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2021-07-10T00:23:23,965 Found link https://files.pythonhosted.org/packages/78/ae/82df7eca71fa9e71ad4638f8c222164ccc3583874cb4a6875a04586312bc/mdtraj-1.5.1.zip#sha256=d97591eebf1e9ae04c2b2e144340a959ed359fe33037c647b174f017bab482c3 (from https://pypi.org/simple/mdtraj/), version: 1.5.1 2021-07-10T00:23:23,965 Found link https://files.pythonhosted.org/packages/40/21/40aeb64c81f480e07b1e1c31c6b3b332bc38df08d5fd30210fc235acdb3d/mdtraj-1.6.0.tar.gz#sha256=6da885f0f3bad7baa27adf6f7cac62282e02e58b319144f1fefeaa6d3ca8fe7a (from https://pypi.org/simple/mdtraj/), version: 1.6.0 2021-07-10T00:23:23,966 Found link https://files.pythonhosted.org/packages/8f/9e/cf5814ce6a29a474dc2b61492ed36dde1397b1707e63248bafe495529c29/mdtraj-1.6.0.zip#sha256=9d281e43cbc7133615dc0b81e63f64e79e39e3d25098103798301f3c06383c0b (from https://pypi.org/simple/mdtraj/), version: 1.6.0 2021-07-10T00:23:23,966 Found link 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https://pypi.org/simple/mdtraj/) 2021-07-10T00:23:23,972 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64, cp37-cp37m-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ce/ee/2015ff88cacb7c75b5e1cf6a57e8a089549b0e76bcd9474a08845f7ef12f/mdtraj-1.9.6-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=49f4251f83a7fdea4a8122369ef47f213bb1c1cfc38b91177e98985484fb63bf (from https://pypi.org/simple/mdtraj/) 2021-07-10T00:23:23,972 Skipping link: none of the wheel's tags (cp38-cp38-manylinux1_x86_64, cp38-cp38-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c0/61/2fb002b9b2ab90567eb1a837ed510152ddadd5b8358ac800b591e37675e0/mdtraj-1.9.6-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=84bf863729d435df0dd1f86c3023cbe85b8940b102f9d6ef6ce00dcb9130883c (from https://pypi.org/simple/mdtraj/) 2021-07-10T00:23:23,972 Skipping link: none of the wheel's tags (cp39-cp39-manylinux1_x86_64, cp39-cp39-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/09/49/85dc22a3c28108dfd0bce8a4268ae3937167b18fac531a0d801505cad7d9/mdtraj-1.9.6-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=44fcc435df4057126c123585e36a8a4563e24588ad438c916751e2e01501e2ff (from https://pypi.org/simple/mdtraj/) 2021-07-10T00:23:23,973 Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz#sha256=5b7c9b98dd0a1c1a2ddd6c1690fba6096a63314da2e79e05a8a1402b8949ad3c (from https://pypi.org/simple/mdtraj/), version: 1.9.6 2021-07-10T00:23:23,973 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-10T00:23:23,981 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates 2021-07-10T00:23:23,999 Collecting mdtraj==1.0.0 2021-07-10T00:23:24,001 Created temporary directory: /tmp/pip-unpack-3hrygcxy 2021-07-10T00:23:24,472 Downloading mdtraj-1.0.0.zip (5.9 MB) 2021-07-10T00:23:26,086 Added mdtraj==1.0.0 from https://files.pythonhosted.org/packages/8e/36/9fd92ca45c2b84384f78020524edb9dfd2d4cefc0595472cc60b64af62ed/mdtraj-1.0.0.zip#sha256=8aa8e04038453b3201d906e1ecb01cb4261f0e9230d72e62786255f68e09d86d to build tracker '/tmp/pip-req-tracker-m0dqoacq' 2021-07-10T00:23:26,087 Running setup.py (path:/tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4/setup.py) egg_info for package mdtraj 2021-07-10T00:23:26,088 Created temporary directory: /tmp/pip-pip-egg-info-gnutyo6a 2021-07-10T00:23:26,088 Running command python setup.py egg_info 2021-07-10T00:23:27,332 Using built-in specs. 2021-07-10T00:23:27,333 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-10T00:23:27,333 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-10T00:23:27,333 Target: arm-linux-gnueabihf 2021-07-10T00:23:27,333 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 2021-07-10T00:23:27,334 Thread model: posix 2021-07-10T00:23:27,334 Supported LTO compression algorithms: zlib zstd 2021-07-10T00:23:27,334 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-10T00:23:28,565 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4/MDTraj/formats/dcd/dcd.pyx 2021-07-10T00:23:28,565 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-10T00:23:30,854 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4/MDTraj/formats/xtc/trr.pyx 2021-07-10T00:23:30,855 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-10T00:23:33,250 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4/MDTraj/geometry/src/_geometry.pyx 2021-07-10T00:23:33,250 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-10T00:23:38,798 C compiler: 2021-07-10T00:23:38,799 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-10T00:23:38,799 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-10T00:23:38,799 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-10T00:23:38,800 Compiling MDTraj/formats/xtc/trr.pyx because it changed. 2021-07-10T00:23:38,800 Compiling MDTraj/formats/dcd/dcd.pyx because it changed. 2021-07-10T00:23:38,800 Compiling MDTraj/geometry/src/_geometry.pyx because it changed. 