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2021-07-13T23:37:28,655 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 2021-07-13T23:37:28,655 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 2021-07-13T23:37:28,659 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 2021-07-13T23:37:28,659 Found link https://files.pythonhosted.org/packages/a7/09/abb145901e09665d3a7931527e34a160049cebf4eba3506a69db2093f5f9/mdtraj-1.6.1.tar.gz#sha256=1d390acb7bbe09c7a2b1c639c641c47eef09c37bd525cd83c201addda37074c8 (from https://pypi.org/simple/mdtraj/), version: 1.6.1 2021-07-13T23:37:28,659 Found link https://files.pythonhosted.org/packages/38/44/179f101e32ab7ceb52864fb4ef2955c0807b9f548c087f39f2cfd18cb498/mdtraj-1.6.1.zip#sha256=bca98c6339d04b36934b37857eae9f42fb667e1745d4d7dc29ebfd4e3c653365 (from https://pypi.org/simple/mdtraj/), version: 1.6.1 2021-07-13T23:37:28,659 Found link https://files.pythonhosted.org/packages/bf/81/6f611041374bd7d2d49a15040d999cc52eed1a44e856a4a8d9c02370ac37/mdtraj-1.7.2.tar.gz#sha256=1bc9fb06e84f6562e51e040946dae0b940eaca4760f78f3ac451f4a89b132a9a (from https://pypi.org/simple/mdtraj/), version: 1.7.2 2021-07-13T23:37:28,660 Found link https://files.pythonhosted.org/packages/ff/b2/8785a8c9c7119e1a7c4e64072ccf428f75a3b0a9782a7ac25e5402b0a59d/mdtraj-1.7.2.zip#sha256=3158176cd2c21d2abdff5b2cbd9cac323f337b831123d5201bbb7d3fbe69e714 (from https://pypi.org/simple/mdtraj/), version: 1.7.2 2021-07-13T23:37:28,660 Found link https://files.pythonhosted.org/packages/cd/9f/027fa58d4e93dd3d700e22d5766961c970f6882c2bffd33daef55219d078/mdtraj-1.8.0.tar.gz#sha256=480fa4c280146e91db0ab7811f6fba5da29e89452b071d366a8e68247a88ffea (from https://pypi.org/simple/mdtraj/), version: 1.8.0 2021-07-13T23:37:28,660 Found link https://files.pythonhosted.org/packages/4a/2e/5bb01aaa8cd2ea9d75dd2ac12fd9f04f7137a8c996bde0138ad1b5e54ecb/mdtraj-1.8.0.zip#sha256=867325cb206dca4a605de4877e17e5e1983f2e778a6ef64594bd4250142561a8 (from https://pypi.org/simple/mdtraj/), version: 1.8.0 2021-07-13T23:37:28,661 Found link https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz#sha256=ca1ae07c5f5ce59940a48388ac9b098f8e22743b5f3ed3f46d5e3d1317b06282 (from https://pypi.org/simple/mdtraj/), version: 1.9.1 2021-07-13T23:37:28,661 Found link https://files.pythonhosted.org/packages/e0/9e/857f613eae8af3fb8cc73904b3edf622c58de3884c5989e4466973c3c9ee/mdtraj-1.9.2.tar.gz#sha256=cdd926f19c007955f0f768d36d696f3e77b4c8030289a2b40eb97a91cebacd0f (from https://pypi.org/simple/mdtraj/), version: 1.9.2 2021-07-13T23:37:28,661 Found link https://files.pythonhosted.org/packages/72/68/1efc74927df6fdaaa4816556a2534f4560cb69ed573ccac728e4fb8e3e09/mdtraj-1.9.3.tar.gz#sha256=5d95e045b1dd093a26bf6fea9895c3c6b52955d8f7fceee867a519ccf29640b3 (from https://pypi.org/simple/mdtraj/), version: 1.9.3 2021-07-13T23:37:28,661 Found link https://files.pythonhosted.org/packages/50/1d/581a080a1900f61bb1c0388e29517a54d4034faa094d40d794e1f96597d9/mdtraj-1.9.4.tar.gz#sha256=d5d28be24dd5f38e8b272c3a445a6cdbffc374b30e891c5535f65bb20f7e8b24 (from https://pypi.org/simple/mdtraj/), version: 1.9.4 2021-07-13T23:37:28,662 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1b/77/3ac1597812fc28964662587d405f85986206192623b434f7d0fa1b4a6a5b/mdtraj-1.9.5-cp36-cp36m-manylinux1_x86_64.whl#sha256=c02a9a589acc98dd3cc4db9b0cb21725f5e2cb9484c14cc4fa032a4663c7a1e9 (from https://pypi.org/simple/mdtraj/) 2021-07-13T23:37:28,662 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/af/da/271e93bb98bc93ccac17bc1f31f814be4f9e7024ac19bf31af892a462030/mdtraj-1.9.5-cp37-cp37m-manylinux1_x86_64.whl#sha256=8816f9a91826e46a413fd1a5ffd663b4076cf4c3b8930bb2046814d1438a88ee (from https://pypi.org/simple/mdtraj/) 2021-07-13T23:37:28,663 Skipping link: none of the wheel's tags (cp38-cp38-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/3b/fd/4ffba665d0b0346072f61d0e8ef7ab281202db445d99136c717c89169a97/mdtraj-1.9.5-cp38-cp38-manylinux1_x86_64.whl#sha256=84bb3ced0ff61c4b3b38a36d71837599f50c8723c5d9e555dced51d0d09e10a1 (from https://pypi.org/simple/mdtraj/) 2021-07-13T23:37:28,663 Skipping link: none of the wheel's tags (cp39-cp39-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/68/53/2f666107565f4735abd859b6af6867353eb08d0e9728d90fb0abc12d578e/mdtraj-1.9.5-cp39-cp39-manylinux1_x86_64.whl#sha256=7eae1adc6aa876396c9797d80db3f71da831601fb1739da731e1de9ca8ac96ab (from https://pypi.org/simple/mdtraj/) 2021-07-13T23:37:28,664 Found link https://files.pythonhosted.org/packages/d8/cb/5dcc31c7e2c4485bd2aea66233def28954f2dc530607f5c43fefab71a963/mdtraj-1.9.5.tar.gz#sha256=f22c28c9dd51aa0f8692078dd3c2c7a338a7ca27cbd9aaeb669a60361e95adc4 (from https://pypi.org/simple/mdtraj/), version: 1.9.5 2021-07-13T23:37:28,664 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64, cp36-cp36m-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/fe/a7/2a1392fe56ddd22a9cf5dcff7d684bdd7ce146d5c32839080dd8de7122dd/mdtraj-1.9.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=8d437742ec45ff619c7a50afacf16f3a791d604cd0be74b5b74d90b0dc3f577a (from https://pypi.org/simple/mdtraj/) 2021-07-13T23:37:28,664 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/) 2021-07-13T23:37:28,665 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/) 2021-07-13T23:37:28,665 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/) 2021-07-13T23:37:28,666 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 2021-07-13T23:37:28,666 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-13T23:37:28,674 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2021-07-13T23:37:28,693 Collecting mdtraj==1.9.2 2021-07-13T23:37:28,694 Created temporary directory: /tmp/pip-unpack-42mrumok 2021-07-13T23:37:28,740 Downloading mdtraj-1.9.2.tar.gz (2.0 MB) 2021-07-13T23:37:30,078 Added mdtraj==1.9.2 from https://files.pythonhosted.org/packages/e0/9e/857f613eae8af3fb8cc73904b3edf622c58de3884c5989e4466973c3c9ee/mdtraj-1.9.2.tar.gz#sha256=cdd926f19c007955f0f768d36d696f3e77b4c8030289a2b40eb97a91cebacd0f to build tracker '/tmp/pip-req-tracker-fnshusda' 2021-07-13T23:37:30,079 Running setup.py (path:/tmp/pip-wheel-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/setup.py) egg_info for package mdtraj 2021-07-13T23:37:30,079 Created temporary directory: /tmp/pip-pip-egg-info-o9ohwer3 2021-07-13T23:37:30,080 Running command python setup.py egg_info 2021-07-13T23:37:31,476 Using built-in specs. 2021-07-13T23:37:31,477 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-13T23:37:31,477 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-13T23:37:31,477 Target: arm-linux-gnueabihf 2021-07-13T23:37:31,477 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 2021-07-13T23:37:31,477 Thread model: posix 2021-07-13T23:37:31,477 Supported LTO compression algorithms: zlib zstd 2021-07-13T23:37:31,478 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-13T23:37:33,449 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/formats/dcd/dcd.pyx 2021-07-13T23:37:33,449 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:37:34,999 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. 2021-07-13T23:37:34,999 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. 2021-07-13T23:37:34,999 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. 