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https://files.pythonhosted.org/packages/5e/07/f6d8703864e39672cb420701e6a8ef0c2d3000e9b0bcc25777d29d526350/mdtraj-1.5.1-cp34-cp34m-macosx_10_5_x86_64.whl#sha256=9554b9bcb0729d9dbc10b9ccc74506544a2c2e37d4a478f83fd8d1cba081b2d7 (from https://pypi.org/simple/mdtraj/) 2021-07-12T14:28:47,299 Skipping link: none of the wheel's tags (cp35-cp35m-macosx_10_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/2b/6e/a791501a9a60b3cb2063fc3db8d4d9b1a27cfa4432261b98f804f9bf34e1/mdtraj-1.5.1-cp35-cp35m-macosx_10_5_x86_64.whl#sha256=a8e1eafa532abd1165e5e15636faf0c0858ab03239dbf8264ad23ac1bd820f13 (from https://pypi.org/simple/mdtraj/) 2021-07-12T14:28:47,299 Found link https://files.pythonhosted.org/packages/dc/6c/2173608f090cf361b8c858e7db974757a8ec9c639ce69b100e9a4608875e/mdtraj-1.5.1.tar.gz#sha256=15d57e229e5be9ba2b4a78d004bf57ae63ba5e86079b47643654751faf41e014 (from https://pypi.org/simple/mdtraj/), version: 1.5.1 2021-07-12T14:28:47,299 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 2021-07-12T14:28:47,300 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 2021-07-12T14:28:47,303 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 2021-07-12T14:28:47,303 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 2021-07-12T14:28:47,303 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 2021-07-12T14:28:47,304 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 2021-07-12T14:28:47,304 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 2021-07-12T14:28:47,304 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 2021-07-12T14:28:47,304 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 2021-07-12T14:28:47,305 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 2021-07-12T14:28:47,305 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 2021-07-12T14:28:47,305 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 2021-07-12T14:28:47,306 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 2021-07-12T14:28:47,306 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/) 2021-07-12T14:28:47,307 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/) 2021-07-12T14:28:47,307 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/) 2021-07-12T14:28:47,307 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/) 2021-07-12T14:28:47,308 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 2021-07-12T14:28:47,308 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/) 2021-07-12T14:28:47,309 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/) 2021-07-12T14:28:47,309 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/) 2021-07-12T14:28:47,310 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/) 2021-07-12T14:28:47,310 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 2021-07-12T14:28:47,310 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-12T14:28:47,318 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2021-07-12T14:28:47,337 Collecting mdtraj==1.9.1 2021-07-12T14:28:47,339 Created temporary directory: /tmp/pip-unpack-dgqw1620 2021-07-12T14:28:48,275 Downloading mdtraj-1.9.1.tar.gz (2.0 MB) 2021-07-12T14:28:49,625 Added mdtraj==1.9.1 from https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz#sha256=ca1ae07c5f5ce59940a48388ac9b098f8e22743b5f3ed3f46d5e3d1317b06282 to build tracker '/tmp/pip-req-tracker-043nzu9g' 2021-07-12T14:28:49,626 Running setup.py (path:/tmp/pip-wheel-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/setup.py) egg_info for package mdtraj 2021-07-12T14:28:49,627 Created temporary directory: /tmp/pip-pip-egg-info-62iklk07 2021-07-12T14:28:49,627 Running command python setup.py egg_info 2021-07-12T14:28:51,039 Using built-in specs. 2021-07-12T14:28:51,040 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-12T14:28:51,040 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-12T14:28:51,040 Target: arm-linux-gnueabihf 2021-07-12T14:28:51,040 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 2021-07-12T14:28:51,041 Thread model: posix 2021-07-12T14:28:51,041 Supported LTO compression algorithms: zlib zstd 2021-07-12T14:28:51,041 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-12T14:28:52,967 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/formats/dcd/dcd.pyx 2021-07-12T14:28:52,968 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:28:55,308 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/geometry/neighborlist.pyx 2021-07-12T14:28:55,308 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:00,618 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/geometry/neighbors.pyx 2021-07-12T14:29:00,619 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:06,043 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/geometry/src/_geometry.pyx 2021-07-12T14:29:06,043 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:13,781 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/rmsd/_lprmsd.pyx 2021-07-12T14:29:13,782 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:17,091 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/formats/binpos/binpos.pyx 2021-07-12T14:29:17,091 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:19,360 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/formats/dtr/dtr.pyx 2021-07-12T14:29:19,360 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:21,643 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/formats/tng/tng.pyx 2021-07-12T14:29:21,643 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:24,471 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/formats/xtc/trr.pyx 2021-07-12T14:29:24,471 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:27,547 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/formats/xtc/xtc.pyx 2021-07-12T14:29:27,547 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:30,454 /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-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/mdtraj/rmsd/_rmsd.pyx 2021-07-12T14:29:30,454 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T14:29:38,065 C compiler: 2021-07-12T14:29:38,065 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-12T14:29:38,065 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-12T14:29:38,066 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-12T14:29:38,066 Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T14:29:38,066 Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T14:29:38,067 Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T14:29:38,067 Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T14:29:38,067 Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T14:29:38,067 Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T14:29:38,067 Compiling mdtraj/rmsd/_rmsd.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T14:29:38,067 Compiling mdtraj/rmsd/_lprmsd.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-12T14:29:38,068 Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-12T14:29:38,068 Compiling mdtraj/geometry/neighbors.