2021-07-10T00:23:38,800 [1/3] Cythonizing MDTraj/formats/dcd/dcd.pyx 2021-07-10T00:23:38,800 [2/3] Cythonizing MDTraj/formats/xtc/trr.pyx 2021-07-10T00:23:38,800 [3/3] Cythonizing MDTraj/geometry/src/_geometry.pyx 2021-07-10T00:23:38,932 running egg_info 2021-07-10T00:23:38,934 creating /tmp/pip-pip-egg-info-gnutyo6a/mdtraj.egg-info 2021-07-10T00:23:38,935 writing /tmp/pip-pip-egg-info-gnutyo6a/mdtraj.egg-info/PKG-INFO 2021-07-10T00:23:38,937 writing dependency_links to /tmp/pip-pip-egg-info-gnutyo6a/mdtraj.egg-info/dependency_links.txt 2021-07-10T00:23:38,939 writing entry points to /tmp/pip-pip-egg-info-gnutyo6a/mdtraj.egg-info/entry_points.txt 2021-07-10T00:23:38,940 writing top-level names to /tmp/pip-pip-egg-info-gnutyo6a/mdtraj.egg-info/top_level.txt 2021-07-10T00:23:38,942 writing manifest file '/tmp/pip-pip-egg-info-gnutyo6a/mdtraj.egg-info/SOURCES.txt' 2021-07-10T00:23:39,157 reading manifest file '/tmp/pip-pip-egg-info-gnutyo6a/mdtraj.egg-info/SOURCES.txt' 2021-07-10T00:23:39,159 reading manifest template 'MANIFEST.in' 2021-07-10T00:23:39,207 writing manifest file '/tmp/pip-pip-egg-info-gnutyo6a/mdtraj.egg-info/SOURCES.txt' 2021-07-10T00:23:39,549 Source in /tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4 has version 1.0.0, which satisfies requirement mdtraj==1.0.0 from https://files.pythonhosted.org/packages/8e/36/9fd92ca45c2b84384f78020524edb9dfd2d4cefc0595472cc60b64af62ed/mdtraj-1.0.0.zip#sha256=8aa8e04038453b3201d906e1ecb01cb4261f0e9230d72e62786255f68e09d86d 2021-07-10T00:23:39,550 Removed mdtraj==1.0.0 from https://files.pythonhosted.org/packages/8e/36/9fd92ca45c2b84384f78020524edb9dfd2d4cefc0595472cc60b64af62ed/mdtraj-1.0.0.zip#sha256=8aa8e04038453b3201d906e1ecb01cb4261f0e9230d72e62786255f68e09d86d from build tracker '/tmp/pip-req-tracker-m0dqoacq' 2021-07-10T00:23:39,555 Created temporary directory: /tmp/pip-unpack-b_tjjzf7 2021-07-10T00:23:39,555 Building wheels for collected packages: mdtraj 2021-07-10T00:23:39,559 Created temporary directory: /tmp/pip-wheel-84zz6cnh 2021-07-10T00:23:39,560 Building wheel for mdtraj (setup.py): started 2021-07-10T00:23:39,560 Destination directory: /tmp/pip-wheel-84zz6cnh 2021-07-10T00:23:39,560 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-84zz6cnh 2021-07-10T00:23:40,669 C compiler: 2021-07-10T00:23:40,677 Using built-in specs. 2021-07-10T00:23:40,678 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-10T00:23:40,678 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-10T00:23:40,678 Target: arm-linux-gnueabihf 2021-07-10T00:23:40,678 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 2021-07-10T00:23:40,678 Thread model: posix 2021-07-10T00:23:40,678 Supported LTO compression algorithms: zlib zstd 2021-07-10T00:23:40,679 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-10T00:23:40,935 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-10T00:23:40,961 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-10T00:23:40,991 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-10T00:23:41,808 running bdist_wheel 2021-07-10T00:23:41,813 running build 2021-07-10T00:23:41,813 running build_py 2021-07-10T00:23:41,948 creating build 2021-07-10T00:23:41,948 creating build/lib.linux-armv7l-3.9 2021-07-10T00:23:41,949 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-10T00:23:41,949 creating build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-10T00:23:41,951 copying scripts/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-10T00:23:41,952 copying scripts/mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-10T00:23:41,955 copying scripts/mdinspect.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-10T00:23:41,958 copying MDTraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-10T00:23:41,961 copying MDTraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-10T00:23:41,963 copying MDTraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-10T00:23:41,966 creating build/lib.linux-armv7l-3.9/mdtraj/html 2021-07-10T00:23:41,967 copying MDTraj/html/linked_heatmap.py -> build/lib.linux-armv7l-3.9/mdtraj/html 2021-07-10T00:23:41,970 copying MDTraj/html/install.py -> build/lib.linux-armv7l-3.9/mdtraj/html 2021-07-10T00:23:41,972 copying MDTraj/html/imagebutton_widget.py -> build/lib.linux-armv7l-3.9/mdtraj/html 2021-07-10T00:23:41,975 copying MDTraj/html/trajectory_widget.py -> build/lib.linux-armv7l-3.9/mdtraj/html 2021-07-10T00:23:41,978 copying MDTraj/html/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/html 2021-07-10T00:23:41,982 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:41,983 copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:41,987 copying MDTraj/geometry/contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:41,990 copying MDTraj/geometry/dssp.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:41,993 copying MDTraj/geometry/sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:41,996 copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:41,999 copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:42,002 copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:42,005 copying MDTraj/geometry/hbond.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:42,009 copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:42,012 copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:42,015 copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-10T00:23:42,020 creating build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,021 copying MDTraj/geometry/tests/test_angles.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,024 copying MDTraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,027 copying MDTraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,031 copying MDTraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,034 copying MDTraj/geometry/tests/test_dssp.