2021-07-13T23:37:35,758 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/geometry/neighborlist.pyx 2021-07-13T23:37:35,759 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:37:41,029 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/geometry/neighbors.pyx 2021-07-13T23:37:41,030 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:37:46,365 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/geometry/src/_geometry.pyx 2021-07-13T23:37:46,365 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:37:54,026 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/rmsd/_lprmsd.pyx 2021-07-13T23:37:54,026 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:37:57,322 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/formats/binpos/binpos.pyx 2021-07-13T23:37:57,322 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:37:59,557 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/formats/dtr/dtr.pyx 2021-07-13T23:37:59,557 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:38:01,854 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/formats/tng/tng.pyx 2021-07-13T23:38:01,854 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:38:04,659 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/formats/xtc/trr.pyx 2021-07-13T23:38:04,659 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:38:07,807 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/formats/xtc/xtc.pyx 2021-07-13T23:38:07,807 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:38:10,776 /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-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/mdtraj/rmsd/_rmsd.pyx 2021-07-13T23:38:10,777 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-13T23:38:18,333 C compiler: 2021-07-13T23:38:18,333 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-13T23:38:18,333 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-13T23:38:18,333 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-13T23:38:18,333 Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-13T23:38:18,334 Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-13T23:38:18,334 Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-13T23:38:18,334 Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-13T23:38:18,334 Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-13T23:38:18,334 Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-13T23:38:18,334 Compiling mdtraj/rmsd/_rmsd.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-13T23:38:18,334 Compiling mdtraj/rmsd/_lprmsd.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-13T23:38:18,334 Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-13T23:38:18,335 Compiling mdtraj/geometry/neighbors.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-13T23:38:18,335 Compiling mdtraj/geometry/neighborlist.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-13T23:38:18,335 [ 1/11] Cythonizing mdtraj/formats/dcd/dcd.pyx 2021-07-13T23:38:18,335 [ 2/11] Cythonizing mdtraj/geometry/neighborlist.pyx 2021-07-13T23:38:18,335 [ 3/11] Cythonizing mdtraj/geometry/neighbors.pyx 2021-07-13T23:38:18,335 [ 4/11] Cythonizing mdtraj/geometry/src/_geometry.pyx 2021-07-13T23:38:18,336 [ 5/11] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2021-07-13T23:38:18,336 [ 6/11] Cythonizing mdtraj/formats/binpos/binpos.pyx 2021-07-13T23:38:18,336 [ 7/11] Cythonizing mdtraj/formats/dtr/dtr.pyx 2021-07-13T23:38:18,336 [ 8/11] Cythonizing mdtraj/formats/tng/tng.pyx 2021-07-13T23:38:18,336 [ 9/11] Cythonizing mdtraj/formats/xtc/trr.pyx 2021-07-13T23:38:18,336 [10/11] Cythonizing mdtraj/formats/xtc/xtc.pyx 2021-07-13T23:38:18,336 [11/11] Cythonizing mdtraj/rmsd/_rmsd.pyx 2021-07-13T23:38:18,824 running egg_info 2021-07-13T23:38:18,827 creating /tmp/pip-pip-egg-info-o9ohwer3/mdtraj.egg-info 2021-07-13T23:38:18,828 writing /tmp/pip-pip-egg-info-o9ohwer3/mdtraj.egg-info/PKG-INFO 2021-07-13T23:38:18,831 writing dependency_links to /tmp/pip-pip-egg-info-o9ohwer3/mdtraj.egg-info/dependency_links.txt 2021-07-13T23:38:18,833 writing entry points to /tmp/pip-pip-egg-info-o9ohwer3/mdtraj.egg-info/entry_points.txt 2021-07-13T23:38:18,834 writing top-level names to /tmp/pip-pip-egg-info-o9ohwer3/mdtraj.egg-info/top_level.txt 2021-07-13T23:38:18,836 writing manifest file '/tmp/pip-pip-egg-info-o9ohwer3/mdtraj.egg-info/SOURCES.txt' 2021-07-13T23:38:19,027 reading manifest file '/tmp/pip-pip-egg-info-o9ohwer3/mdtraj.egg-info/SOURCES.txt' 2021-07-13T23:38:19,029 reading manifest template 'MANIFEST.in' 2021-07-13T23:38:19,076 writing manifest file '/tmp/pip-pip-egg-info-o9ohwer3/mdtraj.egg-info/SOURCES.txt' 2021-07-13T23:38:19,549 Source in /tmp/pip-wheel-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047 has version 1.9.2, which satisfies requirement mdtraj==1.9.2 from https://files.pythonhosted.org/packages/e0/9e/857f613eae8af3fb8cc73904b3edf622c58de3884c5989e4466973c3c9ee/mdtraj-1.9.2.tar.gz#sha256=cdd926f19c007955f0f768d36d696f3e77b4c8030289a2b40eb97a91cebacd0f 2021-07-13T23:38:19,550 Removed mdtraj==1.9.2 from https://files.pythonhosted.org/packages/e0/9e/857f613eae8af3fb8cc73904b3edf622c58de3884c5989e4466973c3c9ee/mdtraj-1.9.2.tar.gz#sha256=cdd926f19c007955f0f768d36d696f3e77b4c8030289a2b40eb97a91cebacd0f from build tracker '/tmp/pip-req-tracker-fnshusda' 2021-07-13T23:38:19,554 Created temporary directory: /tmp/pip-unpack-5p2n9w7s 2021-07-13T23:38:19,555 Building wheels for collected packages: mdtraj 2021-07-13T23:38:19,559 Created temporary directory: /tmp/pip-wheel-t86aazv6 2021-07-13T23:38:19,560 Building wheel for mdtraj (setup.py): started 2021-07-13T23:38:19,560 Destination directory: /tmp/pip-wheel-t86aazv6 2021-07-13T23:38:19,561 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/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-t86aazv6 2021-07-13T23:38:20,966 C compiler: 2021-07-13T23:38:20,975 Using built-in specs. 2021-07-13T23:38:20,975 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-13T23:38:20,976 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-13T23:38:20,976 Target: arm-linux-gnueabihf 2021-07-13T23:38:20,976 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 2021-07-13T23:38:20,976 Thread model: posix 2021-07-13T23:38:20,976 Supported LTO compression algorithms: zlib zstd 2021-07-13T23:38:20,976 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-13T23:38:21,537 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-13T23:38:21,725 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-13T23:38:21,917 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-13T23:38:22,832 running bdist_wheel 2021-07-13T23:38:22,838 running build 2021-07-13T23:38:22,838 running build_py 2021-07-13T23:38:22,975 creating build 2021-07-13T23:38:22,975 creating build/lib.linux-armv7l-3.9 2021-07-13T23:38:22,976 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-13T23:38:22,977 copying mdtraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-13T23:38:22,978 copying mdtraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-13T23:38:22,981 copying mdtraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-13T23:38:22,983 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:22,984 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:22,987 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:22,989 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:22,991 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:22,993 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:22,995 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:22,997 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:22,999 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:23,001 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-13T23:38:23,004 creating build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-13T23:38:23,005 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-13T23:38:23,008 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-13T23:38:23,012 copying mdtraj/core/element.