288 [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx 2023-07-02T16:27:44,288 [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx 2023-07-02T16:27:44,382 running bdist_wheel 2023-07-02T16:27:44,403 running build 2023-07-02T16:27:44,404 running build_py 2023-07-02T16:27:44,414 creating build 2023-07-02T16:27:44,414 creating build/lib.linux-armv7l-cpython-39 2023-07-02T16:27:44,415 creating build/lib.linux-armv7l-cpython-39/mdtraj 2023-07-02T16:27:44,416 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2023-07-02T16:27:44,418 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2023-07-02T16:27:44,420 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2023-07-02T16:27:44,423 creating build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-02T16:27:44,424 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-02T16:27:44,426 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-02T16:27:44,428 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-02T16:27:44,430 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-02T16:27:44,432 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-02T16:27:44,434 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2023-07-02T16:27:44,437 creating build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-02T16:27:44,438 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-02T16:27:44,441 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-02T16:27:44,444 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-02T16:27:44,447 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-02T16:27:44,449 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-02T16:27:44,451 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2023-07-02T16:27:44,454 creating build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2023-07-02T16:27:44,455 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2023-07-02T16:27:44,457 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2023-07-02T16:27:44,460 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2023-07-02T16:27:44,462 creating build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2023-07-02T16:27:44,463 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2023-07-02T16:27:44,465 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2023-07-02T16:27:44,467 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2023-07-02T16:27:44,470 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,471 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,474 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,476 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,478 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,479 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,482 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,484 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,486 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,489 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2023-07-02T16:27:44,492 creating build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,493 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,495 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,497 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,500 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,502 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,504 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,507 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,509 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,512 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,514 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,516 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,519 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,521 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,523 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,525 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:27:44,527 creating build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-02T16:27:44,528 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-02T16:27:44,530 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-02T16:27:44,533 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-02T16:27:44,535 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2023-07-02T16:27:44,538 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,539 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,542 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,545 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,548 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,550 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,552 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,555 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,557 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,560 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,563 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,565 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,567 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,569 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,572 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,574 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,577 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,579 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,581 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,584 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,585 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,587 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,589 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,591 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,594 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,596 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,599 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,602 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,604 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,606 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,608 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,611 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,614 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2023-07-02T16:27:44,616 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2023-07-02T16:27:44,617 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2023-07-02T16:27:44,620 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2023-07-02T16:27:44,623 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2023-07-02T16:27:44,627 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2023-07-02T16:27:44,628 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2023-07-02T16:27:44,631 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2023-07-02T16:27:44,641 running build_ext 2023-07-02T16:27:44,645 building 'mdtraj.formats.xtc' extension 2023-07-02T16:27:44,646 creating build/temp.linux-armv7l-cpython-39 2023-07-02T16:27:44,646 creating build/temp.linux-armv7l-cpython-39/mdtraj 2023-07-02T16:27:44,647 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats 2023-07-02T16:27:44,648 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc 2023-07-02T16:27:44,648 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src 2023-07-02T16:27:44,650 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:27:44,777 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:27:44,923 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-07-02T16:27:44,924 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:27:44,924 788 | int smallnum, smaller, larger, i, is_smaller, run; 2023-07-02T16:27:44,924 | ^~~~~~ 2023-07-02T16:27:44,924 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:27:44,924 785 | int smallidx, minidx, maxidx; 2023-07-02T16:27:44,924 | ^~~~~~ 2023-07-02T16:27:44,931 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-07-02T16:27:44,932 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:27:44,932 1016 | int errval=1; 2023-07-02T16:27:44,932 | ^~~~~~ 2023-07-02T16:27:44,936 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2023-07-02T16:27:44,936 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:27:44,937 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2023-07-02T16:27:44,937 | ^~~~~~ 2023-07-02T16:27:44,937 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:27:44,937 1302 | int smallidx, minidx, maxidx; 2023-07-02T16:27:44,937 | ^~~~~~ 2023-07-02T16:27:44,946 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-07-02T16:27:44,946 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:27:44,946 