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,037 copying MDTraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,040 copying MDTraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,043 copying MDTraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,045 copying MDTraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,048 copying MDTraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,051 copying MDTraj/geometry/tests/test_drid.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-10T00:23:42,054 creating build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-10T00:23:42,056 copying MDTraj/nmr/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-10T00:23:42,059 copying MDTraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-10T00:23:42,062 copying MDTraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-10T00:23:42,066 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-10T00:23:42,067 copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-10T00:23:42,071 copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-10T00:23:42,073 copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-10T00:23:42,076 copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-10T00:23:42,080 copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-10T00:23:42,085 creating build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-10T00:23:42,086 copying MDTraj/core/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-10T00:23:42,089 copying MDTraj/core/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-10T00:23:42,094 copying MDTraj/core/topology.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-10T00:23:42,098 copying MDTraj/core/element.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-10T00:23:42,103 creating build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,104 copying MDTraj/formats/openmmxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,107 copying MDTraj/formats/mol2.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,111 copying MDTraj/formats/lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,114 copying MDTraj/formats/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,118 copying MDTraj/formats/registry.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,120 copying MDTraj/formats/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,124 copying MDTraj/formats/arc.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,127 copying MDTraj/formats/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,130 copying MDTraj/formats/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,133 copying MDTraj/formats/prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-10T00:23:42,137 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-10T00:23:42,138 copying MDTraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-10T00:23:42,143 copying MDTraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-10T00:23:42,145 copying MDTraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-10T00:23:42,150 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-10T00:23:42,152 copying MDTraj/formats/pdb/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-10T00:23:42,155 copying MDTraj/formats/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-10T00:23:42,158 copying MDTraj/formats/pdb/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-10T00:23:42,161 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,162 copying MDTraj/utils/contextmanagers.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,166 copying MDTraj/utils/rotation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,169 copying MDTraj/utils/six.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,173 copying MDTraj/utils/validation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,176 copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,178 copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,181 copying MDTraj/utils/ffi.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,184 copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,186 copying MDTraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-10T00:23:42,191 creating build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,192 copying MDTraj/utils/unit/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,195 copying MDTraj/utils/unit/prefix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,198 copying MDTraj/utils/unit/doctests.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,201 copying MDTraj/utils/unit/quantity.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,205 copying MDTraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,207 copying MDTraj/utils/unit/constants.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,210 copying MDTraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,212 copying MDTraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,216 copying MDTraj/utils/unit/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,219 copying MDTraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,221 copying MDTraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,224 copying MDTraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,227 copying MDTraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-10T00:23:42,232 creating build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,234 copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,237 copying MDTraj/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,240 copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,243 copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,246 copying MDTraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,249 copying MDTraj/tests/test_rmsd_memmap.