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-13T23:38:23,015 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-13T23:38:23,020 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-13T23:38:23,023 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-13T23:38:23,025 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-13T23:38:23,026 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-13T23:38:23,028 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-13T23:38:23,031 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-13T23:38:23,033 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-13T23:38:23,035 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-13T23:38:23,038 creating build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,039 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,042 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,045 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,048 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,051 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,053 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,056 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,059 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,061 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,062 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,065 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,068 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,071 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,073 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,076 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,079 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,082 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,083 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,086 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,089 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,092 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,094 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,096 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,099 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,101 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,104 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,106 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,108 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,111 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,113 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,116 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-13T23:38:23,119 creating build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-13T23:38:23,119 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-13T23:38:23,122 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-13T23:38:23,125 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-13T23:38:23,127 creating build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-13T23:38:23,128 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-13T23:38:23,130 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-13T23:38:23,132 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-13T23:38:23,135 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-13T23:38:23,136 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-13T23:38:23,138 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-13T23:38:23,141 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-13T23:38:23,143 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-13T23:38:23,145 creating build/lib.linux-armv7l-3.9/mdtraj/utils/external 2021-07-13T23:38:23,146 copying mdtraj/utils/external/pyparsing.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external 2021-07-13T23:38:23,154 copying mdtraj/utils/external/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external 2021-07-13T23:38:23,156 creating build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,157 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,160 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,162 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,165 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,167 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,169 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,171 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,173 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,176 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,178 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,181 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,182 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,185 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-13T23:38:23,188 creating build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-13T23:38:23,189 copying mdtraj/utils/external/astor/misc.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-13T23:38:23,192 copying mdtraj/utils/external/astor/treewalk.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-13T23:38:23,194 copying mdtraj/utils/external/astor/codegen.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-13T23:38:23,196 copying mdtraj/utils/external/astor/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-13T23:38:23,199 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-13T23:38:23,200 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-13T23:38:23,203 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-13T23:38:23,207 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-13T23:38:23,210 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-13T23:38:23,211 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-13T23:38:23,214 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-13T23:38:23,228 running build_ext 2021-07-13T23:38:23,233 building 'mdtraj.formats.xtc' extension 2021-07-13T23:38:23,234 creating build/temp.linux-armv7l-3.9 2021-07-13T23:38:23,234 creating build/temp.linux-armv7l-3.9/mdtraj 2021-07-13T23:38:23,235 creating build/temp.linux-armv7l-3.9/mdtraj/formats 2021-07-13T23:38:23,235 creating build/temp.linux-armv7l-3.9/mdtraj/formats/xtc 2021-07-13T23:38:23,236 creating build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src 2021-07-13T23:38:23,237 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/xdr_seek.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:38:23,395 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 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:38:23,569 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-13T23:38:23,569 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:23,570 788 | int smallnum, smaller, larger, i, is_smaller, run; 2021-07-13T23:38:23,570 | ^~~~~~ 2021-07-13T23:38:23,570 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:23,570 785 | int smallidx, minidx, maxidx; 2021-07-13T23:38:23,570 | ^~~~~~ 2021-07-13T23:38:23,578 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2021-07-13T23:38:23,579 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:23,579 1016 | int errval=1; 2021-07-13T23:38:23,579 | ^~~~~~ 2021-07-13T23:38:23,584 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2021-07-13T23:38:23,585 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:23,585 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2021-07-13T23:38:23,585 | ^~~~~~ 2021-07-13T23:38:23,586 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:23,586 1302 | int smallidx, minidx, maxidx; 2021-07-13T23:38:23,586 | ^~~~~~ 2021-07-13T23:38:23,595 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2021-07-13T23:38:23,595 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:23,596 1509 | int errval=1; 2021-07-13T23:38:23,596 | ^~~~~~ 2021-07-13T23:38:25,744 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_xtc.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:38:25,842 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2021-07-13T23:38:25,843 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2021-07-13T23:38:25,843 66 | int i,j,result; 2021-07-13T23:38:25,843 | ^ 2021-07-13T23:38:25,843 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2021-07-13T23:38:25,844 66 | int i,j,result; 2021-07-13T23:38:25,844 | ^ 2021-07-13T23:38:25,845 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2021-07-13T23:38:25,845 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2021-07-13T23:38:25,845 119 | if (NULL == xd) 2021-07-13T23:38:25,845 | ^~ 2021-07-13T23:38:25,846 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’ 2021-07-13T23:38:25,846 122 | do { 2021-07-13T23:38:25,846 | ^~ 2021-07-13T23:38:25,997 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 -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/xtc.