1509 | int errval=1; 2023-07-02T16:27:44,947 | ^~~~~~ 2023-07-02T16:27:47,061 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:27:47,141 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2023-07-02T16:27:47,142 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2023-07-02T16:27:47,142 66 | int i,j,result; 2023-07-02T16:27:47,142 | ^ 2023-07-02T16:27:47,142 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2023-07-02T16:27:47,142 66 | int i,j,result; 2023-07-02T16:27:47,142 | ^ 2023-07-02T16:27:47,143 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2023-07-02T16:27:47,143 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-07-02T16:27:47,143 119 | if (NULL == xd) 2023-07-02T16:27:47,144 | ^~ 2023-07-02T16:27:47,144 mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-07-02T16:27:47,144 122 | do { 2023-07-02T16:27:47,144 | ^~ 2023-07-02T16:27:47,289 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:27:47,622 In file included from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-02T16:27:47,622 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-02T16:27:47,623 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-02T16:27:47,623 from mdtraj/formats/xtc/xtc.c:779: 2023-07-02T16:27:47,623 /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-07-02T16:27:47,623 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-02T16:27:47,623 | ^~~~~~~ 2023-07-02T16:27:54,131 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2023-07-02T16:27:54,131 mdtraj/formats/xtc/xtc.c:691:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:27:54,131 691 | #define PyInt_FromLong PyLong_FromLong 2023-07-02T16:27:54,132 | ^~~~~~~~~~~~~~~ 2023-07-02T16:27:54,138 mdtraj/formats/xtc/xtc.c:9535:7: note: ‘__pyx_v_status’ was declared here 2023-07-02T16:27:54,138 9535 | int __pyx_v_status; 2023-07-02T16:27:54,138 | ^~~~~~~~~~~~~~ 2023-07-02T16:28:03,535 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2023-07-02T16:28:03,540 mdtraj/formats/xtc/xtc.c:8054:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,540 8054 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2023-07-02T16:28:03,540 | ^ 2023-07-02T16:28:03,545 mdtraj/formats/xtc/xtc.c:8050:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,546 8050 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2023-07-02T16:28:03,546 | ^ 2023-07-02T16:28:03,551 mdtraj/formats/xtc/xtc.c:8046:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,551 8046 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-02T16:28:03,551 | ^ 2023-07-02T16:28:03,556 mdtraj/formats/xtc/xtc.c:8006:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,556 8006 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-02T16:28:03,556 | ^ 2023-07-02T16:28:03,561 mdtraj/formats/xtc/xtc.c:7988:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,562 7988 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-02T16:28:03,562 | ^ 2023-07-02T16:28:03,566 mdtraj/formats/xtc/xtc.c:8064:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,566 8064 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-02T16:28:03,567 | ^ 2023-07-02T16:28:03,572 mdtraj/formats/xtc/xtc.c:8026:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,572 8026 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2023-07-02T16:28:03,572 | ^ 2023-07-02T16:28:03,577 mdtraj/formats/xtc/xtc.c:8022:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,577 8022 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2023-07-02T16:28:03,577 | ^ 2023-07-02T16:28:03,582 mdtraj/formats/xtc/xtc.c:8018:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,582 8018 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-02T16:28:03,583 | ^ 2023-07-02T16:28:03,587 mdtraj/formats/xtc/xtc.c:7641:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,588 7641 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2023-07-02T16:28:03,588 | ^ 2023-07-02T16:28:03,592 mdtraj/formats/xtc/xtc.c:7637:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:03,593 7637 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2023-07-02T16:28:03,593 | ^ 2023-07-02T16:28:08,133 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/xtc.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:28:08,305 building 'mdtraj.formats.trr' extension 2023-07-02T16:28:08,306 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:28:08,422 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:28:08,553 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-07-02T16:28:08,554 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:28:08,554 788 | int smallnum, smaller, larger, i, is_smaller, run; 2023-07-02T16:28:08,554 | ^~~~~~ 2023-07-02T16:28:08,554 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:28:08,554 785 | int smallidx, minidx, maxidx; 2023-07-02T16:28:08,554 | ^~~~~~ 2023-07-02T16:28:08,561 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-07-02T16:28:08,561 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:28:08,561 1016 | int errval=1; 2023-07-02T16:28:08,561 | ^~~~~~ 2023-07-02T16:28:08,565 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2023-07-02T16:28:08,566 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:28:08,566 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2023-07-02T16:28:08,566 | ^~~~~~ 2023-07-02T16:28:08,567 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:28:08,567 1302 | int smallidx, minidx, maxidx; 2023-07-02T16:28:08,567 | ^~~~~~ 2023-07-02T16:28:08,575 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-07-02T16:28:08,576 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2023-07-02T16:28:08,576 1509 | int errval=1; 2023-07-02T16:28:08,576 | ^~~~~~ 2023-07-02T16:28:10,699 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:28:11,354 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:28:11,671 In file included from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-02T16:28:11,671 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-02T16:28:11,672 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-02T16:28:11,672 from mdtraj/formats/xtc/trr.c:779: 2023-07-02T16:28:11,672 /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-07-02T16:28:11,672 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-02T16:28:11,672 | ^~~~~~~ 2023-07-02T16:28:18,520 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2023-07-02T16:28:18,521 mdtraj/formats/xtc/trr.c:691:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:18,521 691 | #define PyInt_FromLong PyLong_FromLong 2023-07-02T16:28:18,521 | ^~~~~~~~~~~~~~~ 2023-07-02T16:28:18,527 mdtraj/formats/xtc/trr.c:11061:7: note: ‘__pyx_v_status’ was declared here 2023-07-02T16:28:18,527 11061 | int __pyx_v_status; 2023-07-02T16:28:18,527 | ^~~~~~~~~~~~~~ 2023-07-02T16:28:28,279 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2023-07-02T16:28:28,285 mdtraj/formats/xtc/trr.c:8414:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,285 8414 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2023-07-02T16:28:28,285 | ^ 2023-07-02T16:28:28,290 mdtraj/formats/xtc/trr.c:8410:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,291 8410 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-02T16:28:28,291 | ^ 2023-07-02T16:28:28,292 mdtraj/formats/xtc/trr.c:1927:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,292 1927 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2023-07-02T16:28:28,292 | ^ 2023-07-02T16:28:28,296 mdtraj/formats/xtc/trr.c:6951:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2023-07-02T16:28:28,296 6951 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2023-07-02T16:28:28,296 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:28:28,301 mdtraj/formats/xtc/trr.c:8404:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,301 8404 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2023-07-02T16:28:28,301 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-07-02T16:28:28,307 mdtraj/formats/xtc/trr.c:8357:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,307 8357 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2023-07-02T16:28:28,307 | ^ 2023-07-02T16:28:28,312 mdtraj/formats/xtc/trr.c:8353:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,312 8353 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-02T16:28:28,313 | ^ 2023-07-02T16:28:28,314 mdtraj/formats/xtc/trr.c:1927:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,314 1927 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2023-07-02T16:28:28,314 | ^ 2023-07-02T16:28:28,318 