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,251 copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,254 copying MDTraj/tests/test_nmr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,257 copying MDTraj/tests/test_crd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,259 copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,262 copying MDTraj/tests/test_quaternion.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,264 copying MDTraj/tests/test_lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,267 copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,269 copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,272 copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,275 copying MDTraj/tests/test_prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,277 copying MDTraj/tests/test_arc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,279 copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,282 copying MDTraj/tests/test_mol2.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,284 copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,287 copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,291 copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,294 copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,296 copying MDTraj/tests/test_lprmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,299 copying MDTraj/tests/test_topology.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-10T00:23:42,303 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-10T00:23:42,304 copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-10T00:23:42,306 copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-10T00:23:42,309 copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-10T00:23:42,311 copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-10T00:23:42,314 copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-10T00:23:42,328 creating build/lib.linux-armv7l-3.9/mdtraj/html/static 2021-07-10T00:23:42,329 copying MDTraj/html/static/objexporter.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static 2021-07-10T00:23:42,333 copying MDTraj/html/static/widget_trajectory.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static 2021-07-10T00:23:42,336 copying MDTraj/html/static/widget_imagebutton.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static 2021-07-10T00:23:42,339 copying MDTraj/html/static/surface.min.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static 2021-07-10T00:23:42,343 copying MDTraj/html/static/iview.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static 2021-07-10T00:23:42,348 copying MDTraj/html/static/filesaver.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static 2021-07-10T00:23:42,351 copying MDTraj/html/static/context.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static 2021-07-10T00:23:42,354 creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,355 copying MDTraj/testing/reference/nitrogen.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,382 copying MDTraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,390 copying MDTraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,396 copying MDTraj/testing/reference/nitrogen.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,415 copying MDTraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,420 copying MDTraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,423 copying MDTraj/testing/reference/1am7_protein.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,432 copying MDTraj/testing/reference/alanine-dipeptide-implicit.prmtop -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,435 copying MDTraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,438 copying MDTraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,445 copying MDTraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,448 copying MDTraj/testing/reference/README.md -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,451 copying MDTraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,457 copying MDTraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,477 copying MDTraj/testing/reference/tz2.truncoct.parm7 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,502 copying MDTraj/testing/reference/1am7_corrected.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,516 copying MDTraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,519 copying MDTraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,532 copying MDTraj/testing/reference/lysozyme-ligand-tripos.mol2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,535 copying MDTraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,541 copying MDTraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,544 copying MDTraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,546 copying MDTraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,552 copying MDTraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,556 copying MDTraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,578 copying MDTraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,580 copying MDTraj/testing/reference/alanine-dipeptide-explicit.