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-12T14:29:38,068 Compiling mdtraj/geometry/neighborlist.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-12T14:29:38,068 [ 1/11] Cythonizing mdtraj/formats/dcd/dcd.pyx 2021-07-12T14:29:38,068 [ 2/11] Cythonizing mdtraj/geometry/neighborlist.pyx 2021-07-12T14:29:38,069 [ 3/11] Cythonizing mdtraj/geometry/neighbors.pyx 2021-07-12T14:29:38,069 [ 4/11] Cythonizing mdtraj/geometry/src/_geometry.pyx 2021-07-12T14:29:38,069 [ 5/11] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2021-07-12T14:29:38,069 [ 6/11] Cythonizing mdtraj/formats/binpos/binpos.pyx 2021-07-12T14:29:38,069 [ 7/11] Cythonizing mdtraj/formats/dtr/dtr.pyx 2021-07-12T14:29:38,069 [ 8/11] Cythonizing mdtraj/formats/tng/tng.pyx 2021-07-12T14:29:38,069 [ 9/11] Cythonizing mdtraj/formats/xtc/trr.pyx 2021-07-12T14:29:38,070 [10/11] Cythonizing mdtraj/formats/xtc/xtc.pyx 2021-07-12T14:29:38,070 [11/11] Cythonizing mdtraj/rmsd/_rmsd.pyx 2021-07-12T14:29:38,593 running egg_info 2021-07-12T14:29:38,596 creating /tmp/pip-pip-egg-info-62iklk07/mdtraj.egg-info 2021-07-12T14:29:38,597 writing /tmp/pip-pip-egg-info-62iklk07/mdtraj.egg-info/PKG-INFO 2021-07-12T14:29:38,600 writing dependency_links to /tmp/pip-pip-egg-info-62iklk07/mdtraj.egg-info/dependency_links.txt 2021-07-12T14:29:38,602 writing entry points to /tmp/pip-pip-egg-info-62iklk07/mdtraj.egg-info/entry_points.txt 2021-07-12T14:29:38,603 writing top-level names to /tmp/pip-pip-egg-info-62iklk07/mdtraj.egg-info/top_level.txt 2021-07-12T14:29:38,605 writing manifest file '/tmp/pip-pip-egg-info-62iklk07/mdtraj.egg-info/SOURCES.txt' 2021-07-12T14:29:38,798 reading manifest file '/tmp/pip-pip-egg-info-62iklk07/mdtraj.egg-info/SOURCES.txt' 2021-07-12T14:29:38,800 reading manifest template 'MANIFEST.in' 2021-07-12T14:29:38,849 writing manifest file '/tmp/pip-pip-egg-info-62iklk07/mdtraj.egg-info/SOURCES.txt' 2021-07-12T14:29:39,339 Source in /tmp/pip-wheel-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d has version 1.9.1, which satisfies requirement mdtraj==1.9.1 from https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz#sha256=ca1ae07c5f5ce59940a48388ac9b098f8e22743b5f3ed3f46d5e3d1317b06282 2021-07-12T14:29:39,340 Removed mdtraj==1.9.1 from https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz#sha256=ca1ae07c5f5ce59940a48388ac9b098f8e22743b5f3ed3f46d5e3d1317b06282 from build tracker '/tmp/pip-req-tracker-043nzu9g' 2021-07-12T14:29:39,344 Created temporary directory: /tmp/pip-unpack-p_h17b48 2021-07-12T14:29:39,345 Building wheels for collected packages: mdtraj 2021-07-12T14:29:39,349 Created temporary directory: /tmp/pip-wheel-fbxzni2w 2021-07-12T14:29:39,350 Building wheel for mdtraj (setup.py): started 2021-07-12T14:29:39,350 Destination directory: /tmp/pip-wheel-fbxzni2w 2021-07-12T14:29:39,350 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/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-fbxzni2w 2021-07-12T14:29:40,748 C compiler: 2021-07-12T14:29:40,758 Using built-in specs. 2021-07-12T14:29:40,758 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-12T14:29:40,759 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-12T14:29:40,759 Target: arm-linux-gnueabihf 2021-07-12T14:29:40,759 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 2021-07-12T14:29:40,759 Thread model: posix 2021-07-12T14:29:40,760 Supported LTO compression algorithms: zlib zstd 2021-07-12T14:29:40,760 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-12T14:29:41,345 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-12T14:29:41,535 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-12T14:29:41,722 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-12T14:29:42,604 running bdist_wheel 2021-07-12T14:29:42,611 running build 2021-07-12T14:29:42,611 running build_py 2021-07-12T14:29:42,747 creating build 2021-07-12T14:29:42,747 creating build/lib.linux-armv7l-3.9 2021-07-12T14:29:42,748 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-12T14:29:42,749 copying mdtraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-12T14:29:42,751 copying mdtraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-12T14:29:42,754 copying mdtraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-12T14:29:42,756 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,757 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,759 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,762 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,764 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,766 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,768 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,770 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,773 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,775 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,778 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,780 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,782 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,785 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,787 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-12T14:29:42,791 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-12T14:29:42,791 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-12T14:29:42,793 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-12T14:29:42,796 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-12T14:29:42,798 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-12T14:29:42,800 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-12T14:29:42,803 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-12T14:29:42,804 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-12T14:29:42,806 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-12T14:29:42,809 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-12T14:29:42,811 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-12T14:29:42,814 creating build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-12T14:29:42,815 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-12T14:29:42,817 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-12T14:29:42,820 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-12T14:29:42,823 creating build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-12T14:29:42,824 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-12T14:29:42,826 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-12T14:29:42,828 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-12T14:29:42,832 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-12T14:29:42,835 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-12T14:29:42,839 copying mdtraj/core/element.