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:38:26,398 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-13T23:38:26,398 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-13T23:38:26,398 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-13T23:38:26,398 from mdtraj/formats/xtc/xtc.c:637: 2021-07-13T23:38:26,399 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-13T23:38:26,399 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-13T23:38:26,399 | ^~~~~~~ 2021-07-13T23:38:32,549 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2021-07-13T23:38:32,550 mdtraj/formats/xtc/xtc.c:551:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:38:32,550 551 | #define PyInt_FromLong PyLong_FromLong 2021-07-13T23:38:32,550 | ^~~~~~~~~~~~~~~ 2021-07-13T23:38:32,556 mdtraj/formats/xtc/xtc.c:9214:7: note: ‘__pyx_v_status’ was declared here 2021-07-13T23:38:32,556 9214 | int __pyx_v_status; 2021-07-13T23:38:32,556 | ^~~~~~~~~~~~~~ 2021-07-13T23:38:41,728 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2021-07-13T23:38:41,733 mdtraj/formats/xtc/xtc.c:7389:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:38:41,733 7389 | } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_5 = 1; 2021-07-13T23:38:41,733 | ^ 2021-07-13T23:38:41,738 mdtraj/formats/xtc/xtc.c:7385:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:38:41,738 7385 | } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_5 = 0; 2021-07-13T23:38:41,738 | ^ 2021-07-13T23:38:46,188 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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 build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/xtc.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so 2021-07-13T23:38:46,476 building 'mdtraj.formats.trr' extension 2021-07-13T23:38:46,477 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/xdr_seek.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:38:46,611 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 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:38:46,772 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-13T23:38:46,773 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:46,773 788 | int smallnum, smaller, larger, i, is_smaller, run; 2021-07-13T23:38:46,773 | ^~~~~~ 2021-07-13T23:38:46,774 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:46,774 785 | int smallidx, minidx, maxidx; 2021-07-13T23:38:46,774 | ^~~~~~ 2021-07-13T23:38:46,782 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2021-07-13T23:38:46,782 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:46,783 1016 | int errval=1; 2021-07-13T23:38:46,783 | ^~~~~~ 2021-07-13T23:38:46,788 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2021-07-13T23:38:46,789 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:46,789 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2021-07-13T23:38:46,789 | ^~~~~~ 2021-07-13T23:38:46,790 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:46,790 1302 | int smallidx, minidx, maxidx; 2021-07-13T23:38:46,790 | ^~~~~~ 2021-07-13T23:38:46,799 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2021-07-13T23:38:46,800 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2021-07-13T23:38:46,800 1509 | int errval=1; 2021-07-13T23:38:46,800 | ^~~~~~ 2021-07-13T23:38:48,940 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_trr.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:38:49,052 mdtraj/formats/xtc/src/xdrfile_trr.c: In function ‘read_trr_nframes’: 2021-07-13T23:38:49,052 mdtraj/formats/xtc/src/xdrfile_trr.c:504:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2021-07-13T23:38:49,052 504 | if (NULL == xd) 2021-07-13T23:38:49,052 | ^~ 2021-07-13T23:38:49,053 mdtraj/formats/xtc/src/xdrfile_trr.c:507:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2021-07-13T23:38:49,053 507 | do { 2021-07-13T23:38:49,053 | ^~ 2021-07-13T23:38:49,652 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 -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/trr.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:38:50,061 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-13T23:38:50,062 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-13T23:38:50,062 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-13T23:38:50,062 from mdtraj/formats/xtc/trr.c:637: 2021-07-13T23:38:50,062 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-13T23:38:50,062 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-13T23:38:50,062 | ^~~~~~~ 2021-07-13T23:38:57,031 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2021-07-13T23:38:57,031 mdtraj/formats/xtc/trr.c:551:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:38:57,032 551 | #define PyInt_FromLong PyLong_FromLong 2021-07-13T23:38:57,032 | ^~~~~~~~~~~~~~~ 2021-07-13T23:38:57,041 mdtraj/formats/xtc/trr.c:10882:7: note: ‘__pyx_v_status’ was declared here 2021-07-13T23:38:57,041 10882 | int __pyx_v_status; 2021-07-13T23:38:57,041 | ^~~~~~~~~~~~~~ 2021-07-13T23:39:06,492 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2021-07-13T23:39:06,499 mdtraj/formats/xtc/trr.c:8257:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,499 8257 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2021-07-13T23:39:06,499 | ^ 2021-07-13T23:39:06,506 mdtraj/formats/xtc/trr.c:8253:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,506 8253 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2021-07-13T23:39:06,506 | ^ 2021-07-13T23:39:06,508 mdtraj/formats/xtc/trr.c:1782:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,508 1782 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2021-07-13T23:39:06,508 | ^ 2021-07-13T23:39:06,513 mdtraj/formats/xtc/trr.c:6794:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2021-07-13T23:39:06,513 6794 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2021-07-13T23:39:06,513 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:39:06,520 mdtraj/formats/xtc/trr.c:8247:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,520 8247 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2021-07-13T23:39:06,520 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2021-07-13T23:39:06,527 mdtraj/formats/xtc/trr.c:8200:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,527 8200 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2021-07-13T23:39:06,527 | ^ 2021-07-13T23:39:06,534 mdtraj/formats/xtc/trr.c:8196:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,534 8196 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2021-07-13T23:39:06,534 | ^ 2021-07-13T23:39:06,536 mdtraj/formats/xtc/trr.c:1782:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,536 1782 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2021-07-13T23:39:06,536 | ^ 2021-07-13T23:39:06,541 mdtraj/formats/xtc/trr.c:6810:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2021-07-13T23:39:06,541 6810 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2021-07-13T23:39:06,541 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:39:06,548 mdtraj/formats/xtc/trr.c:8190:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,548 8190 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2021-07-13T23:39:06,548 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2021-07-13T23:39:06,554 mdtraj/formats/xtc/trr.c:8590:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,554 8590 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2021-07-13T23:39:06,554 | ^ 2021-07-13T23:39:06,562 mdtraj/formats/xtc/trr.c:8586:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,562 8586 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2021-07-13T23:39:06,562 | ^ 2021-07-13T23:39:06,569 mdtraj/formats/xtc/trr.c:8431:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,569 8431 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2021-07-13T23:39:06,569 | ^ 2021-07-13T23:39:06,576 mdtraj/formats/xtc/trr.c:8427:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,576 8427 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2021-07-13T23:39:06,577 | ^ 2021-07-13T23:39:06,583 mdtraj/formats/xtc/trr.c:8483:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,583 8483 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2021-07-13T23:39:06,583 | ^ 2021-07-13T23:39:06,590 mdtraj/formats/xtc/trr.c:8479:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:06,590 8479 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2021-07-13T23:39:06,590 | ^ 2021-07-13T23:39:13,018 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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 build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/trr.