mdtraj/formats/xtc/trr.c:6967:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2023-07-02T16:28:28,318 6967 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2023-07-02T16:28:28,318 | ^~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:28:28,323 mdtraj/formats/xtc/trr.c:8347:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,323 8347 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2023-07-02T16:28:28,323 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2023-07-02T16:28:28,328 mdtraj/formats/xtc/trr.c:8747:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,328 8747 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-02T16:28:28,328 | ^ 2023-07-02T16:28:28,334 mdtraj/formats/xtc/trr.c:8743:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,334 8743 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-07-02T16:28:28,334 | ^ 2023-07-02T16:28:28,339 mdtraj/formats/xtc/trr.c:8588:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,340 8588 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-02T16:28:28,340 | ^ 2023-07-02T16:28:28,345 mdtraj/formats/xtc/trr.c:8584:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,345 8584 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-07-02T16:28:28,345 | ^ 2023-07-02T16:28:28,350 mdtraj/formats/xtc/trr.c:8640:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,350 8640 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2023-07-02T16:28:28,350 | ^ 2023-07-02T16:28:28,356 mdtraj/formats/xtc/trr.c:8636:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:28,356 8636 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2023-07-02T16:28:28,356 | ^ 2023-07-02T16:28:34,720 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/trr.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:28:34,906 building 'mdtraj.formats.tng' extension 2023-07-02T16:28:34,907 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng 2023-07-02T16:28:34,908 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src 2023-07-02T16:28:34,909 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression 2023-07-02T16:28:34,910 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib 2023-07-02T16:28:34,911 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwlzh.o 2023-07-02T16:28:35,617 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwt.o 2023-07-02T16:28:35,990 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/coder.o 2023-07-02T16:28:36,690 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/dict.o 2023-07-02T16:28:36,817 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/fixpoint.o 2023-07-02T16:28:36,997 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffman.o 2023-07-02T16:28:37,674 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffmem.o 2023-07-02T16:28:38,111 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/lz77.o 2023-07-02T16:28:38,413 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/merge_sort.o 2023-07-02T16:28:38,586 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/mtf.o 2023-07-02T16:28:38,671 mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: 2023-07-02T16:28:38,671 mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-07-02T16:28:38,671 196 | while (dict[ptr]!=v) 2023-07-02T16:28:38,671 | ^~ 2023-07-02T16:28:38,975 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/rle.o 2023-07-02T16:28:39,024 mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: 2023-07-02T16:28:39,024 mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-07-02T16:28:39,024 56 | if (v==vals[i]) 2023-07-02T16:28:39,025 | ^~ 2023-07-02T16:28:39,150 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/tng_compress.o 2023-07-02T16:28:41,372 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/vals16.o 2023-07-02T16:28:41,503 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/warnmalloc.o 2023-07-02T16:28:41,643 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/widemuldiv.o 2023-07-02T16:28:41,878 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc2.o 2023-07-02T16:28:43,498 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc3.o 2023-07-02T16:28:45,750 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/md5.o 2023-07-02T16:28:46,161 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/tng_io.o 2023-07-02T16:28:46,319 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: 2023-07-02T16:28:46,322 mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-02T16:28:46,322 1064 | tng_data->input_endianness_swap_func_32 = 2023-07-02T16:28:46,322 | ^ 2023-07-02T16:28:46,323 mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-02T16:28:46,323 1073 | tng_data->input_endianness_swap_func_64 = 2023-07-02T16:28:46,323 | ^ 2023-07-02T16:28:46,324 mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-02T16:28:46,324 1089 | tng_data->input_endianness_swap_func_32 = 2023-07-02T16:28:46,324 | ^ 2023-07-02T16:28:46,324 mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-02T16:28:46,324 1098 | tng_data->input_endianness_swap_func_64 = 2023-07-02T16:28:46,325 | ^ 2023-07-02T16:28:46,409 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: 2023-07-02T16:28:46,414 mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 2023-07-02T16:28:46,414 9565 | if(tng_data->output_endianness_swap_func_32 == 2023-07-02T16:28:46,414 | ^~ 2023-07-02T16:28:46,418 mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 2023-07-02T16:28:46,418 9570 | else if(tng_data->output_endianness_swap_func_32 == 2023-07-02T16:28:46,419 | ^~ 2023-07-02T16:28:46,423 mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 2023-07-02T16:28:46,423 9588 | if(tng_data->output_endianness_swap_func_64 == 2023-07-02T16:28:46,423 | ^~ 2023-07-02T16:28:46,428 mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 2023-07-02T16:28:46,428 9593 | else if(tng_data->output_endianness_swap_func_64 == 2023-07-02T16:28:46,428 | ^~ 2023-07-02T16:28:46,430 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: 2023-07-02T16:28:46,435 mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-02T16:28:46,435 9651 | tng_data->output_endianness_swap_func_32 = 2023-07-02T16:28:46,435 | ^ 2023-07-02T16:28:46,439 mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-02T16:28:46,440 9660 | tng_data->output_endianness_swap_func_64 = 2023-07-02T16:28:46,440 | ^ 2023-07-02T16:28:46,444 mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-02T16:28:46,444 9673 | tng_data->output_endianness_swap_func_32 = 2023-07-02T16:28:46,445 | ^ 2023-07-02T16:28:46,449 mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const, int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const, uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const, long long unsigned int *)’} [-Wincompatible-pointer-types] 2023-07-02T16:28:46,449 9682 | tng_data->output_endianness_swap_func_64 = 2023-07-02T16:28:46,449 | ^ 2023-07-02T16:28:48,302 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: 2023-07-02T16:28:48,308 mdtraj/formats/tng/src/lib/tng_io.c:12613:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2023-07-02T16:28:48,309 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2023-07-02T16:28:48,309 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:28:48,315 mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 2023-07-02T16:28:48,316 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2023-07-02T16:28:48,316 | ^~~~~~~~~~~~~~~~~~ 2023-07-02T16:28:49,354 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: 2023-07-02T16:28:49,358 mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:49,358 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; 2023-07-02T16:28:49,358 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2023-07-02T16:28:49,360 mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:28:49,360 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, 2023-07-02T16:28:49,360 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:28:49,360 4309 | (int)n_frames, 2023-07-02T16:28:49,360 | ~~~~~~~~~~~~~~ 2023-07-02T16:28:49,360 4310 | f_precision, 2023-07-02T16:28:49,360 | ~~~~~~~~~~~~ 2023-07-02T16:28:49,361 4311 | 0, alt_algo, 2023-07-02T16:28:49,361 | ~~~~~~~~~~~~ 2023-07-02T16:28:49,361 4312 | &compressed_len); 2023-07-02T16:28:49,361 | ~~~~~~~~~~~~~~~~ 2023-07-02T16:28:49,363 mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 2023-07-02T16:28:49,364 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; 2023-07-02T16:28:49,364 | ^~~~~~~~~~~ 2023-07-02T16:29:00,293 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/tng.