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,583 copying MDTraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,598 copying MDTraj/testing/reference/1am7_uncorrected.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,614 copying MDTraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,617 copying MDTraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,622 copying MDTraj/testing/reference/freesolve_v0.3.tar.bz2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,632 copying MDTraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,634 copying MDTraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,639 copying MDTraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,644 copying MDTraj/testing/reference/native.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,647 copying MDTraj/testing/reference/imatinib.mol2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,650 copying MDTraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,698 copying MDTraj/testing/reference/imatinib.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,703 copying MDTraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,715 copying MDTraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,726 copying MDTraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,728 copying MDTraj/testing/reference/overflow.crd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,764 copying MDTraj/testing/reference/3nch.pdb.gz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,774 copying MDTraj/testing/reference/alanine-dipeptide-explicit.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,780 copying MDTraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,782 copying MDTraj/testing/reference/alanine-dipeptide-explicit.prmtop -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,794 copying MDTraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,796 copying MDTraj/testing/reference/1ncw.pdb.gz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,804 copying MDTraj/testing/reference/alanine.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,806 copying MDTraj/testing/reference/1vii.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,811 copying MDTraj/testing/reference/1vii.pdb.gz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,814 copying MDTraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,821 copying MDTraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,842 copying MDTraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,847 copying MDTraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,856 copying MDTraj/testing/reference/native2.xml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-10T00:23:42,859 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-10T00:23:42,860 copying MDTraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-10T00:23:42,863 copying MDTraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-10T00:23:42,882 running build_ext 2021-07-10T00:23:42,885 building 'mdtraj.formats.xtc' extension 2021-07-10T00:23:42,886 creating build/temp.linux-armv7l-3.9 2021-07-10T00:23:42,886 creating build/temp.linux-armv7l-3.9/MDTraj 2021-07-10T00:23:42,887 creating build/temp.linux-armv7l-3.9/MDTraj/formats 2021-07-10T00:23:42,887 creating build/temp.linux-armv7l-3.9/MDTraj/formats/xtc 2021-07-10T00:23:42,888 creating build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src 2021-07-10T00:23:42,889 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IMDTraj/formats/xtc/include/ -IMDTraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src/xdrfile.o 2021-07-10T00:23:43,067 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-10T00:23:43,068 MDTraj/formats/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T00:23:43,068 478 | while (size >= num && num_of_bits < 32) 2021-07-10T00:23:43,068 | ^~ 2021-07-10T00:23:43,068 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-10T00:23:43,068 MDTraj/formats/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T00:23:43,068 524 | while (bytes[num_of_bytes] >= num) 2021-07-10T00:23:43,068 | ^~ 2021-07-10T00:23:43,069 MDTraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-10T00:23:43,069 MDTraj/formats/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T00:23:43,069 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-10T00:23:43,070 | ^~ 2021-07-10T00:23:43,070 MDTraj/formats/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T00:23:43,070 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-10T00:23:43,070 | ^ 2021-07-10T00:23:43,070 MDTraj/formats/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T00:23:43,070 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-10T00:23:43,070 | ^ 2021-07-10T00:23:43,071 MDTraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-10T00:23:43,071 MDTraj/formats/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T00:23:43,071 683 | if (lastbits < num_of_bits) 2021-07-10T00:23:43,071 | ^ 2021-07-10T00:23:43,072 MDTraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-10T00:23:43,073 MDTraj/formats/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T00:23:43,073 797 | if(size3>xfp->buf1size) 2021-07-10T00:23:43,073 | ^ 2021-07-10T00:23:43,074 