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so 2021-07-13T23:39:13,216 building 'mdtraj.formats.tng' extension 2021-07-13T23:39:13,217 creating build/temp.linux-armv7l-3.9/mdtraj/formats/tng 2021-07-13T23:39:13,218 creating build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src 2021-07-13T23:39:13,218 creating build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression 2021-07-13T23:39:13,220 creating build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/lib 2021-07-13T23:39:13,220 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwlzh.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/bwlzh.o 2021-07-13T23:39:13,992 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/bwt.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/bwt.o 2021-07-13T23:39:14,407 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/coder.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/coder.o 2021-07-13T23:39:15,127 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/dict.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/dict.o 2021-07-13T23:39:15,266 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/fixpoint.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/fixpoint.o 2021-07-13T23:39:15,466 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffman.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/huffman.o 2021-07-13T23:39:16,185 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/huffmem.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/huffmem.o 2021-07-13T23:39:16,646 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/lz77.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/lz77.o 2021-07-13T23:39:16,981 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/merge_sort.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/merge_sort.o 2021-07-13T23:39:17,191 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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/mtf.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/mtf.o 2021-07-13T23:39:17,296 mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: 2021-07-13T23:39:17,296 mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-13T23:39:17,297 196 | while (dict[ptr]!=v) 2021-07-13T23:39:17,297 | ^~ 2021-07-13T23:39:17,603 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/rle.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/rle.o 2021-07-13T23:39:17,658 mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: 2021-07-13T23:39:17,659 mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-13T23:39:17,659 56 | if (v==vals[i]) 2021-07-13T23:39:17,659 | ^~ 2021-07-13T23:39:17,790 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/tng_compress.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/tng_compress.o 2021-07-13T23:39:20,066 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/vals16.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/vals16.o 2021-07-13T23:39:20,210 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/warnmalloc.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o 2021-07-13T23:39:20,384 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/widemuldiv.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o 2021-07-13T23:39:20,648 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc2.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/xtc2.o 2021-07-13T23:39:22,283 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/compression/xtc3.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/xtc3.o 2021-07-13T23:39:24,605 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/md5.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/lib/md5.o 2021-07-13T23:39:25,036 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/src/lib/tng_io.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/lib/tng_io.o 2021-07-13T23:39:25,253 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: 2021-07-13T23:39:25,257 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] 2021-07-13T23:39:25,257 1064 | tng_data->input_endianness_swap_func_32 = 2021-07-13T23:39:25,257 | ^ 2021-07-13T23:39:25,257 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] 2021-07-13T23:39:25,257 1073 | tng_data->input_endianness_swap_func_64 = 2021-07-13T23:39:25,257 | ^ 2021-07-13T23:39:25,258 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] 2021-07-13T23:39:25,258 1089 | tng_data->input_endianness_swap_func_32 = 2021-07-13T23:39:25,258 | ^ 2021-07-13T23:39:25,258 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] 2021-07-13T23:39:25,258 1098 | tng_data->input_endianness_swap_func_64 = 2021-07-13T23:39:25,258 | ^ 2021-07-13T23:39:25,342 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: 2021-07-13T23:39:25,347 mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 2021-07-13T23:39:25,347 9565 | if(tng_data->output_endianness_swap_func_32 == 2021-07-13T23:39:25,347 | ^~ 2021-07-13T23:39:25,351 mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 2021-07-13T23:39:25,351 9570 | else if(tng_data->output_endianness_swap_func_32 == 2021-07-13T23:39:25,351 | ^~ 2021-07-13T23:39:25,355 mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 2021-07-13T23:39:25,355 9588 | if(tng_data->output_endianness_swap_func_64 == 2021-07-13T23:39:25,355 | ^~ 2021-07-13T23:39:25,359 mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 2021-07-13T23:39:25,359 9593 | else if(tng_data->output_endianness_swap_func_64 == 2021-07-13T23:39:25,360 | ^~ 2021-07-13T23:39:25,361 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: 2021-07-13T23:39:25,365 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] 2021-07-13T23:39:25,366 9651 | tng_data->output_endianness_swap_func_32 = 2021-07-13T23:39:25,366 | ^ 2021-07-13T23:39:25,370 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] 2021-07-13T23:39:25,370 9660 | tng_data->output_endianness_swap_func_64 = 2021-07-13T23:39:25,370 | ^ 2021-07-13T23:39:25,374 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] 2021-07-13T23:39:25,374 9673 | tng_data->output_endianness_swap_func_32 = 2021-07-13T23:39:25,374 | ^ 2021-07-13T23:39:25,378 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] 2021-07-13T23:39:25,378 9682 | tng_data->output_endianness_swap_func_64 = 2021-07-13T23:39:25,379 | ^ 2021-07-13T23:39:27,339 In file included from /usr/include/string.h:495, 2021-07-13T23:39:27,339 from mdtraj/formats/tng/include/tng/tng_io.h:302, 2021-07-13T23:39:27,339 from mdtraj/formats/tng/src/lib/tng_io.c:20: 2021-07-13T23:39:27,339 In function ‘strncpy’, 2021-07-13T23:39:27,339 inlined from ‘tng_gen_data_block_add’ at mdtraj/formats/tng/src/lib/tng_io.c:12613:9: 2021-07-13T23:39:27,340 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2021-07-13T23:39:27,340 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-13T23:39:27,340 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:39:27,340 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: 2021-07-13T23:39:27,345 mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 2021-07-13T23:39:27,345 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2021-07-13T23:39:27,346 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T23:39:28,601 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: 2021-07-13T23:39:28,604 mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:28,604 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; 2021-07-13T23:39:28,604 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2021-07-13T23:39:28,605 mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:39:28,605 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, 2021-07-13T23:39:28,606 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:39:28,606 4309 | (int)n_frames, 2021-07-13T23:39:28,606 | ~~~~~~~~~~~~~~ 2021-07-13T23:39:28,606 4310 | f_precision, 2021-07-13T23:39:28,606 | ~~~~~~~~~~~~ 2021-07-13T23:39:28,606 4311 | 0, alt_algo, 2021-07-13T23:39:28,606 | ~~~~~~~~~~~~ 2021-07-13T23:39:28,606 4312 | &compressed_len); 2021-07-13T23:39:28,606 | ~~~~~~~~~~~~~~~~ 2021-07-13T23:39:28,608 mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 2021-07-13T23:39:28,608 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; 2021-07-13T23:39:28,608 | ^~~~~~~~~~~ 2021-07-13T23:39:39,890 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 -DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/tng/tng.