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/tng.o 2023-07-02T16:29:00,610 In file included from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-02T16:29:00,611 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-02T16:29:00,611 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-02T16:29:00,611 from mdtraj/formats/tng/tng.c:805: 2023-07-02T16:29:00,611 /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-07-02T16:29:00,611 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-02T16:29:00,611 | ^~~~~~~ 2023-07-02T16:29:00,692 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’: 2023-07-02T16:29:00,694 mdtraj/formats/tng/tng.c:3688:104: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,694 3688 | __pyx_t_1 = ((tng_util_trajectory_open(__pyx_v_filename, __pyx_v_self->mode, (&__pyx_v_self->_traj)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,694 | ^~ 2023-07-02T16:29:00,696 mdtraj/formats/tng/tng.c:3743:88: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,696 3743 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,697 | ^~ 2023-07-02T16:29:00,698 mdtraj/formats/tng/tng.c:3775:90: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,699 3775 | __pyx_t_1 = ((tng_num_frames_get(__pyx_v_self->_traj, (&__pyx_v_self->tot_n_frames)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,699 | ^~ 2023-07-02T16:29:00,700 mdtraj/formats/tng/tng.c:3807:95: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,701 3807 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,701 | ^~ 2023-07-02T16:29:00,703 mdtraj/formats/tng/tng.c:3877:113: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,703 3877 | __pyx_t_1 = ((tng_num_frames_per_frame_set_get(__pyx_v_self->_traj, (&__pyx_v_self->_frames_per_frame_set)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,703 | ^~ 2023-07-02T16:29:00,706 mdtraj/formats/tng/tng.c:3921:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,707 3921 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,707 | ^~ 2023-07-02T16:29:00,723 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’: 2023-07-02T16:29:00,725 mdtraj/formats/tng/tng.c:4717:106: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,725 4717 | __pyx_t_7 = ((tng_chain_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,726 | ^~ 2023-07-02T16:29:00,728 mdtraj/formats/tng/tng.c:4762:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,728 4762 | __pyx_t_7 = ((tng_residue_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,728 | ^~ 2023-07-02T16:29:00,734 mdtraj/formats/tng/tng.c:4869:115: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,734 4869 | __pyx_t_8 = ((tng_global_residue_id_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, (&__pyx_v_residue_id)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,734 | ^~ 2023-07-02T16:29:00,736 mdtraj/formats/tng/tng.c:4899:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,736 4899 | __pyx_t_8 = ((tng_atom_name_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,736 | ^~ 2023-07-02T16:29:00,742 mdtraj/formats/tng/tng.c:5027:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,742 5027 | __pyx_t_8 = ((tng_atom_type_of_particle_nr_get(__pyx_v_self->_traj, __pyx_v_i, __pyx_v_text, 0x400) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,742 | ^~ 2023-07-02T16:29:00,762 mdtraj/formats/tng/tng.c:5628:126: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,762 5628 | __pyx_t_7 = ((tng_molsystem_bonds_get(__pyx_v_self->_traj, (&__pyx_v_n_bonds), (&__pyx_v_from_atoms), (&__pyx_v_to_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,763 | ^~ 2023-07-02T16:29:00,771 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’: 2023-07-02T16:29:00,774 mdtraj/formats/tng/tng.c:6038:152: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,774 6038 | __pyx_t_1 = ((tng_util_pos_read_range(__pyx_v_self->_traj, __pyx_v_self->_pos, __pyx_v_self->_pos, (&__pyx_v_positions), (&__pyx_v_stride_length)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,774 | ^~ 2023-07-02T16:29:00,789 mdtraj/formats/tng/tng.c:6306:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,790 6306 | __pyx_t_1 = ((tng_util_time_of_frame_get(__pyx_v_self->_traj, __pyx_v_self->_pos, (&__pyx_v_frame_time)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,790 | ^~ 2023-07-02T16:29:00,795 mdtraj/formats/tng/tng.c:6408:304: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,795 6408 | __pyx_t_1 = ((tng_data_vector_interval_get(__pyx_v_self->_traj, __pyx_v_6mdtraj_7formats_3tng_TNG_TRAJ_BOX_SHAPE, __pyx_v_self->_pos, __pyx_v_self->_pos, __pyx_e_6mdtraj_7formats_3tng_TNG_USE_HASH, (&__pyx_v_box_shape), (&__pyx_v_stride_length), (&__pyx_v_n_values_per_frame), (&__pyx_v_data_type)) == __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,796 | ^~ 2023-07-02T16:29:00,867 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’: 2023-07-02T16:29:00,872 mdtraj/formats/tng/tng.c:8900:94: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,872 8900 | __pyx_t_1 = ((tng_implicit_num_particles_set(__pyx_v_self->_traj, __pyx_v_self->n_atoms) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,872 | ^~ 2023-07-02T16:29:00,877 mdtraj/formats/tng/tng.c:8932:75: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,877 8932 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,877 | ^~ 2023-07-02T16:29:00,882 mdtraj/formats/tng/tng.c:8964:81: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,882 8964 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,882 | ^~ 2023-07-02T16:29:00,897 mdtraj/formats/tng/tng.c:9287:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,897 9287 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,897 | ^~ 2023-07-02T16:29:00,919 mdtraj/formats/tng/tng.c:9478:372: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,919 9478 | __pyx_t_1 = ((tng_util_pos_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz_array.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,919 | ^~ 2023-07-02T16:29:00,938 mdtraj/formats/tng/tng.c:9530:378: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,938 9530 | __pyx_t_1 = ((tng_util_box_shape_write(__pyx_v_self->_traj, __pyx_v_self->tot_n_frames, (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box_array.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,939 | ^~ 2023-07-02T16:29:00,945 mdtraj/formats/tng/tng.c:9592:89: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2023-07-02T16:29:00,945 9592 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_15) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2023-07-02T16:29:00,945 | ^~ 2023-07-02T16:29:16,921 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/tng/tng.o -L/usr/lib -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:29:17,172 building 'mdtraj.formats.dcd' extension 2023-07-02T16:29:17,173 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd 2023-07-02T16:29:17,174 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src 2023-07-02T16:29:17,175 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:29:17,505 In file included from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-02T16:29:17,506 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-02T16:29:17,506 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-02T16:29:17,506 from mdtraj/formats/dcd/dcd.c:777: 2023-07-02T16:29:17,506 /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-07-02T16:29:17,507 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-02T16:29:17,507 | ^~~~~~~ 2023-07-02T16:29:24,796 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2023-07-02T16:29:24,796 mdtraj/formats/dcd/dcd.c:689:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:29:24,797 689 | #define PyInt_FromLong PyLong_FromLong 2023-07-02T16:29:24,797 | ^~~~~~~~~~~~~~~ 2023-07-02T16:29:24,799 mdtraj/formats/dcd/dcd.c:5430:7: note: ‘__pyx_v_i’ was declared here 2023-07-02T16:29:24,799 5430 | int __pyx_v_i; 2023-07-02T16:29:24,799 | ^~~~~~~~~ 2023-07-02T16:29:27,895 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:29:29,227 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:29:29,369 building 'mdtraj.formats.binpos' extension 2023-07-02T16:29:29,370 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos 2023-07-02T16:29:29,371 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src 2023-07-02T16:29:29,372 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:29:29,699 In file included from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-02T16:29:29,699 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-02T16:29:29,700 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-02T16:29:29,700 from mdtraj/formats/binpos/binpos.c:777: 2023-07-02T16:29:29,700 /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-07-02T16:29:29,700 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-02T16:29:29,700 | ^~~~~~~ 2023-07-02T16:29:37,605 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2023-07-02T16:29:37,608 mdtraj/formats/binpos/binpos.c:5508:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:29:37,608 5508 | if (__pyx_t_2) { 2023-07-02T16:29:37,608 | ^ 2023-07-02T16:29:37,611 mdtraj/formats/binpos/binpos.c:4988:7: note: ‘__pyx_v_status’ was declared here 2023-07-02T16:29:37,611 4988 | int __pyx_v_status; 2023-07-02T16:29:37,611 | ^~~~~~~~~~~~~~ 2023-07-02T16:29:37,611 mdtraj/formats/binpos/binpos.c:689:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:29:37,612 689 | #define PyInt_FromLong PyLong_FromLong 2023-07-02T16:29:37,612 | ^~~~~~~~~~~~~~~ 2023-07-02T16:29:37,614 mdtraj/formats/binpos/binpos.c:4985:7: note: ‘__pyx_v_i’ was declared here 2023-07-02T16:29:37,614 4985 | int __pyx_v_i; 2023-07-02T16:29:37,614 | ^~~~~~~~~ 2023-07-02T16:29:39,054 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:29:39,365 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/binpos.