MDTraj/formats/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T00:23:43,075 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-10T00:23:43,079 | ^ 2021-07-10T00:23:43,084 MDTraj/formats/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T00:23:43,084 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-10T00:23:43,085 | ^ 2021-07-10T00:23:43,085 MDTraj/formats/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T00:23:43,085 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-10T00:23:43,093 | ^ 2021-07-10T00:23:43,095 MDTraj/formats/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T00:23:43,095 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-10T00:23:43,101 | ^ 2021-07-10T00:23:43,108 MDTraj/formats/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T00:23:43,109 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-10T00:23:43,109 | ^ 2021-07-10T00:23:43,109 MDTraj/formats/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T00:23:43,110 1611 | maxidx = (LASTIDXn_frames == -1) != 0); 2021-07-10T00:23:46,241 | ^~ 2021-07-10T00:23:46,256 MDTraj/formats/xtc/xtc.c:7931:5: warning: implicit declaration of function ‘read_xtc_nframes’; did you mean ‘read_xtc_natoms’? [-Wimplicit-function-declaration] 2021-07-10T00:23:46,256 7931 | read_xtc_nframes(__pyx_t_4, (&__pyx_v_self->n_frames)); 2021-07-10T00:23:46,256 | ^~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,256 | read_xtc_natoms 2021-07-10T00:23:46,302 MDTraj/formats/xtc/xtc.c: In function ‘PyInit_xtc’: 2021-07-10T00:23:46,308 MDTraj/formats/xtc/xtc.c:10785:36: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-10T00:23:46,308 10785 | __pyx_type_3xtc_XTCTrajectoryFile.tp_print = 0; 2021-07-10T00:23:46,308 | ^ 2021-07-10T00:23:46,321 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-10T00:23:46,327 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,327 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,327 | ^ 2021-07-10T00:23:46,327 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,328 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,328 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,328 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,328 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,328 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,335 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,335 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,335 | ^ 2021-07-10T00:23:46,335 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,335 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,335 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,335 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-10T00:23:46,336 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-10T00:23:46,336 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,342 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,342 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,342 | ^ 2021-07-10T00:23:46,342 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,342 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,343 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,343 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,343 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,343 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,349 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,349 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,349 | ^ 2021-07-10T00:23:46,349 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,349 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,350 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,350 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,350 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,350 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,356 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,356 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,356 | ^ 2021-07-10T00:23:46,356 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,357 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,357 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,357 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-10T00:23:46,357 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-10T00:23:46,357 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,363 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,363 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,363 | ^ 2021-07-10T00:23:46,364 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,364 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,364 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,364 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,364 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,364 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,374 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,374 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,374 | ^ 2021-07-10T00:23:46,374 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,374 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,374 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,375 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,375 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,375 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,381 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,381 