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/tng.o 2021-07-13T23:39:40,267 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-13T23:39:40,268 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-13T23:39:40,268 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-13T23:39:40,268 from mdtraj/formats/tng/tng.c:664: 2021-07-13T23:39:40,268 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-13T23:39:40,268 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-13T23:39:40,268 | ^~~~~~~ 2021-07-13T23:39:40,357 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’: 2021-07-13T23:39:40,359 mdtraj/formats/tng/tng.c:3509:104: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,360 3509 | __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); 2021-07-13T23:39:40,360 | ^~ 2021-07-13T23:39:40,362 mdtraj/formats/tng/tng.c:3564:88: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,362 3564 | __pyx_t_1 = ((tng_num_particles_get(__pyx_v_self->_traj, (&__pyx_v_self->n_atoms)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,362 | ^~ 2021-07-13T23:39:40,365 mdtraj/formats/tng/tng.c:3596:90: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,365 3596 | __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); 2021-07-13T23:39:40,365 | ^~ 2021-07-13T23:39:40,367 mdtraj/formats/tng/tng.c:3628:95: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,368 3628 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,368 | ^~ 2021-07-13T23:39:40,370 mdtraj/formats/tng/tng.c:3698:113: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,370 3698 | __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); 2021-07-13T23:39:40,370 | ^~ 2021-07-13T23:39:40,373 mdtraj/formats/tng/tng.c:3742:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,373 3742 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,374 | ^~ 2021-07-13T23:39:40,395 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’: 2021-07-13T23:39:40,397 mdtraj/formats/tng/tng.c:4536:106: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,398 4536 | __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); 2021-07-13T23:39:40,398 | ^~ 2021-07-13T23:39:40,401 mdtraj/formats/tng/tng.c:4581:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,401 4581 | __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); 2021-07-13T23:39:40,401 | ^~ 2021-07-13T23:39:40,405 mdtraj/formats/tng/tng.c:4688:115: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,406 4688 | __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); 2021-07-13T23:39:40,406 | ^~ 2021-07-13T23:39:40,408 mdtraj/formats/tng/tng.c:4718:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,408 4718 | __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); 2021-07-13T23:39:40,408 | ^~ 2021-07-13T23:39:40,414 mdtraj/formats/tng/tng.c:4846:105: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,414 4846 | __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); 2021-07-13T23:39:40,414 | ^~ 2021-07-13T23:39:40,433 mdtraj/formats/tng/tng.c:5447:126: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,433 5447 | __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); 2021-07-13T23:39:40,433 | ^~ 2021-07-13T23:39:40,443 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’: 2021-07-13T23:39:40,446 mdtraj/formats/tng/tng.c:5855:152: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,446 5855 | __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); 2021-07-13T23:39:40,446 | ^~ 2021-07-13T23:39:40,461 mdtraj/formats/tng/tng.c:6123:108: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,461 6123 | __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); 2021-07-13T23:39:40,461 | ^~ 2021-07-13T23:39:40,466 mdtraj/formats/tng/tng.c:6225:304: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,467 6225 | __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); 2021-07-13T23:39:40,467 | ^~ 2021-07-13T23:39:40,537 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’: 2021-07-13T23:39:40,541 mdtraj/formats/tng/tng.c:8714:94: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,541 8714 | __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); 2021-07-13T23:39:40,542 | ^~ 2021-07-13T23:39:40,546 mdtraj/formats/tng/tng.c:8746:75: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,546 8746 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,547 | ^~ 2021-07-13T23:39:40,551 mdtraj/formats/tng/tng.c:8778:81: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,551 8778 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,551 | ^~ 2021-07-13T23:39:40,567 mdtraj/formats/tng/tng.c:9069:77: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,567 9069 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_14) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,567 | ^~ 2021-07-13T23:39:40,588 mdtraj/formats/tng/tng.c:9260:372: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,588 9260 | __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_17, __pyx_pybuffernd_xyz_array.diminfo[0].strides, __pyx_t_18, __pyx_pybuffernd_xyz_array.diminfo[1].strides, __pyx_t_19, __pyx_pybuffernd_xyz_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,588 | ^~ 2021-07-13T23:39:40,605 mdtraj/formats/tng/tng.c:9312:378: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,605 9312 | __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_19, __pyx_pybuffernd_box_array.diminfo[0].strides, __pyx_t_18, __pyx_pybuffernd_box_array.diminfo[1].strides, __pyx_t_17, __pyx_pybuffernd_box_array.diminfo[2].strides)))) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,606 | ^~ 2021-07-13T23:39:40,612 mdtraj/formats/tng/tng.c:9374:89: warning: comparison between ‘tng_function_status’ and ‘enum __pyx_t_6mdtraj_7formats_3tng_tng_function_status’ [-Wenum-compare] 2021-07-13T23:39:40,612 9374 | __pyx_t_1 = ((tng_frame_set_first_frame_time_set(__pyx_v_self->_traj, __pyx_t_14) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-13T23:39:40,612 | ^~ 2021-07-13T23:39:56,333 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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 build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/bwlzh.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/bwt.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/coder.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/dict.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/fixpoint.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/huffman.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/huffmem.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/lz77.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/merge_sort.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/mtf.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/rle.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/tng_compress.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/vals16.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/warnmalloc.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/widemuldiv.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/xtc2.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression/xtc3.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/lib/md5.