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:29:39,503 building 'mdtraj.formats.dtr' extension 2023-07-02T16:29:39,504 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr 2023-07-02T16:29:39,505 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src 2023-07-02T16:29:39,506 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:29:39,768 In file included from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-02T16:29:39,768 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-02T16:29:39,768 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-02T16:29:39,768 from mdtraj/formats/dtr/dtr.cpp:798: 2023-07-02T16:29:39,769 /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-07-02T16:29:39,769 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-02T16:29:39,769 | ^~~~~~~ 2023-07-02T16:29:52,077 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:29:53,767 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2023-07-02T16:29:53,767 mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2023-07-02T16:29:53,767 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2023-07-02T16:29:53,768 | ~~^ ~ 2023-07-02T16:29:53,768 | | | 2023-07-02T16:29:53,768 | | size_t {aka unsigned int} 2023-07-02T16:29:53,768 | long int 2023-07-02T16:29:53,768 | %d 2023-07-02T16:29:53,768 mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-07-02T16:29:53,769 487 | printf("size %d framesize %d\n\n", 2023-07-02T16:29:53,769 | ~^ 2023-07-02T16:29:53,769 | | 2023-07-02T16:29:53,769 | int 2023-07-02T16:29:53,769 | %lld 2023-07-02T16:29:53,769 488 | keys[i].size(), m_framesize); 2023-07-02T16:29:53,769 | ~~~~~~~~~~~~~~ 2023-07-02T16:29:53,770 | | 2023-07-02T16:29:53,770 | uint64_t {aka long long unsigned int} 2023-07-02T16:29:53,770 mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-07-02T16:29:53,770 487 | printf("size %d framesize %d\n\n", 2023-07-02T16:29:53,770 | ~^ 2023-07-02T16:29:53,770 | | 2023-07-02T16:29:53,770 | int 2023-07-02T16:29:53,770 | %lld 2023-07-02T16:29:53,771 488 | keys[i].size(), m_framesize); 2023-07-02T16:29:53,771 | ~~~~~~~~~~~ 2023-07-02T16:29:53,771 | | 2023-07-02T16:29:53,771 | uint64_t {aka long long unsigned int} 2023-07-02T16:29:53,771 mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2023-07-02T16:29:53,772 494 | "non-constant time interval at frame %ld\n", i); 2023-07-02T16:29:53,772 | ~~^ ~ 2023-07-02T16:29:53,772 | | | 2023-07-02T16:29:53,772 | | size_t {aka unsigned int} 2023-07-02T16:29:53,772 | long int 2023-07-02T16:29:53,772 | %d 2023-07-02T16:29:53,772 mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2023-07-02T16:29:53,773 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2023-07-02T16:29:53,773 | ~~^ ~ 2023-07-02T16:29:53,773 | | | 2023-07-02T16:29:53,773 | | size_t {aka unsigned int} 2023-07-02T16:29:53,773 | long int 2023-07-02T16:29:53,773 | %d 2023-07-02T16:29:53,897 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2023-07-02T16:29:53,898 mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-07-02T16:29:53,898 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2023-07-02T16:29:53,898 | ~~^ 2023-07-02T16:29:53,898 | | 2023-07-02T16:29:53,898 | long int 2023-07-02T16:29:53,898 | %lld 2023-07-02T16:29:53,898 1302 | 3*natoms, pos.count); 2023-07-02T16:29:53,899 | ~~~~~~~~~ 2023-07-02T16:29:53,899 | | 2023-07-02T16:29:53,899 | uint64_t {aka long long unsigned int} 2023-07-02T16:29:53,899 mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-07-02T16:29:53,899 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2023-07-02T16:29:53,899 | ~~^ 2023-07-02T16:29:53,899 | | 2023-07-02T16:29:53,900 | long int 2023-07-02T16:29:53,900 | %lld 2023-07-02T16:29:53,900 1311 | 3*natoms, vel.count); 2023-07-02T16:29:53,900 | ~~~~~~~~~ 2023-07-02T16:29:53,900 | | 2023-07-02T16:29:53,900 | uint64_t {aka long long unsigned int} 2023-07-02T16:29:53,923 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2023-07-02T16:29:53,923 mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2023-07-02T16:29:53,923 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2023-07-02T16:29:53,923 | ~~^ 2023-07-02T16:29:53,924 | | 2023-07-02T16:29:53,924 | long int 2023-07-02T16:29:53,924 | %lld 2023-07-02T16:29:53,924 1573 | velblob.count, 3*natoms); 2023-07-02T16:29:53,924 | ~~~~~~~~~~~~~ 2023-07-02T16:29:53,924 | | 2023-07-02T16:29:53,924 | uint64_t {aka long long unsigned int} 2023-07-02T16:29:54,945 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: 2023-07-02T16:29:54,945 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 2023-07-02T16:29:54,945 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2023-07-02T16:29:54,945 | ~~~~~~~~^~~~~ 2023-07-02T16:29:57,170 In file included from /usr/include/c++/10/map:60, 2023-07-02T16:29:57,171 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2023-07-02T16:29:57,171 /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2023-07-02T16:29:57,171 /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2023-07-02T16:29:57,171 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-07-02T16:29:57,171 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:29:57,233 /usr/include/c++/10/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2023-07-02T16:29:57,233 /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2023-07-02T16:29:57,233 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2023-07-02T16:29:57,234 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:29:57,234 /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2023-07-02T16:29:57,289 In file included from /usr/include/c++/10/map:61, 2023-07-02T16:29:57,289 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2023-07-02T16:29:57,289 /usr/include/c++/10/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2023-07-02T16:29:57,289 /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2023-07-02T16:29:57,289 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-07-02T16:29:57,289 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:29:57,289 521 | std::forward_as_tuple(std::move(__k)), 2023-07-02T16:29:57,290 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:29:57,290 522 | std::tuple<>()); 2023-07-02T16:29:57,290 | ~~~~~~~~~~~~~~~ 2023-07-02T16:29:58,060 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: 2023-07-02T16:29:58,060 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2023-07-02T16:29:58,060 706 | sprintf(sub, "%03x/", i); 2023-07-02T16:29:58,060 | ^~~~ 2023-07-02T16:29:58,061 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 2023-07-02T16:29:58,061 706 | sprintf(sub, "%03x/", i); 2023-07-02T16:29:58,061 | ^~~~~~~ 2023-07-02T16:29:58,061 mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2023-07-02T16:29:58,061 706 | sprintf(sub, "%03x/", i); 2023-07-02T16:29:58,061 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2023-07-02T16:29:58,062 mdtraj/formats/dtr/src/dtrplugin.cxx:714:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2023-07-02T16:29:58,062 714 | sprintf(subsub, "%03x", j); 2023-07-02T16:29:58,062 | ^~~~ 2023-07-02T16:29:58,062 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 2023-07-02T16:29:58,062 714 | sprintf(subsub, "%03x", j); 2023-07-02T16:29:58,062 | ^~~~~~ 2023-07-02T16:29:58,062 mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2023-07-02T16:29:58,063 714 | sprintf(subsub, "%03x", j); 