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-12T14:29:42,843 creating build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,844 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,846 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,848 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,851 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,854 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,857 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,860 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,862 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,865 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,868 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,871 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,874 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,877 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,880 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,883 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,885 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:42,889 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,890 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,893 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,895 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,898 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,900 copying mdtraj/utils/six.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,903 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,906 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,908 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-12T14:29:42,911 creating build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-12T14:29:42,912 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-12T14:29:42,914 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-12T14:29:42,917 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-12T14:29:42,920 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-12T14:29:42,921 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-12T14:29:42,923 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-12T14:29:42,927 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-12T14:29:42,931 creating build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,932 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,935 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,937 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,940 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,942 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,945 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,947 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,950 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,953 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,955 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,958 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,960 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,963 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-12T14:29:42,966 creating build/lib.linux-armv7l-3.9/mdtraj/utils/external 2021-07-12T14:29:42,967 copying mdtraj/utils/external/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external 2021-07-12T14:29:42,969 copying mdtraj/utils/external/pyparsing.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external 2021-07-12T14:29:42,977 creating build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-12T14:29:42,978 copying mdtraj/utils/external/astor/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-12T14:29:42,980 copying mdtraj/utils/external/astor/treewalk.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-12T14:29:42,982 copying mdtraj/utils/external/astor/misc.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-12T14:29:42,985 copying mdtraj/utils/external/astor/codegen.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor 2021-07-12T14:29:42,990 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-12T14:29:42,991 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-12T14:29:42,994 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-12T14:29:43,010 running build_ext 2021-07-12T14:29:43,015 building 'mdtraj.formats.xtc' extension 2021-07-12T14:29:43,016 creating build/temp.linux-armv7l-3.9 2021-07-12T14:29:43,017 creating build/temp.linux-armv7l-3.9/mdtraj 2021-07-12T14:29:43,018 creating build/temp.linux-armv7l-3.9/mdtraj/formats 2021-07-12T14:29:43,018 creating build/temp.linux-armv7l-3.9/mdtraj/formats/xtc 2021-07-12T14:29:43,019 creating build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src 2021-07-12T14:29:43,020 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 2021-07-12T14:29:43,164 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 2021-07-12T14:29:43,336 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-12T14:29:43,336 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:29:43,337 788 | int smallnum, smaller, larger, i, is_smaller, run; 2021-07-12T14:29:43,337 | ^~~~~~ 2021-07-12T14:29:43,337 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:29:43,337 785 | int smallidx, minidx, maxidx; 2021-07-12T14:29:43,337 | ^~~~~~ 2021-07-12T14:29:43,344 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2021-07-12T14:29:43,345 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:29:43,345 1016 | int errval=1; 2021-07-12T14:29:43,345 | ^~~~~~ 2021-07-12T14:29:43,349 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2021-07-12T14:29:43,350 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:29:43,350 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2021-07-12T14:29:43,350 | ^~~~~~ 2021-07-12T14:29:43,350 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:29:43,351 1302 | int smallidx, minidx, maxidx; 2021-07-12T14:29:43,351 | ^~~~~~ 2021-07-12T14:29:43,359 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2021-07-12T14:29:43,360 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:29:43,360 1509 | int errval=1; 2021-07-12T14:29:43,360 | ^~~~~~ 2021-07-12T14:29:45,528 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 2021-07-12T14:29:45,625 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2021-07-12T14:29:45,626 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2021-07-12T14:29:45,626 66 | int i,j,result; 2021-07-12T14:29:45,626 | ^ 2021-07-12T14:29:45,626 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2021-07-12T14:29:45,626 66 | int i,j,result; 2021-07-12T14:29:45,626 | ^ 2021-07-12T14:29:45,627 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2021-07-12T14:29:45,627 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2021-07-12T14:29:45,628 119 | if (NULL == xd) 2021-07-12T14:29:45,628 | ^~ 2021-07-12T14:29:45,628 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’ 2021-07-12T14:29:45,628 122 | do { 2021-07-12T14:29:45,628 | ^~ 2021-07-12T14:29:45,771 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 2021-07-12T14:29:46,174 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-12T14:29:46,174 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-12T14:29:46,174 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-12T14:29:46,174 from mdtraj/formats/xtc/xtc.c:637: 2021-07-12T14:29:46,175 /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] 2021-07-12T14:29:46,175 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-12T14:29:46,175 | ^~~~~~~ 2021-07-12T14:29:52,166 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2021-07-12T14:29:52,167 mdtraj/formats/xtc/xtc.c:551:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:29:52,167 551 | #define PyInt_FromLong PyLong_FromLong 2021-07-12T14:29:52,167 | ^~~~~~~~~~~~~~~ 2021-07-12T14:29:52,171 mdtraj/formats/xtc/xtc.c:8584:7: note: ‘__pyx_v_status’ was declared here 2021-07-12T14:29:52,172 8584 | int __pyx_v_status; 2021-07-12T14:29:52,172 | ^~~~~~~~~~~~~~ 2021-07-12T14:30:04,672 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 2021-07-12T14:30:04,865 building 'mdtraj.formats.trr' extension 2021-07-12T14:30:04,865 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 2021-07-12T14:30:05,002 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 2021-07-12T14:30:05,161 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-12T14:30:05,162 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:30:05,162 788 | int smallnum, smaller, larger, i, is_smaller, run; 2021-07-12T14:30:05,162 | ^~~~~~ 2021-07-12T14:30:05,162 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:30:05,162 785 | int smallidx, minidx, maxidx; 2021-07-12T14:30:05,162 | ^~~~~~ 2021-07-12T14:30:05,169 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2021-07-12T14:30:05,170 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:30:05,170 1016 | int errval=1; 2021-07-12T14:30:05,170 | ^~~~~~ 2021-07-12T14:30:05,174 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2021-07-12T14:30:05,175 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:30:05,175 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2021-07-12T14:30:05,175 | ^~~~~~ 2021-07-12T14:30:05,175 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:30:05,175 1302 | int smallidx, minidx, maxidx; 2021-07-12T14:30:05,175 | ^~~~~~ 2021-07-12T14:30:05,184 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2021-07-12T14:30:05,184 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2021-07-12T14:30:05,185 1509 | int errval=1; 2021-07-12T14:30:05,185 | ^~~~~~ 2021-07-12T14:30:07,332 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 2021-07-12T14:30:07,446 mdtraj/formats/xtc/src/xdrfile_trr.c: In function ‘read_trr_nframes’: 2021-07-12T14:30:07,446 mdtraj/formats/xtc/src/xdrfile_trr.c:504:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2021-07-12T14:30:07,446 504 | if (NULL == xd) 2021-07-12T14:30:07,447 | ^~ 2021-07-12T14:30:07,447 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’ 2021-07-12T14:30:07,447 507 | do { 2021-07-12T14:30:07,448 | ^~ 2021-07-12T14:30:08,015 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 2021-07-12T14:30:08,392 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-12T14:30:08,392 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-12T14:30:08,392 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-12T14:30:08,392 from mdtraj/formats/xtc/trr.c:637: 2021-07-12T14:30:08,392 /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] 2021-07-12T14:30:08,392 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-12T14:30:08,393 | ^~~~~~~ 2021-07-12T14:30:14,927 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2021-07-12T14:30:14,927 mdtraj/formats/xtc/trr.c:551:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:14,928 551 | #define PyInt_FromLong PyLong_FromLong 2021-07-12T14:30:14,928 | ^~~~~~~~~~~~~~~ 2021-07-12T14:30:14,934 mdtraj/formats/xtc/trr.c:10352:7: note: ‘__pyx_v_status’ was declared here 2021-07-12T14:30:14,935 10352 | int __pyx_v_status; 2021-07-12T14:30:14,935 | ^~~~~~~~~~~~~~ 2021-07-12T14:30:24,454 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2021-07-12T14:30:24,460 mdtraj/formats/xtc/trr.c:8063:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,460 8063 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_4 = 2; 2021-07-12T14:30:24,460 | ^ 2021-07-12T14:30:24,465 mdtraj/formats/xtc/trr.c:8059:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,466 8059 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_4 = 1; 2021-07-12T14:30:24,466 | ^ 2021-07-12T14:30:24,467 mdtraj/formats/xtc/trr.c:1782:90: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,467 1782 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2021-07-12T14:30:24,467 | ^ 2021-07-12T14:30:24,471 mdtraj/formats/xtc/trr.c:6884:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2021-07-12T14:30:24,471 6884 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2021-07-12T14:30:24,471 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:30:24,476 mdtraj/formats/xtc/trr.c:8055:19: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,476 8055 | } else if (unlikely(__pyx_t_25 >= __pyx_pybuffernd_forces.diminfo[0].shape)) __pyx_t_4 = 0; 2021-07-12T14:30:24,476 | ^ 2021-07-12T14:30:24,481 mdtraj/formats/xtc/trr.c:8006:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,482 8006 | } else if (unlikely(__pyx_t_25 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_4 = 2; 2021-07-12T14:30:24,482 | ^ 2021-07-12T14:30:24,487 mdtraj/formats/xtc/trr.c:8002:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,487 8002 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_4 = 1; 2021-07-12T14:30:24,487 | ^ 2021-07-12T14:30:24,488 mdtraj/formats/xtc/trr.c:1782:90: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,488 1782 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2021-07-12T14:30:24,488 | ^ 2021-07-12T14:30:24,493 mdtraj/formats/xtc/trr.c:6894:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2021-07-12T14:30:24,493 6894 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2021-07-12T14:30:24,493 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:30:24,497 mdtraj/formats/xtc/trr.c:7998:19: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,498 7998 | } else if (unlikely(__pyx_t_23 >= __pyx_pybuffernd_vel.diminfo[0].shape)) __pyx_t_4 = 0; 2021-07-12T14:30:24,498 | ^ 2021-07-12T14:30:24,502 mdtraj/formats/xtc/trr.c:8396:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,503 8396 | } else if (unlikely(__pyx_t_24 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2021-07-12T14:30:24,503 | ^ 2021-07-12T14:30:24,508 mdtraj/formats/xtc/trr.c:8392:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,508 8392 | } else if (unlikely(__pyx_t_25 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2021-07-12T14:30:24,508 | ^ 2021-07-12T14:30:24,514 mdtraj/formats/xtc/trr.c:8237:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,514 8237 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2021-07-12T14:30:24,514 | ^ 2021-07-12T14:30:24,519 mdtraj/formats/xtc/trr.c:8233:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,519 8233 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2021-07-12T14:30:24,520 | ^ 2021-07-12T14:30:24,524 mdtraj/formats/xtc/trr.c:8289:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,524 8289 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_4 = 1; 2021-07-12T14:30:24,524 | ^ 2021-07-12T14:30:24,530 