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/lib/tng_io.o build/temp.linux-armv7l-3.9/mdtraj/formats/tng/tng.o -lz -o build/lib.linux-armv7l-3.9/mdtraj/formats/tng.cpython-39-arm-linux-gnueabihf.so 2021-07-13T23:39:56,628 building 'mdtraj.formats.dcd' extension 2021-07-13T23:39:56,629 creating build/temp.linux-armv7l-3.9/mdtraj/formats/dcd 2021-07-13T23:39:56,630 creating build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/src 2021-07-13T23:39:56,634 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/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:39:57,031 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-13T23:39:57,031 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-13T23:39:57,032 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-13T23:39:57,032 from mdtraj/formats/dcd/dcd.c:635: 2021-07-13T23:39:57,032 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-13T23:39:57,032 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-13T23:39:57,032 | ^~~~~~~ 2021-07-13T23:40:04,307 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2021-07-13T23:40:04,307 mdtraj/formats/dcd/dcd.c:549:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:40:04,307 549 | #define PyInt_FromLong PyLong_FromLong 2021-07-13T23:40:04,308 | ^~~~~~~~~~~~~~~ 2021-07-13T23:40:04,310 mdtraj/formats/dcd/dcd.c:5260:7: note: ‘__pyx_v_i’ was declared here 2021-07-13T23:40:04,310 5260 | int __pyx_v_i; 2021-07-13T23:40:04,310 | ^~~~~~~~~ 2021-07-13T23:40:07,453 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/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:40:08,894 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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 build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/src/dcdplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so 2021-07-13T23:40:09,051 building 'mdtraj.formats.binpos' extension 2021-07-13T23:40:09,052 creating build/temp.linux-armv7l-3.9/mdtraj/formats/binpos 2021-07-13T23:40:09,053 creating build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/src 2021-07-13T23:40:09,055 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/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/binpos.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:40:09,456 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-13T23:40:09,457 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-13T23:40:09,457 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-13T23:40:09,457 from mdtraj/formats/binpos/binpos.c:635: 2021-07-13T23:40:09,457 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-13T23:40:09,457 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-13T23:40:09,457 | ^~~~~~~ 2021-07-13T23:40:17,146 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2021-07-13T23:40:17,149 mdtraj/formats/binpos/binpos.c:5341:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:40:17,149 5341 | if (__pyx_t_2) { 2021-07-13T23:40:17,149 | ^ 2021-07-13T23:40:17,151 mdtraj/formats/binpos/binpos.c:4821:7: note: ‘__pyx_v_status’ was declared here 2021-07-13T23:40:17,152 4821 | int __pyx_v_status; 2021-07-13T23:40:17,152 | ^~~~~~~~~~~~~~ 2021-07-13T23:40:17,152 mdtraj/formats/binpos/binpos.c:549:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-13T23:40:17,152 549 | #define PyInt_FromLong PyLong_FromLong 2021-07-13T23:40:17,152 | ^~~~~~~~~~~~~~~ 2021-07-13T23:40:17,155 mdtraj/formats/binpos/binpos.c:4818:7: note: ‘__pyx_v_i’ was declared here 2021-07-13T23:40:17,155 4818 | int __pyx_v_i; 2021-07-13T23:40:17,155 | ^~~~~~~~~ 2021-07-13T23:40:18,627 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/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/src/binposplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:40:18,995 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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 build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/binpos.o build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/src/binposplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so 2021-07-13T23:40:19,148 building 'mdtraj.formats.dtr' extension 2021-07-13T23:40:19,149 creating build/temp.linux-armv7l-3.9/mdtraj/formats/dtr 2021-07-13T23:40:19,151 creating build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/src 2021-07-13T23:40:19,151 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 -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:40:19,460 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-13T23:40:19,461 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-13T23:40:19,461 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-13T23:40:19,461 from mdtraj/formats/dtr/dtr.cpp:656: 2021-07-13T23:40:19,461 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-13T23:40:19,461 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-13T23:40:19,461 | ^~~~~~~ 2021-07-13T23:40:31,767 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 -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:40:33,598 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2021-07-13T23:40:33,598 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=] 2021-07-13T23:40:33,598 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2021-07-13T23:40:33,599 | ~~^ ~ 2021-07-13T23:40:33,599 | | | 2021-07-13T23:40:33,599 | | size_t {aka unsigned int} 2021-07-13T23:40:33,599 | long int 2021-07-13T23:40:33,599 | %d 2021-07-13T23:40:33,599 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=] 2021-07-13T23:40:33,600 487 | printf("size %d framesize %d\n\n", 2021-07-13T23:40:33,600 | ~^ 2021-07-13T23:40:33,600 | | 2021-07-13T23:40:33,600 | int 2021-07-13T23:40:33,600 | %lld 2021-07-13T23:40:33,600 488 | keys[i].size(), m_framesize); 2021-07-13T23:40:33,600 | ~~~~~~~~~~~~~~ 2021-07-13T23:40:33,600 | | 2021-07-13T23:40:33,600 | uint64_t {aka long long unsigned int} 2021-07-13T23:40:33,601 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=] 2021-07-13T23:40:33,601 487 | printf("size %d framesize %d\n\n", 2021-07-13T23:40:33,601 | ~^ 2021-07-13T23:40:33,601 | | 2021-07-13T23:40:33,601 | int 2021-07-13T23:40:33,601 | %lld 2021-07-13T23:40:33,601 488 | keys[i].size(), m_framesize); 2021-07-13T23:40:33,602 | ~~~~~~~~~~~ 2021-07-13T23:40:33,602 | | 2021-07-13T23:40:33,602 | uint64_t {aka long long unsigned int} 2021-07-13T23:40:33,602 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=] 2021-07-13T23:40:33,602 494 | "non-constant time interval at frame %ld\n", i); 2021-07-13T23:40:33,602 | ~~^ ~ 2021-07-13T23:40:33,602 | | | 2021-07-13T23:40:33,603 | | size_t {aka unsigned int} 2021-07-13T23:40:33,603 | long int 2021-07-13T23:40:33,603 | %d 2021-07-13T23:40:33,603 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=] 2021-07-13T23:40:33,603 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2021-07-13T23:40:33,603 | ~~^ ~ 2021-07-13T23:40:33,603 | | | 2021-07-13T23:40:33,604 | | size_t {aka unsigned int} 2021-07-13T23:40:33,604 | long int 2021-07-13T23:40:33,604 | %d 2021-07-13T23:40:33,729 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2021-07-13T23:40:33,729 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=] 2021-07-13T23:40:33,729 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2021-07-13T23:40:33,729 | ~~^ 2021-07-13T23:40:33,729 | | 2021-07-13T23:40:33,729 | long int 2021-07-13T23:40:33,730 | %lld 2021-07-13T23:40:33,730 1302 | 3*natoms, pos.count); 2021-07-13T23:40:33,730 | ~~~~~~~~~ 2021-07-13T23:40:33,730 | | 2021-07-13T23:40:33,730 | uint64_t {aka long long unsigned int} 2021-07-13T23:40:33,730 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=] 2021-07-13T23:40:33,730 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2021-07-13T23:40:33,731 | ~~^ 2021-07-13T23:40:33,731 | | 2021-07-13T23:40:33,731 | long int 2021-07-13T23:40:33,731 | %lld 2021-07-13T23:40:33,731 1311 | 3*natoms, vel.count); 2021-07-13T23:40:33,731 | ~~~~~~~~~ 2021-07-13T23:40:33,731 | | 2021-07-13T23:40:33,731 | uint64_t {aka long long unsigned int} 2021-07-13T23:40:33,754 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2021-07-13T23:40:33,754 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=] 2021-07-13T23:40:33,755 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2021-07-13T23:40:33,755 | ~~^ 2021-07-13T23:40:33,755 | | 2021-07-13T23:40:33,755 | long int 2021-07-13T23:40:33,755 | %lld 2021-07-13T23:40:33,755 1573 | velblob.count, 3*natoms); 2021-07-13T23:40:33,756 | ~~~~~~~~~~~~~ 2021-07-13T23:40:33,756 | | 2021-07-13T23:40:33,756 | uint64_t {aka long long unsigned int} 2021-07-13T23:40:34,790 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: 2021-07-13T23:40:34,791 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 2021-07-13T23:40:34,791 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2021-07-13T23:40:34,791 | ~~~~~~~~^~~~~ 2021-07-13T23:40:37,037 In file included from /usr/include/c++/10/map:60, 2021-07-13T23:40:37,037 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2021-07-13T23:40:37,038 /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> >]’: 2021-07-13T23:40:37,038 /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 2021-07-13T23:40:37,038 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2021-07-13T23:40:37,038 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:37,919 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: 2021-07-13T23:40:37,920 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=] 2021-07-13T23:40:37,920 706 | sprintf(sub, "%03x/", i); 2021-07-13T23:40:37,920 | ^~~~ 2021-07-13T23:40:37,920 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 2021-07-13T23:40:37,920 706 | sprintf(sub, "%03x/", i); 2021-07-13T23:40:37,920 | ^~~~~~~ 2021-07-13T23:40:37,921 In file included from /usr/include/stdio.h:867, 2021-07-13T23:40:37,921 from mdtraj/formats/dtr/include/molfile_plugin.h:35, 2021-07-13T23:40:37,921 from mdtraj/formats/dtr/include/dtrplugin.hxx:46, 2021-07-13T23:40:37,921 from mdtraj/formats/dtr/src/dtrplugin.cxx:42: 2021-07-13T23:40:37,921 /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 2021-07-13T23:40:37,921 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-13T23:40:37,921 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:37,921 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-13T23:40:37,921 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:37,922 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=] 2021-07-13T23:40:37,922 714 | sprintf(subsub, "%03x", j); 2021-07-13T23:40:37,922 | ^~~~ 2021-07-13T23:40:37,922 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 2021-07-13T23:40:37,922 714 | sprintf(subsub, "%03x", j); 2021-07-13T23:40:37,922 | ^~~~~~ 2021-07-13T23:40:37,922 In file included from /usr/include/stdio.h:867, 2021-07-13T23:40:37,923 from mdtraj/formats/dtr/include/molfile_plugin.h:35, 2021-07-13T23:40:37,923 from mdtraj/formats/dtr/include/dtrplugin.hxx:46, 2021-07-13T23:40:37,923 from mdtraj/formats/dtr/src/dtrplugin.cxx:42: 2021-07-13T23:40:37,923 /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 2021-07-13T23:40:37,923 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-13T23:40:37,923 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:37,923 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-13T23:40:37,924 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:38,329 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: 2021-07-13T23:40:38,329 mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2021-07-13T23:40:38,329 667 | sprintf(answer, "%03x/", d1); 2021-07-13T23:40:38,330 | ^ 2021-07-13T23:40:38,330 In file included from /usr/include/stdio.h:867, 2021-07-13T23:40:38,330 from mdtraj/formats/dtr/include/molfile_plugin.h:35, 2021-07-13T23:40:38,330 from mdtraj/formats/dtr/include/dtrplugin.hxx:46, 2021-07-13T23:40:38,330 from mdtraj/formats/dtr/src/dtrplugin.cxx:42: 2021-07-13T23:40:38,330 /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 2021-07-13T23:40:38,330 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-13T23:40:38,331 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:38,331 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-13T23:40:38,331 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:38,331 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=] 2021-07-13T23:40:38,331 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2021-07-13T23:40:38,331 | ^~~~ 2021-07-13T23:40:38,331 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2021-07-13T23:40:38,331 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2021-07-13T23:40:38,332 | ^~~~~~~~~~~~ 2021-07-13T23:40:38,332 In file included from /usr/include/stdio.h:867, 2021-07-13T23:40:38,332 from mdtraj/formats/dtr/include/molfile_plugin.h:35, 2021-07-13T23:40:38,332 from mdtraj/formats/dtr/include/dtrplugin.hxx:46, 2021-07-13T23:40:38,332 from mdtraj/formats/dtr/src/dtrplugin.cxx:42: 2021-07-13T23:40:38,332 /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 2021-07-13T23:40:38,332 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-13T23:40:38,332 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:38,332 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-13T23:40:38,333 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T23:40:46,188 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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 build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/src/dtrplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so 2021-07-13T23:40:46,589 building 'mdtraj._rmsd' extension 2021-07-13T23:40:46,590 creating build/temp.linux-armv7l-3.9/mdtraj/rmsd 2021-07-13T23:40:46,591 creating build/temp.linux-armv7l-3.9/mdtraj/rmsd/src 2021-07-13T23:40:46,591 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/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.c -o build/temp.linux-armv7l-3.9/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -O3 -funroll-loops -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2021-07-13T23:40:46,609 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’ 2021-07-13T23:40:46,611 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-13T23:40:46,759 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-13T23:40:46,760 ERROR: Failed building wheel for mdtraj 2021-07-13T23:40:46,760 Running setup.py clean for mdtraj 2021-07-13T23:40:46,761 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-6agn7a7f/mdtraj_a62c9ce4c4b041a0bffe0f8cfa48b047/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 2021-07-13T23:40:48,242 C compiler: 2021-07-13T23:40:48,251 Using built-in specs. 2021-07-13T23:40:48,251 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-13T23:40:48,251 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-13T23:40:48,252 Target: arm-linux-gnueabihf 2021-07-13T23:40:48,252 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 2021-07-13T23:40:48,252 Thread model: posix 2021-07-13T23:40:48,252 Supported LTO compression algorithms: zlib zstd 2021-07-13T23:40:48,252 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-13T23:40:48,826 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-13T23:40:49,015 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-13T23:40:49,205 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-13T23:40:50,088 running clean 2021-07-13T23:40:50,091 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-13T23:40:50,120 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-13T23:40:50,170 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-13T23:40:50,170 'build/scripts-3.9' does not exist -- can't clean it 2021-07-13T23:40:50,170 removing 'build' 2021-07-13T23:40:50,303 Failed to build mdtraj 2021-07-13T23:40:50,304 ERROR: Failed to build one or more wheels 2021-07-13T23:40:50,304 Exception information: 2021-07-13T23:40:50,304 Traceback (most recent call last): 2021-07-13T23:40:50,304 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-13T23:40:50,304 status = self.run(options, args) 2021-07-13T23:40:50,304 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-13T23:40:50,304 return func(self, options, args) 2021-07-13T23:40:50,304 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-13T23:40:50,304 raise CommandError( 2021-07-13T23:40:50,304 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-13T23:40:50,308 Removed build tracker: '/tmp/pip-req-tracker-fnshusda'