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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/) 2021-07-09T22:19:56,278 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/) 2021-07-09T22:19:56,278 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 2021-07-09T22:19:56,278 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 2021-07-09T22:19:56,279 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 2021-07-09T22:19:56,279 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 2021-07-09T22:19:56,279 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 2021-07-09T22:19:56,280 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 2021-07-09T22:19:56,280 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 2021-07-09T22:19:56,280 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 2021-07-09T22:19:56,280 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 2021-07-09T22:19:56,281 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 2021-07-09T22:19:56,281 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 2021-07-09T22:19:56,281 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 2021-07-09T22:19:56,281 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 2021-07-09T22:19:56,282 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 2021-07-09T22:19:56,282 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/) 2021-07-09T22:19:56,283 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/) 2021-07-09T22:19:56,283 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/) 2021-07-09T22:19:56,284 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/) 2021-07-09T22:19:56,284 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 2021-07-09T22:19:56,284 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/) 2021-07-09T22:19:56,285 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/) 2021-07-09T22:19:56,285 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/) 2021-07-09T22:19:56,286 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/) 2021-07-09T22:19:56,286 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 2021-07-09T22:19:56,286 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-09T22:19:56,294 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates 2021-07-09T22:19:56,312 Collecting mdtraj==0.9.0 2021-07-09T22:19:56,314 Created temporary directory: /tmp/pip-unpack-f1fx97ta 2021-07-09T22:19:58,347 Downloading mdtraj-0.9.0.zip (5.2 MB) 2021-07-09T22:19:59,898 Added mdtraj==0.9.0 from https://files.pythonhosted.org/packages/5a/a4/ab877500acc0e0b953d8ffa8de21719fcbb78749c2fd682f82601a0f3a3d/mdtraj-0.9.0.zip#sha256=dcc380dbcea821f50bceb6f3492d46122a6b15336a12cb50cd49d31d9700e687 to build tracker '/tmp/pip-req-tracker-yfjvr3vd' 2021-07-09T22:19:59,900 Running setup.py (path:/tmp/pip-wheel-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76/setup.py) egg_info for package mdtraj 2021-07-09T22:19:59,900 Created temporary directory: /tmp/pip-pip-egg-info-1xk8x9l7 2021-07-09T22:19:59,901 Running command python setup.py egg_info 2021-07-09T22:20:02,279 /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-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76/MDTraj/formats/binpos/binpos.pyx 2021-07-09T22:20:02,280 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T22:20:04,333 /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-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76/MDTraj/formats/dcd/dcd.pyx 2021-07-09T22:20:04,334 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T22:20:06,589 /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-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76/MDTraj/formats/xtc/trr.pyx 2021-07-09T22:20:06,590 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T22:20:08,992 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T22:20:08,993 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-09T22:20:08,993 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-09T22:20:08,993 Compiling MDTraj/formats/xtc/trr.pyx because it changed. 2021-07-09T22:20:08,993 Compiling MDTraj/formats/dcd/dcd.pyx because it changed. 2021-07-09T22:20:08,993 Compiling MDTraj/formats/binpos/binpos.pyx because it changed. 2021-07-09T22:20:08,993 [1/3] Cythonizing MDTraj/formats/binpos/binpos.pyx 2021-07-09T22:20:08,994 [2/3] Cythonizing MDTraj/formats/dcd/dcd.pyx 2021-07-09T22:20:08,994 [3/3] Cythonizing MDTraj/formats/xtc/trr.pyx 2021-07-09T22:20:09,128 running egg_info 2021-07-09T22:20:09,131 creating /tmp/pip-pip-egg-info-1xk8x9l7/mdtraj.egg-info 2021-07-09T22:20:09,132 writing /tmp/pip-pip-egg-info-1xk8x9l7/mdtraj.egg-info/PKG-INFO 2021-07-09T22:20:09,134 writing dependency_links to /tmp/pip-pip-egg-info-1xk8x9l7/mdtraj.egg-info/dependency_links.txt 2021-07-09T22:20:09,136 writing entry points to /tmp/pip-pip-egg-info-1xk8x9l7/mdtraj.egg-info/entry_points.txt 2021-07-09T22:20:09,138 writing top-level names to /tmp/pip-pip-egg-info-1xk8x9l7/mdtraj.egg-info/top_level.txt 2021-07-09T22:20:09,140 writing manifest file '/tmp/pip-pip-egg-info-1xk8x9l7/mdtraj.egg-info/SOURCES.txt' 2021-07-09T22:20:09,341 reading manifest file '/tmp/pip-pip-egg-info-1xk8x9l7/mdtraj.egg-info/SOURCES.txt' 2021-07-09T22:20:09,342 reading manifest template 'MANIFEST.in' 2021-07-09T22:20:09,386 writing manifest file '/tmp/pip-pip-egg-info-1xk8x9l7/mdtraj.egg-info/SOURCES.txt' 2021-07-09T22:20:09,602 Source in /tmp/pip-wheel-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76 has version 0.9.0, which satisfies requirement mdtraj==0.9.0 from https://files.pythonhosted.org/packages/5a/a4/ab877500acc0e0b953d8ffa8de21719fcbb78749c2fd682f82601a0f3a3d/mdtraj-0.9.0.zip#sha256=dcc380dbcea821f50bceb6f3492d46122a6b15336a12cb50cd49d31d9700e687 2021-07-09T22:20:09,603 Removed mdtraj==0.9.0 from https://files.pythonhosted.org/packages/5a/a4/ab877500acc0e0b953d8ffa8de21719fcbb78749c2fd682f82601a0f3a3d/mdtraj-0.9.0.zip#sha256=dcc380dbcea821f50bceb6f3492d46122a6b15336a12cb50cd49d31d9700e687 from build tracker '/tmp/pip-req-tracker-yfjvr3vd' 2021-07-09T22:20:09,607 Created temporary directory: /tmp/pip-unpack-blnyzoft 2021-07-09T22:20:09,608 Building wheels for collected packages: mdtraj 2021-07-09T22:20:09,612 Created temporary directory: /tmp/pip-wheel-g_m0ncxc 2021-07-09T22:20:09,612 Building wheel for mdtraj (setup.py): started 2021-07-09T22:20:09,613 Destination directory: /tmp/pip-wheel-g_m0ncxc 2021-07-09T22:20:09,613 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76/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-g_m0ncxc 2021-07-09T22:20:10,973 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T22:20:10,995 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-09T22:20:11,024 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-09T22:20:11,845 running bdist_wheel 2021-07-09T22:20:11,849 running build 2021-07-09T22:20:11,850 running build_py 2021-07-09T22:20:11,987 creating build 2021-07-09T22:20:11,988 creating build/lib.linux-armv7l-3.9 2021-07-09T22:20:11,988 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T22:20:11,989 creating build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T22:20:11,990 copying scripts/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T22:20:11,992 copying scripts/mdinspect.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T22:20:11,994 copying scripts/mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T22:20:11,997 copying MDTraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T22:20:11,999 copying MDTraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T22:20:12,002 copying MDTraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T22:20:12,005 creating build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,006 copying MDTraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,008 copying MDTraj/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,010 copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,012 copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,015 copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,016 copying MDTraj/tests/test_lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,019 copying MDTraj/tests/test_mol2.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,021 copying MDTraj/tests/test_prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,023 copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,025 copying MDTraj/tests/test_rmsd_memmap.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,027 copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,030 copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,033 copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,035 copying MDTraj/tests/test_lprmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,037 copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,040 copying MDTraj/tests/test_crd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,042 copying MDTraj/tests/test_topology.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,045 copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,048 copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,050 copying MDTraj/tests/test_arc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,053 copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,055 copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,058 copying MDTraj/tests/test_nmr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,060 copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,063 copying MDTraj/tests/test_quaternion.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T22:20:12,066 creating build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T22:20:12,067 copying MDTraj/core/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T22:20:12,069 copying MDTraj/core/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T22:20:12,073 copying MDTraj/core/topology.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T22:20:12,076 copying MDTraj/core/element.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T22:20:12,080 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,081 copying MDTraj/geometry/hbond.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,084 copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,086 copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,088 copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,091 copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,094 copying MDTraj/geometry/sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,096 copying MDTraj/geometry/contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,099 copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,101 copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,103 copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T22:20:12,107 creating build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,108 copying MDTraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,111 copying MDTraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,113 copying MDTraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,115 copying MDTraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,118 copying MDTraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,119 copying MDTraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,121 copying MDTraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,123 copying MDTraj/geometry/tests/test_drid.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,125 copying MDTraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,128 copying MDTraj/geometry/tests/test_angles.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T22:20:12,131 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T22:20:12,132 copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T22:20:12,134 copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T22:20:12,136 copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T22:20:12,138 copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T22:20:12,141 copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T22:20:12,144 creating build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-09T22:20:12,145 copying MDTraj/nmr/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-09T22:20:12,147 copying MDTraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-09T22:20:12,150 copying MDTraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr 2021-07-09T22:20:12,154 creating build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,155 copying MDTraj/formats/mol2.