2023-07-02T16:29:58,063 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-07-02T16:29:58,472 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: 2023-07-02T16:29:58,473 mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2023-07-02T16:29:58,473 667 | sprintf(answer, "%03x/", d1); 2023-07-02T16:29:58,473 | ^ 2023-07-02T16:29:58,473 mdtraj/formats/dtr/src/dtrplugin.cxx:667:13: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2023-07-02T16:29:58,473 667 | sprintf(answer, "%03x/", d1); 2023-07-02T16:29:58,473 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:29:58,474 mdtraj/formats/dtr/src/dtrplugin.cxx:665:28: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 2023-07-02T16:29:58,474 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-07-02T16:29:58,474 | ^~~~ 2023-07-02T16:29:58,474 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2023-07-02T16:29:58,474 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-07-02T16:29:58,474 | ^~~~~~~~~~~~ 2023-07-02T16:29:58,474 mdtraj/formats/dtr/src/dtrplugin.cxx:665:13: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2023-07-02T16:29:58,475 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2023-07-02T16:29:58,475 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:30:01,179 In file included from /usr/include/c++/10/map:61, 2023-07-02T16:30:01,179 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2023-07-02T16:30:01,179 /usr/include/c++/10/bits/stl_map.h: In member function ‘int desres::molfile::DtrReader::frame_from_bytes(const void*, uint64_t, molfile_timestep_t*) const’: 2023-07-02T16:30:01,180 /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2023-07-02T16:30:01,180 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2023-07-02T16:30:01,180 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:30:01,180 521 | std::forward_as_tuple(std::move(__k)), 2023-07-02T16:30:01,180 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:30:01,180 522 | std::tuple<>()); 2023-07-02T16:30:01,181 | ~~~~~~~~~~~~~~~ 2023-07-02T16:30:06,326 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:30:06,696 building 'mdtraj._rmsd' extension 2023-07-02T16:30:06,697 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd 2023-07-02T16:30:06,698 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src 2023-07-02T16:30:06,699 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:30:40,862 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:30:41,064 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:30:41,309 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:30:41,969 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:30:42,335 building 'mdtraj._lprmsd' extension 2023-07-02T16:30:42,336 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:30:42,590 In file included from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-02T16:30:42,590 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-02T16:30:42,591 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-02T16:30:42,591 from mdtraj/rmsd/_lprmsd.cpp:807: 2023-07-02T16:30:42,591 /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-07-02T16:30:42,591 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-02T16:30:42,591 | ^~~~~~~ 2023-07-02T16:30:53,297 mdtraj/rmsd/_lprmsd.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: 2023-07-02T16:30:53,297 mdtraj/rmsd/_lprmsd.cpp:4080:14: warning: ‘__pyx_pybuffernd_ref_xyz_frame_dis.__Pyx_LocalBuf_ND::diminfo[0].__Pyx_Buf_DimInfo::shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:30:53,298 4080 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; 2023-07-02T16:30:53,298 | ^~ 2023-07-02T16:31:03,801 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:06,180 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:06,378 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:07,411 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:07,712 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:07,958 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:08,618 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:31:08,940 building 'mdtraj.core.lib.libtheobald' extension 2023-07-02T16:31:08,941 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2023-07-02T16:31:09,599 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/rmsd/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2023-07-02T16:31:09,794 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o 2023-07-02T16:31:09,828 building 'mdtraj.geometry._geometry' extension 2023-07-02T16:31:09,829 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry 2023-07-02T16:31:09,829 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src 2023-07-02T16:31:09,831 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:10,093 In file included from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-07-02T16:31:10,093 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-07-02T16:31:10,093 from /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-07-02T16:31:10,093 from mdtraj/geometry/src/_geometry.cpp:809: 2023-07-02T16:31:10,093 /tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-07-02T16:31:10,094 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-07-02T16:31:10,094 | ^~~~~~~ 2023-07-02T16:31:15,318 mdtraj/geometry/src/_geometry.cpp: In function ‘void __pyx_f_6mdtraj_8geometry_9_geometry_make_whole(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’: 2023-07-02T16:31:15,318 mdtraj/geometry/src/_geometry.cpp:6080:224: warning: ‘__pyx_v_delta[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:31:15,319 6080 | (__pyx_v_offset[__pyx_v_k]) = ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_8 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_7)) ))) * roundf(((__pyx_v_delta[2]) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_5 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_4)) )))))); 2023-07-02T16:31:15,319 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:31:15,319 mdtraj/geometry/src/_geometry.cpp:6094:277: warning: ‘__pyx_v_delta[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:31:15,319 6094 | (__pyx_v_offset[__pyx_t_9]) = ((__pyx_v_offset[__pyx_t_9]) + ((*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_4 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_5)) ))) * roundf((((__pyx_v_delta[1]) - (__pyx_v_offset[1])) / (*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_frame_unitcell_vectors.data + __pyx_t_7 * __pyx_v_frame_unitcell_vectors.strides[0]) )) + __pyx_t_8)) ))))))); 2023-07-02T16:31:15,319 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2023-07-02T16:31:15,319 mdtraj/geometry/src/_geometry.cpp:6094:277: warning: ‘__pyx_v_offset[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:31:39,082 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:55,448 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:58,938 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:31:59,925 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/sasa.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:32:00,355 building 'mdtraj.geometry.drid' extension 2023-07-02T16:32:00,356 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:32:24,588 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:32:25,199 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:32:25,311 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/moments.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:32:25,650 building 'mdtraj.geometry.neighbors' extension 2023-07-02T16:32:25,652 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:32:48,436 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:32:49,571 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighbors.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:32:49,922 building 'mdtraj.geometry.neighborlist' extension 2023-07-02T16:32:49,922 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:33:10,191 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/geometry/include -I/tmp/pip-build-env-dkc13pqe/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2023-07-02T16:33:14,477 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2023-07-02T16:33:14,477 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors[0][0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:33:14,477 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2023-07-02T16:33:14,477 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-07-02T16:33:14,478 mdtraj/geometry/src/neighborlist.cpp:51:53: warning: ‘periodicBoxVectors[1][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:33:14,478 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; 2023-07-02T16:33:14,478 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-07-02T16:33:14,478 mdtraj/geometry/src/neighborlist.cpp:52:53: warning: ‘periodicBoxVectors[2][2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:33:14,478 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; 2023-07-02T16:33:14,478 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-07-02T16:33:14,478 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors[0][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-07-02T16:33:14,479 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2023-07-02T16:33:14,479 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2023-07-02T16:33:15,471 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighborlist.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so 2023-07-02T16:33:15,857 installing to build/bdist.linux-armv7l/wheel 2023-07-02T16:33:15,857 running install 2023-07-02T16:33:15,882 running install_lib 2023-07-02T16:33:15,891 creating build/bdist.linux-armv7l 2023-07-02T16:33:15,892 creating build/bdist.linux-armv7l/wheel 2023-07-02T16:33:15,893 creating build/bdist.linux-armv7l/wheel/mdtraj 2023-07-02T16:33:15,895 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-02T16:33:15,896 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-02T16:33:15,898 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-02T16:33:15,901 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-02T16:33:15,903 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-02T16:33:15,904 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-02T16:33:15,907 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2023-07-02T16:33:15,909 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-02T16:33:15,910 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-02T16:33:15,913 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-02T16:33:15,917 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-02T16:33:15,920 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-02T16:33:15,922 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-02T16:33:15,925 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-07-02T16:33:15,926 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-07-02T16:33:15,928 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-07-02T16:33:15,931 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2023-07-02T16:33:15,933 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2023-07-02T16:33:15,935 copying build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-02T16:33:15,964 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-07-02T16:33:15,965 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-07-02T16:33:15,967 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-07-02T16:33:15,970 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2023-07-02T16:33:15,971 copying build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-02T16:33:15,990 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-07-02T16:33:15,991 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-07-02T16:33:15,994 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-07-02T16:33:15,996 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2023-07-02T16:33:15,999 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,000 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/six.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,004 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,005 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,008 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,011 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,013 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,016 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,019 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,022 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,025 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,028 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,030 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,033 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,036 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,039 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2023-07-02T16:33:16,041 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,043 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,045 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,048 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,050 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,053 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,055 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,058 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2023-07-02T16:33:16,060 copying build/lib.linux-armv7l-cpython-39/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-02T16:33:16,063 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,064 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,067 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,069 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,095 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,098 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,100 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,103 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,106 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,108 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,164 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,167 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,169 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,172 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,174 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,176 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,198 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,200 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,202 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,204 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2023-07-02T16:33:16,233 copying build/lib.linux-armv7l-cpython-39/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-02T16:33:16,235 copying build/lib.linux-armv7l-cpython-39/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2023-07-02T16:33:16,238 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-02T16:33:16,239 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-02T16:33:16,242 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-02T16:33:16,245 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-02T16:33:16,246 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2023-07-02T16:33:16,250 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,250 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,254 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,276 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,278 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,281 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,284 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,286 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,288 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,291 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,294 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,296 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,332 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,375 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-07-02T16:33:16,377 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-07-02T16:33:16,378 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-07-02T16:33:16,381 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2023-07-02T16:33:16,384 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-07-02T16:33:16,388 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-07-02T16:33:16,391 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2023-07-02T16:33:16,394 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,397 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,400 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,403 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,407 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,421 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,442 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,444 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,446 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,448 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,463 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,465 