mdtraj/formats/xtc/trr.c:8285:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:24,530 8285 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_4 = 0; 2021-07-12T14:30:24,530 | ^ 2021-07-12T14:30:29,366 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 2021-07-12T14:30:29,565 building 'mdtraj.formats.tng' extension 2021-07-12T14:30:29,566 creating build/temp.linux-armv7l-3.9/mdtraj/formats/tng 2021-07-12T14:30:29,566 creating build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src 2021-07-12T14:30:29,567 creating build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/compression 2021-07-12T14:30:29,569 creating build/temp.linux-armv7l-3.9/mdtraj/formats/tng/src/lib 2021-07-12T14:30:29,570 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 2021-07-12T14:30:30,350 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 2021-07-12T14:30:30,771 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 2021-07-12T14:30:31,495 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 2021-07-12T14:30:31,637 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 2021-07-12T14:30:31,842 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 2021-07-12T14:30:32,555 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 2021-07-12T14:30:33,020 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 2021-07-12T14:30:33,360 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 2021-07-12T14:30:33,569 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 2021-07-12T14:30:33,674 mdtraj/formats/tng/src/compression/mtf.c: In function ‘Ptngc_comp_conv_to_mtf’: 2021-07-12T14:30:33,675 mdtraj/formats/tng/src/compression/mtf.c:196:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-12T14:30:33,675 196 | while (dict[ptr]!=v) 2021-07-12T14:30:33,675 | ^~ 2021-07-12T14:30:33,984 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 2021-07-12T14:30:34,044 mdtraj/formats/tng/src/compression/rle.c: In function ‘Ptngc_comp_conv_to_rle’: 2021-07-12T14:30:34,044 mdtraj/formats/tng/src/compression/rle.c:56:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-12T14:30:34,044 56 | if (v==vals[i]) 2021-07-12T14:30:34,045 | ^~ 2021-07-12T14:30:34,179 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 2021-07-12T14:30:36,458 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 2021-07-12T14:30:36,600 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 2021-07-12T14:30:36,770 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 2021-07-12T14:30:37,039 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 2021-07-12T14:30:38,710 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 2021-07-12T14:30:41,038 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 2021-07-12T14:30:41,474 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 2021-07-12T14:30:41,677 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’: 2021-07-12T14:30:41,681 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] 2021-07-12T14:30:41,681 1064 | tng_data->input_endianness_swap_func_32 = 2021-07-12T14:30:41,681 | ^ 2021-07-12T14:30:41,681 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] 2021-07-12T14:30:41,682 1073 | tng_data->input_endianness_swap_func_64 = 2021-07-12T14:30:41,682 | ^ 2021-07-12T14:30:41,682 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] 2021-07-12T14:30:41,682 1089 | tng_data->input_endianness_swap_func_32 = 2021-07-12T14:30:41,682 | ^ 2021-07-12T14:30:41,682 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] 2021-07-12T14:30:41,682 1098 | tng_data->input_endianness_swap_func_64 = 2021-07-12T14:30:41,683 | ^ 2021-07-12T14:30:41,768 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’: 2021-07-12T14:30:41,774 mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast 2021-07-12T14:30:41,774 9565 | if(tng_data->output_endianness_swap_func_32 == 2021-07-12T14:30:41,774 | ^~ 2021-07-12T14:30:41,780 mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast 2021-07-12T14:30:41,780 9570 | else if(tng_data->output_endianness_swap_func_32 == 2021-07-12T14:30:41,780 | ^~ 2021-07-12T14:30:41,785 mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast 2021-07-12T14:30:41,785 9588 | if(tng_data->output_endianness_swap_func_64 == 2021-07-12T14:30:41,785 | ^~ 2021-07-12T14:30:41,791 mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast 2021-07-12T14:30:41,791 9593 | else if(tng_data->output_endianness_swap_func_64 == 2021-07-12T14:30:41,791 | ^~ 2021-07-12T14:30:41,793 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’: 2021-07-12T14:30:41,799 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] 2021-07-12T14:30:41,799 9651 | tng_data->output_endianness_swap_func_32 = 2021-07-12T14:30:41,799 | ^ 2021-07-12T14:30:41,805 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] 2021-07-12T14:30:41,805 9660 | tng_data->output_endianness_swap_func_64 = 2021-07-12T14:30:41,805 | ^ 2021-07-12T14:30:41,810 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] 2021-07-12T14:30:41,810 9673 | tng_data->output_endianness_swap_func_32 = 2021-07-12T14:30:41,811 | ^ 2021-07-12T14:30:41,816 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] 2021-07-12T14:30:41,816 9682 | tng_data->output_endianness_swap_func_64 = 2021-07-12T14:30:41,816 | ^ 2021-07-12T14:30:43,796 In file included from /usr/include/string.h:495, 2021-07-12T14:30:43,796 from mdtraj/formats/tng/include/tng/tng_io.h:302, 2021-07-12T14:30:43,796 from mdtraj/formats/tng/src/lib/tng_io.c:20: 2021-07-12T14:30:43,796 In function ‘strncpy’, 2021-07-12T14:30:43,796 inlined from ‘tng_gen_data_block_add’ at mdtraj/formats/tng/src/lib/tng_io.c:12613:9: 2021-07-12T14:30:43,796 /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=] 2021-07-12T14:30:43,796 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-12T14:30:43,797 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:30:43,797 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_gen_data_block_add’: 2021-07-12T14:30:43,804 mdtraj/formats/tng/src/lib/tng_io.c:12613:47: note: length computed here 2021-07-12T14:30:43,804 12613 | strncpy(data->block_name, block_name, strlen(block_name) + 1); 2021-07-12T14:30:43,805 | ^~~~~~~~~~~~~~~~~~ 2021-07-12T14:30:45,061 mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_data_block_write.isra’: 2021-07-12T14:30:45,065 mdtraj/formats/tng/src/lib/tng_io.c:5986:72: warning: ‘num_first_particle’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:45,065 5986 | for(j = num_first_particle; j < num_first_particle + n_particles; 2021-07-12T14:30:45,065 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2021-07-12T14:30:45,067 mdtraj/formats/tng/src/lib/tng_io.c:4308:24: warning: ‘n_particles’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:30:45,067 4308 | dest = tng_compress_pos_float((float *)*data, (int)n_particles, 2021-07-12T14:30:45,067 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:30:45,068 4309 | (int)n_frames, 2021-07-12T14:30:45,068 | ~~~~~~~~~~~~~~ 2021-07-12T14:30:45,068 4310 | f_precision, 2021-07-12T14:30:45,068 | ~~~~~~~~~~~~ 2021-07-12T14:30:45,068 4311 | 0, alt_algo, 2021-07-12T14:30:45,068 | ~~~~~~~~~~~~ 2021-07-12T14:30:45,068 4312 | &compressed_len); 2021-07-12T14:30:45,068 | ~~~~~~~~~~~~~~~~ 2021-07-12T14:30:45,070 mdtraj/formats/tng/src/lib/tng_io.c:5684:13: note: ‘n_particles’ was declared here 2021-07-12T14:30:45,071 5684 | int64_t n_particles, num_first_particle, n_frames, stride_length; 2021-07-12T14:30:45,071 | ^~~~~~~~~~~ 2021-07-12T14:30:56,359 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 2021-07-12T14:30:56,743 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-12T14:30:56,744 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-12T14:30:56,744 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-12T14:30:56,744 from mdtraj/formats/tng/tng.c:664: 2021-07-12T14:30:56,744 /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] 2021-07-12T14:30:56,744 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-12T14:30:56,744 | ^~~~~~~ 2021-07-12T14:30:56,833 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile___cinit__’: 2021-07-12T14:30:56,834 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] 2021-07-12T14:30:56,835 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); 2021-07-12T14:30:56,835 | ^~ 2021-07-12T14:30:56,837 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] 2021-07-12T14:30:56,837 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); 2021-07-12T14:30:56,837 | ^~ 2021-07-12T14:30:56,839 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] 2021-07-12T14:30:56,839 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); 2021-07-12T14:30:56,839 | ^~ 2021-07-12T14:30:56,841 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] 2021-07-12T14:30:56,841 3628 | __pyx_t_1 = ((tng_distance_unit_exponential_get(__pyx_v_self->_traj, (&__pyx_v_exponent)) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-12T14:30:56,841 | ^~ 2021-07-12T14:30:56,843 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] 2021-07-12T14:30:56,844 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); 2021-07-12T14:30:56,844 | ^~ 2021-07-12T14:30:56,847 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] 2021-07-12T14:30:56,847 3742 | __pyx_t_1 = ((tng_last_program_name_set(__pyx_v_self->_traj, __pyx_t_8) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-12T14:30:56,847 | ^~ 2021-07-12T14:30:56,864 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_8_read_topology’: 2021-07-12T14:30:56,866 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] 2021-07-12T14:30:56,866 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); 2021-07-12T14:30:56,866 | ^~ 2021-07-12T14:30:56,868 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] 2021-07-12T14:30:56,869 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); 2021-07-12T14:30:56,869 | ^~ 2021-07-12T14:30:56,873 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] 2021-07-12T14:30:56,874 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); 2021-07-12T14:30:56,874 | ^~ 2021-07-12T14:30:56,876 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] 2021-07-12T14:30:56,876 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); 2021-07-12T14:30:56,876 | ^~ 2021-07-12T14:30:56,882 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] 2021-07-12T14:30:56,882 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); 2021-07-12T14:30:56,882 | ^~ 2021-07-12T14:30:56,901 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] 2021-07-12T14:30:56,901 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); 2021-07-12T14:30:56,901 | ^~ 2021-07-12T14:30:56,911 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_10_read_frame’: 2021-07-12T14:30:56,914 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] 2021-07-12T14:30:56,914 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); 2021-07-12T14:30:56,914 | ^~ 2021-07-12T14:30:56,929 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] 2021-07-12T14:30:56,929 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); 2021-07-12T14:30:56,929 | ^~ 2021-07-12T14:30:56,934 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] 2021-07-12T14:30:56,935 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); 2021-07-12T14:30:56,935 | ^~ 2021-07-12T14:30:57,005 mdtraj/formats/tng/tng.c: In function ‘__pyx_pf_6mdtraj_7formats_3tng_17TNGTrajectoryFile_16write’: 2021-07-12T14:30:57,010 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] 2021-07-12T14:30:57,010 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); 2021-07-12T14:30:57,010 | ^~ 2021-07-12T14:30:57,014 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] 2021-07-12T14:30:57,015 8746 | __pyx_t_1 = ((tng_util_pos_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-12T14:30:57,015 | ^~ 2021-07-12T14:30:57,019 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] 2021-07-12T14:30:57,020 8778 | __pyx_t_1 = ((tng_util_box_shape_write_interval_set(__pyx_v_self->_traj, 1) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-12T14:30:57,020 | ^~ 2021-07-12T14:30:57,035 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] 2021-07-12T14:30:57,036 9069 | __pyx_t_9 = ((tng_time_per_frame_set(__pyx_v_self->_traj, __pyx_t_14) != __pyx_e_6mdtraj_7formats_3tng_TNG_SUCCESS) != 0); 2021-07-12T14:30:57,036 | ^~ 2021-07-12T14:30:57,056 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] 2021-07-12T14:30:57,057 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); 2021-07-12T14:30:57,057 | ^~ 2021-07-12T14:30:57,074 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] 2021-07-12T14:30:57,074 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); 2021-07-12T14:30:57,074 | ^~ 2021-07-12T14:30:57,080 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] 2021-07-12T14:30:57,081 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); 2021-07-12T14:30:57,081 | ^~ 2021-07-12T14:31:12,933 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 2021-07-12T14:31:13,230 building 'mdtraj.formats.dcd' extension 2021-07-12T14:31:13,231 creating build/temp.linux-armv7l-3.9/mdtraj/formats/dcd 2021-07-12T14:31:13,232 creating build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/src 2021-07-12T14:31:13,232 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 2021-07-12T14:31:13,862 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-12T14:31:13,862 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-12T14:31:13,862 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-12T14:31:13,862 from mdtraj/formats/dcd/dcd.c:635: 2021-07-12T14:31:13,862 /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] 2021-07-12T14:31:13,863 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-12T14:31:13,863 | ^~~~~~~ 2021-07-12T14:31:21,164 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2021-07-12T14:31:21,164 mdtraj/formats/dcd/dcd.c:549:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:31:21,165 549 | #define PyInt_FromLong PyLong_FromLong 2021-07-12T14:31:21,165 | ^~~~~~~~~~~~~~~ 2021-07-12T14:31:21,167 