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,381 | ^ 2021-07-10T00:23:46,381 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,381 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,381 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,382 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-10T00:23:46,382 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-10T00:23:46,382 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,388 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,388 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,388 | ^ 2021-07-10T00:23:46,388 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,388 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,389 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,389 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,389 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,389 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,395 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,395 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,395 | ^ 2021-07-10T00:23:46,396 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,396 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,396 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,396 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,396 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,396 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,402 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,402 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,402 | ^ 2021-07-10T00:23:46,403 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,403 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,403 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,403 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-10T00:23:46,403 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-10T00:23:46,403 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,409 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,409 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-10T00:23:46,410 | ^ 2021-07-10T00:23:46,410 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,410 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,410 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,410 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,410 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,410 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,448 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_ExceptionSave’: 2021-07-10T00:23:46,458 MDTraj/formats/xtc/xtc.c:11628:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-10T00:23:46,459 11628 | *type = tstate->exc_type; 2021-07-10T00:23:46,459 | ^~~~~~~~ 2021-07-10T00:23:46,459 | curexc_type 2021-07-10T00:23:46,469 MDTraj/formats/xtc/xtc.c:11629:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-10T00:23:46,469 11629 | *value = tstate->exc_value; 2021-07-10T00:23:46,470 | ^~~~~~~~~ 2021-07-10T00:23:46,470 | curexc_value 2021-07-10T00:23:46,480 MDTraj/formats/xtc/xtc.c:11630:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-10T00:23:46,481 11630 | *tb = tstate->exc_traceback; 2021-07-10T00:23:46,481 | ^~~~~~~~~~~~~ 2021-07-10T00:23:46,481 | curexc_traceback 2021-07-10T00:23:46,481 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_ExceptionReset’: 2021-07-10T00:23:46,491 MDTraj/formats/xtc/xtc.c:11642:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-10T00:23:46,492 11642 | tmp_type = tstate->exc_type; 2021-07-10T00:23:46,492 | ^~~~~~~~ 2021-07-10T00:23:46,492 | curexc_type 2021-07-10T00:23:46,502 MDTraj/formats/xtc/xtc.c:11643:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-10T00:23:46,503 11643 | tmp_value = tstate->exc_value; 2021-07-10T00:23:46,503 | ^~~~~~~~~ 2021-07-10T00:23:46,503 | curexc_value 2021-07-10T00:23:46,513 MDTraj/formats/xtc/xtc.c:11644:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-10T00:23:46,513 11644 | tmp_tb = tstate->exc_traceback; 2021-07-10T00:23:46,514 | ^~~~~~~~~~~~~ 2021-07-10T00:23:46,514 | curexc_traceback 2021-07-10T00:23:46,524 MDTraj/formats/xtc/xtc.c:11645:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-10T00:23:46,524 11645 | tstate->exc_type = type; 2021-07-10T00:23:46,524 | ^~~~~~~~ 2021-07-10T00:23:46,525 | curexc_type 2021-07-10T00:23:46,535 MDTraj/formats/xtc/xtc.c:11646:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-10T00:23:46,535 11646 | tstate->exc_value = value; 2021-07-10T00:23:46,535 | ^~~~~~~~~ 2021-07-10T00:23:46,535 | curexc_value 2021-07-10T00:23:46,546 MDTraj/formats/xtc/xtc.c:11647:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-10T00:23:46,546 11647 | tstate->exc_traceback = tb; 2021-07-10T00:23:46,546 | ^~~~~~~~~~~~~ 2021-07-10T00:23:46,546 | curexc_traceback 2021-07-10T00:23:46,549 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_GetException’: 2021-07-10T00:23:46,560 MDTraj/formats/xtc/xtc.c:11690:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-10T00:23:46,560 11690 | tmp_type = tstate->exc_type; 2021-07-10T00:23:46,560 | ^~~~~~~~ 2021-07-10T00:23:46,560 | curexc_type 2021-07-10T00:23:46,571 MDTraj/formats/xtc/xtc.c:11691:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-10T00:23:46,571 11691 | tmp_value = tstate->exc_value; 2021-07-10T00:23:46,571 | ^~~~~~~~~ 2021-07-10T00:23:46,571 | curexc_value 2021-07-10T00:23:46,582 MDTraj/formats/xtc/xtc.c:11692:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-10T00:23:46,582 11692 | tmp_tb = tstate->exc_traceback; 2021-07-10T00:23:46,582 | ^~~~~~~~~~~~~ 2021-07-10T00:23:46,582 | curexc_traceback 2021-07-10T00:23:46,593 MDTraj/formats/xtc/xtc.c:11693:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-10T00:23:46,593 11693 | tstate->exc_type = local_type; 2021-07-10T00:23:46,593 | ^~~~~~~~ 2021-07-10T00:23:46,593 | curexc_type 2021-07-10T00:23:46,604 MDTraj/formats/xtc/xtc.c:11694:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-10T00:23:46,604 11694 | tstate->exc_value = local_value; 2021-07-10T00:23:46,604 | ^~~~~~~~~ 2021-07-10T00:23:46,604 | curexc_value 2021-07-10T00:23:46,615 MDTraj/formats/xtc/xtc.c:11695:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-10T00:23:46,615 11695 | tstate->exc_traceback = local_tb; 2021-07-10T00:23:46,615 | ^~~~~~~~~~~~~ 2021-07-10T00:23:46,615 | curexc_traceback 2021-07-10T00:23:46,792 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_PyObject_AsStringAndSize’: 2021-07-10T00:23:46,799 MDTraj/formats/xtc/xtc.c:13710:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,799 13710 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-10T00:23:46,799 | ^ 2021-07-10T00:23:46,799 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,799 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,799 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,799 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,800 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,800 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,807 MDTraj/formats/xtc/xtc.c:13710:13: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,808 13710 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-10T00:23:46,808 | ^ 2021-07-10T00:23:46,808 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,808 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,808 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,808 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-10T00:23:46,808 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-10T00:23:46,808 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,816 MDTraj/formats/xtc/xtc.c:13710:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-10T00:23:46,816 13710 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-10T00:23:46,816 | ^ 2021-07-10T00:23:46,816 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-10T00:23:46,817 from /usr/include/python3.9/Python.h:97, 2021-07-10T00:23:46,817 from MDTraj/formats/xtc/xtc.c:16: 2021-07-10T00:23:46,817 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-10T00:23:46,817 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-10T00:23:46,817 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,823 MDTraj/formats/xtc/xtc.c:13711:20: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-10T00:23:46,824 13711 | return PyUnicode_AsUTF8(o); 2021-07-10T00:23:46,824 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T00:23:46,956 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-10T00:23:47,105 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-10T00:23:47,105 ERROR: Failed building wheel for mdtraj 2021-07-10T00:23:47,106 Running setup.py clean for mdtraj 2021-07-10T00:23:47,106 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-zzu3pn77/mdtraj_ac40d224549a402791f876fe034c19c4/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2021-07-10T00:23:48,277 C compiler: 2021-07-10T00:23:48,285 Using built-in specs. 2021-07-10T00:23:48,285 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-10T00:23:48,286 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-10T00:23:48,286 Target: arm-linux-gnueabihf 2021-07-10T00:23:48,286 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 2021-07-10T00:23:48,286 Thread model: posix 2021-07-10T00:23:48,286 Supported LTO compression algorithms: zlib zstd 2021-07-10T00:23:48,286 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-10T00:23:48,544 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-10T00:23:48,571 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-10T00:23:48,597 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-10T00:23:49,422 running clean 2021-07-10T00:23:49,424 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-10T00:23:49,428 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-10T00:23:49,504 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-10T00:23:49,504 'build/scripts-3.9' does not exist -- can't clean it 2021-07-10T00:23:49,504 removing 'build' 2021-07-10T00:23:49,640 Failed to build mdtraj 2021-07-10T00:23:49,640 ERROR: Failed to build one or more wheels 2021-07-10T00:23:49,641 Exception information: 2021-07-10T00:23:49,641 Traceback (most recent call last): 2021-07-10T00:23:49,641 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-10T00:23:49,641 status = self.run(options, args) 2021-07-10T00:23:49,641 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-10T00:23:49,641 return func(self, options, args) 2021-07-10T00:23:49,641 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-10T00:23:49,641 raise CommandError( 2021-07-10T00:23:49,641 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-10T00:23:49,644 Removed build tracker: '/tmp/pip-req-tracker-m0dqoacq'