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2023-07-02T16:33:16,467 running install_egg_info 2023-07-02T16:33:16,498 running egg_info 2023-07-02T16:33:16,504 writing mdtraj.egg-info/PKG-INFO 2023-07-02T16:33:16,506 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2023-07-02T16:33:16,508 writing entry points to mdtraj.egg-info/entry_points.txt 2023-07-02T16:33:16,509 writing requirements to mdtraj.egg-info/requires.txt 2023-07-02T16:33:16,511 writing top-level names to mdtraj.egg-info/top_level.txt 2023-07-02T16:33:16,558 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-07-02T16:33:16,583 reading manifest template 'MANIFEST.in' 2023-07-02T16:33:17,476 no previously-included directories found matching '__pycache__' 2023-07-02T16:33:17,478 no previously-included directories found matching '*.pyc' 2023-07-02T16:33:17,478 adding license file 'LICENSE' 2023-07-02T16:33:17,505 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2023-07-02T16:33:17,507 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.9.8-py3.9.egg-info 2023-07-02T16:33:17,524 running install_scripts 2023-07-02T16:33:17,576 creating build/bdist.linux-armv7l/wheel/mdtraj-1.9.8.dist-info/WHEEL 2023-07-02T16:33:17,580 creating '/tmp/pip-wheel-d7930_73/.tmp-6_kllcpm/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-07-02T16:33:17,582 adding 'mdtraj/__init__.py' 2023-07-02T16:33:17,830 adding 'mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:18,211 adding 'mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:18,225 adding 'mdtraj/io.py' 2023-07-02T16:33:18,226 adding 'mdtraj/version.py' 2023-07-02T16:33:18,228 adding 'mdtraj/core/__init__.py' 2023-07-02T16:33:18,231 adding 'mdtraj/core/element.py' 2023-07-02T16:33:18,234 adding 'mdtraj/core/residue_names.py' 2023-07-02T16:33:18,236 adding 'mdtraj/core/selection.py' 2023-07-02T16:33:18,244 adding 'mdtraj/core/topology.py' 2023-07-02T16:33:18,253 adding 'mdtraj/core/trajectory.py' 2023-07-02T16:33:18,255 adding 'mdtraj/core/lib/center.h' 2023-07-02T16:33:18,265 adding 'mdtraj/core/lib/libtheobald.a' 2023-07-02T16:33:18,266 adding 'mdtraj/core/lib/theobald_rmsd.h' 2023-07-02T16:33:18,268 adding 'mdtraj/formats/__init__.py' 2023-07-02T16:33:18,272 adding 'mdtraj/formats/amberrst.py' 2023-07-02T16:33:18,274 adding 'mdtraj/formats/arc.py' 2023-07-02T16:33:18,416 adding 'mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:18,581 adding 'mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:19,013 adding 'mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:19,030 adding 'mdtraj/formats/gro.py' 2023-07-02T16:33:19,032 adding 'mdtraj/formats/gsd.py' 2023-07-02T16:33:19,037 adding 'mdtraj/formats/hdf5.py' 2023-07-02T16:33:19,039 adding 'mdtraj/formats/hoomdxml.py' 2023-07-02T16:33:19,042 adding 'mdtraj/formats/lammpstrj.py' 2023-07-02T16:33:19,045 adding 'mdtraj/formats/lh5.py' 2023-07-02T16:33:19,047 adding 'mdtraj/formats/mdcrd.py' 2023-07-02T16:33:19,050 adding 'mdtraj/formats/mol2.py' 2023-07-02T16:33:19,053 adding 'mdtraj/formats/netcdf.py' 2023-07-02T16:33:19,054 adding 'mdtraj/formats/openmmxml.py' 2023-07-02T16:33:19,057 adding 'mdtraj/formats/pdbx.py' 2023-07-02T16:33:19,059 adding 'mdtraj/formats/prmtop.py' 2023-07-02T16:33:19,061 adding 'mdtraj/formats/psf.py' 2023-07-02T16:33:19,062 adding 'mdtraj/formats/registry.py' 2023-07-02T16:33:19,483 adding 'mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:19,773 adding 'mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:20,047 adding 'mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:20,057 adding 'mdtraj/formats/xyzfile.py' 2023-07-02T16:33:20,059 adding 'mdtraj/formats/pdb/__init__.py' 2023-07-02T16:33:20,063 adding 'mdtraj/formats/pdb/pdbfile.py' 2023-07-02T16:33:20,068 adding 'mdtraj/formats/pdb/pdbstructure.py' 2023-07-02T16:33:20,070 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2023-07-02T16:33:20,072 adding 'mdtraj/formats/pdb/data/residues.xml' 2023-07-02T16:33:20,075 adding 'mdtraj/geometry/__init__.py' 2023-07-02T16:33:20,609 adding 'mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:20,629 adding 'mdtraj/geometry/alignment.py' 2023-07-02T16:33:20,631 adding 'mdtraj/geometry/angle.py' 2023-07-02T16:33:20,633 adding 'mdtraj/geometry/contact.py' 2023-07-02T16:33:20,636 adding 'mdtraj/geometry/dihedral.py' 2023-07-02T16:33:20,639 adding 'mdtraj/geometry/distance.py' 2023-07-02T16:33:20,926 adding 'mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:20,936 adding 'mdtraj/geometry/dssp.py' 2023-07-02T16:33:20,939 adding 'mdtraj/geometry/hbond.py' 2023-07-02T16:33:20,942 adding 'mdtraj/geometry/internal.py' 2023-07-02T16:33:21,248 adding 'mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:21,539 adding 'mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so' 2023-07-02T16:33:21,550 adding 'mdtraj/geometry/order.py' 2023-07-02T16:33:21,552 adding 'mdtraj/geometry/rdf.py' 2023-07-02T16:33:21,553 adding 'mdtraj/geometry/rg.py' 2023-07-02T16:33:21,555 adding 'mdtraj/geometry/sasa.py' 2023-07-02T16:33:21,557 adding 'mdtraj/geometry/shape.py' 2023-07-02T16:33:21,558 adding 'mdtraj/geometry/thermodynamic_properties.py' 2023-07-02T16:33:21,560 adding 'mdtraj/nmr/__init__.py' 2023-07-02T16:33:21,562 adding 'mdtraj/nmr/scalar_couplings.py' 2023-07-02T16:33:21,564 adding 'mdtraj/nmr/shift_wrappers.py' 2023-07-02T16:33:21,566 adding 'mdtraj/reporters/__init__.py' 2023-07-02T16:33:21,567 adding 'mdtraj/reporters/basereporter.py' 2023-07-02T16:33:21,569 adding 'mdtraj/reporters/dcdreporter.py' 2023-07-02T16:33:21,570 adding 'mdtraj/reporters/hdf5reporter.py' 2023-07-02T16:33:21,572 adding 'mdtraj/reporters/netcdfreporter.py' 2023-07-02T16:33:21,573 adding 'mdtraj/reporters/xtcreporter.py' 2023-07-02T16:33:21,575 adding 'mdtraj/scripts/__init__.py' 2023-07-02T16:33:21,578 adding 'mdtraj/scripts/mdconvert.py' 2023-07-02T16:33:21,580 adding 'mdtraj/scripts/mdinspect.py' 2023-07-02T16:33:21,582 adding 'mdtraj/testing/__init__.py' 2023-07-02T16:33:21,584 adding 'mdtraj/testing/docscrape.py' 2023-07-02T16:33:21,586 adding 'mdtraj/testing/docstrings.py' 2023-07-02T16:33:21,588 adding 'mdtraj/testing/testing.py' 2023-07-02T16:33:21,590 adding 'mdtraj/utils/__init__.py' 2023-07-02T16:33:21,591 adding 'mdtraj/utils/contextmanagers.py' 2023-07-02T16:33:21,593 adding 'mdtraj/utils/delay_import.py' 2023-07-02T16:33:21,595 adding 'mdtraj/utils/rotation.py' 2023-07-02T16:33:21,596 adding 'mdtraj/utils/singleton.py' 2023-07-02T16:33:21,598 adding 'mdtraj/utils/six.py' 2023-07-02T16:33:21,600 adding 'mdtraj/utils/unitcell.py' 2023-07-02T16:33:21,602 adding 'mdtraj/utils/validation.py' 2023-07-02T16:33:21,604 adding 'mdtraj/utils/zipped.py' 2023-07-02T16:33:21,606 adding 'mdtraj/utils/unit/__init__.py' 2023-07-02T16:33:21,607 adding 'mdtraj/utils/unit/basedimension.py' 2023-07-02T16:33:21,609 adding 'mdtraj/utils/unit/baseunit.py' 2023-07-02T16:33:21,611 adding 'mdtraj/utils/unit/constants.py' 2023-07-02T16:33:21,614 adding 'mdtraj/utils/unit/doctests.py' 2023-07-02T16:33:21,616 adding 'mdtraj/utils/unit/mymatrix.py' 2023-07-02T16:33:21,618 adding 'mdtraj/utils/unit/prefix.py' 2023-07-02T16:33:21,622 adding 'mdtraj/utils/unit/quantity.py' 2023-07-02T16:33:21,623 adding 'mdtraj/utils/unit/standard_dimensions.py' 2023-07-02T16:33:21,627 adding 'mdtraj/utils/unit/unit.py' 2023-07-02T16:33:21,629 adding 'mdtraj/utils/unit/unit_definitions.py' 2023-07-02T16:33:21,631 adding 'mdtraj/utils/unit/unit_math.py' 2023-07-02T16:33:21,632 adding 'mdtraj/utils/unit/unit_operators.py' 2023-07-02T16:33:21,638 adding 'mdtraj-1.9.8.dist-info/LICENSE' 2023-07-02T16:33:21,639 adding 'mdtraj-1.9.8.dist-info/METADATA' 2023-07-02T16:33:21,640 adding 'mdtraj-1.9.8.dist-info/WHEEL' 2023-07-02T16:33:21,641 adding 'mdtraj-1.9.8.dist-info/entry_points.txt' 2023-07-02T16:33:21,642 adding 'mdtraj-1.9.8.dist-info/top_level.txt' 2023-07-02T16:33:21,644 adding 'mdtraj-1.9.8.dist-info/RECORD' 2023-07-02T16:33:21,720 removing build/bdist.linux-armv7l/wheel 2023-07-02T16:33:22,497 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2023-07-02T16:33:22,652 Created wheel for mdtraj: filename=mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl size=7082284 sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 2023-07-02T16:33:22,653 Stored in directory: /tmp/pip-ephem-wheel-cache-ow4nlj1b/wheels/cb/91/3a/33a9f153e7604eba7b22d3df7312c713e8bedeb70143e4ec2b 2023-07-02T16:33:22,672 Successfully built mdtraj 2023-07-02T16:33:22,856 Removed build tracker: '/tmp/pip-build-tracker-rpzkf5fk'