mdtraj/formats/dcd/dcd.c:5262:7: note: ‘__pyx_v_i’ was declared here 2021-07-12T14:31:21,167 5262 | int __pyx_v_i; 2021-07-12T14:31:21,168 | ^~~~~~~~~ 2021-07-12T14:31:24,237 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/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 2021-07-12T14:31:25,674 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 2021-07-12T14:31:25,835 building 'mdtraj.formats.binpos' extension 2021-07-12T14:31:25,836 creating build/temp.linux-armv7l-3.9/mdtraj/formats/binpos 2021-07-12T14:31:25,836 creating build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/src 2021-07-12T14:31:25,837 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 2021-07-12T14:31:26,237 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-12T14:31:26,237 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-12T14:31:26,238 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-12T14:31:26,238 from mdtraj/formats/binpos/binpos.c:635: 2021-07-12T14:31:26,238 /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] 2021-07-12T14:31:26,238 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-12T14:31:26,238 | ^~~~~~~ 2021-07-12T14:31:34,014 mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’: 2021-07-12T14:31:34,018 mdtraj/formats/binpos/binpos.c:5341:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:31:34,018 5341 | if (__pyx_t_2) { 2021-07-12T14:31:34,018 | ^ 2021-07-12T14:31:34,021 mdtraj/formats/binpos/binpos.c:4821:7: note: ‘__pyx_v_status’ was declared here 2021-07-12T14:31:34,022 4821 | int __pyx_v_status; 2021-07-12T14:31:34,022 | ^~~~~~~~~~~~~~ 2021-07-12T14:31:34,022 mdtraj/formats/binpos/binpos.c:549:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-12T14:31:34,022 549 | #define PyInt_FromLong PyLong_FromLong 2021-07-12T14:31:34,022 | ^~~~~~~~~~~~~~~ 2021-07-12T14:31:34,025 mdtraj/formats/binpos/binpos.c:4818:7: note: ‘__pyx_v_i’ was declared here 2021-07-12T14:31:34,026 4818 | int __pyx_v_i; 2021-07-12T14:31:34,026 | ^~~~~~~~~ 2021-07-12T14:31:35,511 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 2021-07-12T14:31:35,862 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 2021-07-12T14:31:36,008 building 'mdtraj.formats.dtr' extension 2021-07-12T14:31:36,009 creating build/temp.linux-armv7l-3.9/mdtraj/formats/dtr 2021-07-12T14:31:36,010 creating build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/src 2021-07-12T14:31:36,011 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 2021-07-12T14:31:36,337 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-12T14:31:36,337 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-12T14:31:36,338 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-12T14:31:36,338 from mdtraj/formats/dtr/dtr.cpp:656: 2021-07-12T14:31:36,338 /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] 2021-07-12T14:31:36,338 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-12T14:31:36,338 | ^~~~~~~ 2021-07-12T14:31:48,663 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 2021-07-12T14:31:50,526 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2021-07-12T14:31:50,526 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=] 2021-07-12T14:31:50,526 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2021-07-12T14:31:50,527 | ~~^ ~ 2021-07-12T14:31:50,527 | | | 2021-07-12T14:31:50,527 | | size_t {aka unsigned int} 2021-07-12T14:31:50,527 | long int 2021-07-12T14:31:50,527 | %d 2021-07-12T14:31:50,527 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=] 2021-07-12T14:31:50,528 487 | printf("size %d framesize %d\n\n", 2021-07-12T14:31:50,528 | ~^ 2021-07-12T14:31:50,528 | | 2021-07-12T14:31:50,528 | int 2021-07-12T14:31:50,528 | %lld 2021-07-12T14:31:50,528 488 | keys[i].size(), m_framesize); 2021-07-12T14:31:50,528 | ~~~~~~~~~~~~~~ 2021-07-12T14:31:50,529 | | 2021-07-12T14:31:50,529 | uint64_t {aka long long unsigned int} 2021-07-12T14:31:50,529 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=] 2021-07-12T14:31:50,529 487 | printf("size %d framesize %d\n\n", 2021-07-12T14:31:50,529 | ~^ 2021-07-12T14:31:50,529 | | 2021-07-12T14:31:50,530 | int 2021-07-12T14:31:50,530 | %lld 2021-07-12T14:31:50,530 488 | keys[i].size(), m_framesize); 2021-07-12T14:31:50,530 | ~~~~~~~~~~~ 2021-07-12T14:31:50,530 | | 2021-07-12T14:31:50,530 | uint64_t {aka long long unsigned int} 2021-07-12T14:31:50,530 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=] 2021-07-12T14:31:50,530 494 | "non-constant time interval at frame %ld\n", i); 2021-07-12T14:31:50,531 | ~~^ ~ 2021-07-12T14:31:50,531 | | | 2021-07-12T14:31:50,531 | | size_t {aka unsigned int} 2021-07-12T14:31:50,531 | long int 2021-07-12T14:31:50,531 | %d 2021-07-12T14:31:50,531 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=] 2021-07-12T14:31:50,531 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2021-07-12T14:31:50,532 | ~~^ ~ 2021-07-12T14:31:50,532 | | | 2021-07-12T14:31:50,532 | | size_t {aka unsigned int} 2021-07-12T14:31:50,532 | long int 2021-07-12T14:31:50,532 | %d 2021-07-12T14:31:50,657 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2021-07-12T14:31:50,658 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=] 2021-07-12T14:31:50,658 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2021-07-12T14:31:50,658 | ~~^ 2021-07-12T14:31:50,658 | | 2021-07-12T14:31:50,658 | long int 2021-07-12T14:31:50,658 | %lld 2021-07-12T14:31:50,659 1302 | 3*natoms, pos.count); 2021-07-12T14:31:50,659 | ~~~~~~~~~ 2021-07-12T14:31:50,659 | | 2021-07-12T14:31:50,659 | uint64_t {aka long long unsigned int} 2021-07-12T14:31:50,659 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=] 2021-07-12T14:31:50,659 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2021-07-12T14:31:50,659 | ~~^ 2021-07-12T14:31:50,660 | | 2021-07-12T14:31:50,660 | long int 2021-07-12T14:31:50,660 | %lld 2021-07-12T14:31:50,660 1311 | 3*natoms, vel.count); 2021-07-12T14:31:50,660 | ~~~~~~~~~ 2021-07-12T14:31:50,660 | | 2021-07-12T14:31:50,660 | uint64_t {aka long long unsigned int} 2021-07-12T14:31:50,683 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2021-07-12T14:31:50,683 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=] 2021-07-12T14:31:50,684 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2021-07-12T14:31:50,684 | ~~^ 2021-07-12T14:31:50,684 | | 2021-07-12T14:31:50,684 | long int 2021-07-12T14:31:50,684 | %lld 2021-07-12T14:31:50,684 1573 | velblob.count, 3*natoms); 2021-07-12T14:31:50,684 | ~~~~~~~~~~~~~ 2021-07-12T14:31:50,684 | | 2021-07-12T14:31:50,685 | uint64_t {aka long long unsigned int} 2021-07-12T14:31:51,725 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: 2021-07-12T14:31:51,725 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 2021-07-12T14:31:51,725 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2021-07-12T14:31:51,725 | ~~~~~~~~^~~~~ 2021-07-12T14:31:53,983 In file included from /usr/include/c++/10/map:60, 2021-07-12T14:31:53,983 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2021-07-12T14:31:53,983 /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> >]’: 2021-07-12T14:31:53,984 /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 2021-07-12T14:31:53,984 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2021-07-12T14:31:53,984 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:31:54,866 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: 2021-07-12T14:31:54,866 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=] 2021-07-12T14:31:54,866 706 | sprintf(sub, "%03x/", i); 2021-07-12T14:31:54,866 | ^~~~ 2021-07-12T14:31:54,866 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 2021-07-12T14:31:54,867 706 | sprintf(sub, "%03x/", i); 2021-07-12T14:31:54,867 | ^~~~~~~ 2021-07-12T14:31:54,867 In file included from /usr/include/stdio.h:867, 2021-07-12T14:31:54,867 from mdtraj/formats/dtr/include/molfile_plugin.h:35, 2021-07-12T14:31:54,867 from mdtraj/formats/dtr/include/dtrplugin.hxx:46, 2021-07-12T14:31:54,867 from mdtraj/formats/dtr/src/dtrplugin.cxx:42: 2021-07-12T14:31:54,867 /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 2021-07-12T14:31:54,867 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-12T14:31:54,868 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:31:54,868 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-12T14:31:54,868 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:31:54,868 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=] 2021-07-12T14:31:54,868 714 | sprintf(subsub, "%03x", j); 2021-07-12T14:31:54,868 | ^~~~ 2021-07-12T14:31:54,868 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 2021-07-12T14:31:54,869 714 | sprintf(subsub, "%03x", j); 2021-07-12T14:31:54,869 | ^~~~~~ 2021-07-12T14:31:54,869 In file included from /usr/include/stdio.h:867, 2021-07-12T14:31:54,869 from mdtraj/formats/dtr/include/molfile_plugin.h:35, 2021-07-12T14:31:54,869 from mdtraj/formats/dtr/include/dtrplugin.hxx:46, 2021-07-12T14:31:54,869 from mdtraj/formats/dtr/src/dtrplugin.cxx:42: 2021-07-12T14:31:54,869 /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 2021-07-12T14:31:54,870 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-12T14:31:54,870 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:31:54,870 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-12T14:31:54,870 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:31:55,278 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: 2021-07-12T14:31:55,278 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=] 2021-07-12T14:31:55,278 667 | sprintf(answer, "%03x/", d1); 2021-07-12T14:31:55,278 | ^ 2021-07-12T14:31:55,278 In file included from /usr/include/stdio.h:867, 2021-07-12T14:31:55,279 from mdtraj/formats/dtr/include/molfile_plugin.h:35, 2021-07-12T14:31:55,279 from mdtraj/formats/dtr/include/dtrplugin.hxx:46, 2021-07-12T14:31:55,279 from mdtraj/formats/dtr/src/dtrplugin.cxx:42: 2021-07-12T14:31:55,279 /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 2021-07-12T14:31:55,279 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-12T14:31:55,279 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:31:55,279 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-12T14:31:55,280 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:31:55,280 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=] 2021-07-12T14:31:55,280 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2021-07-12T14:31:55,280 | ^~~~ 2021-07-12T14:31:55,280 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2021-07-12T14:31:55,280 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2021-07-12T14:31:55,280 | ^~~~~~~~~~~~ 2021-07-12T14:31:55,280 In file included from /usr/include/stdio.h:867, 2021-07-12T14:31:55,281 from mdtraj/formats/dtr/include/molfile_plugin.h:35, 2021-07-12T14:31:55,281 from mdtraj/formats/dtr/include/dtrplugin.hxx:46, 2021-07-12T14:31:55,281 from mdtraj/formats/dtr/src/dtrplugin.cxx:42: 2021-07-12T14:31:55,281 /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 2021-07-12T14:31:55,281 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-12T14:31:55,281 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:31:55,281 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-12T14:31:55,281 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T14:32:03,213 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 2021-07-12T14:32:03,631 building 'mdtraj._rmsd' extension 2021-07-12T14:32:03,632 creating build/temp.linux-armv7l-3.9/mdtraj/rmsd 2021-07-12T14:32:03,633 creating build/temp.linux-armv7l-3.9/mdtraj/rmsd/src 2021-07-12T14:32:03,633 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 2021-07-12T14:32:03,654 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’ 2021-07-12T14:32:03,656 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-12T14:32:03,808 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-12T14:32:03,808 ERROR: Failed building wheel for mdtraj 2021-07-12T14:32:03,809 Running setup.py clean for mdtraj 2021-07-12T14:32:03,809 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ui4m6p9c/mdtraj_88a322e277954b8d80747a504870113d/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 2021-07-12T14:32:05,290 C compiler: 2021-07-12T14:32:05,299 Using built-in specs. 2021-07-12T14:32:05,300 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2021-07-12T14:32:05,300 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2021-07-12T14:32:05,300 Target: arm-linux-gnueabihf 2021-07-12T14:32:05,300 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 2021-07-12T14:32:05,300 Thread model: posix 2021-07-12T14:32:05,300 Supported LTO compression algorithms: zlib zstd 2021-07-12T14:32:05,301 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2021-07-12T14:32:05,884 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-12T14:32:06,085 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-12T14:32:06,268 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-12T14:32:07,172 running clean 2021-07-12T14:32:07,175 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-12T14:32:07,204 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-12T14:32:07,252 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-12T14:32:07,253 'build/scripts-3.9' does not exist -- can't clean it 2021-07-12T14:32:07,253 removing 'build' 2021-07-12T14:32:07,387 Failed to build mdtraj 2021-07-12T14:32:07,388 ERROR: Failed to build one or more wheels 2021-07-12T14:32:07,389 Exception information: 2021-07-12T14:32:07,389 Traceback (most recent call last): 2021-07-12T14:32:07,389 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-12T14:32:07,389 status = self.run(options, args) 2021-07-12T14:32:07,389 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-12T14:32:07,389 return func(self, options, args) 2021-07-12T14:32:07,389 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-12T14:32:07,389 raise CommandError( 2021-07-12T14:32:07,389 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-12T14:32:07,393 Removed build tracker: '/tmp/pip-req-tracker-043nzu9g'