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,157 copying MDTraj/formats/openmmxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,159 copying MDTraj/formats/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,161 copying MDTraj/formats/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,164 copying MDTraj/formats/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,167 copying MDTraj/formats/registry.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,170 copying MDTraj/formats/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,172 copying MDTraj/formats/arc.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,175 copying MDTraj/formats/prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,178 copying MDTraj/formats/lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T22:20:12,181 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-09T22:20:12,182 copying MDTraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-09T22:20:12,184 copying MDTraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-09T22:20:12,187 copying MDTraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-09T22:20:12,191 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-09T22:20:12,192 copying MDTraj/formats/pdb/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-09T22:20:12,194 copying MDTraj/formats/pdb/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-09T22:20:12,195 copying MDTraj/formats/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-09T22:20:12,198 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T22:20:12,199 copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T22:20:12,202 copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T22:20:12,204 copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T22:20:12,206 copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T22:20:12,207 copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T22:20:12,210 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,211 copying MDTraj/utils/validation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,214 copying MDTraj/utils/ffi.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,216 copying MDTraj/utils/six.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,218 copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,220 copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,222 copying MDTraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,225 copying MDTraj/utils/rotation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,227 copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,229 copying MDTraj/utils/contextmanagers.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T22:20:12,232 creating build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,233 copying MDTraj/utils/unit/quantity.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,236 copying MDTraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,238 copying MDTraj/utils/unit/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,241 copying MDTraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,243 copying MDTraj/utils/unit/doctests.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,245 copying MDTraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,248 copying MDTraj/utils/unit/prefix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,251 copying MDTraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,253 copying MDTraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,255 copying MDTraj/utils/unit/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,258 copying MDTraj/utils/unit/constants.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,260 copying MDTraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,262 copying MDTraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T22:20:12,272 creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,273 copying MDTraj/testing/reference/alanine-dipeptide-explicit.prmtop -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,290 copying MDTraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,292 copying MDTraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,298 copying MDTraj/testing/reference/1am7_corrected.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,314 copying MDTraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,317 copying MDTraj/testing/reference/README.md -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,319 copying MDTraj/testing/reference/tz2.truncoct.parm7 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,345 copying MDTraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,347 copying MDTraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,353 copying MDTraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,373 copying MDTraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,382 copying MDTraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,393 copying MDTraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,395 copying MDTraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,398 copying MDTraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,402 copying MDTraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,412 copying MDTraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,417 copying MDTraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,440 copying MDTraj/testing/reference/alanine-dipeptide-explicit.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,448 copying MDTraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,450 copying MDTraj/testing/reference/alanine.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,453 copying MDTraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,456 copying MDTraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,460 copying MDTraj/testing/reference/imatinib.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,463 copying MDTraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,469 copying MDTraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,471 copying MDTraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,488 copying MDTraj/testing/reference/nitrogen.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,512 copying MDTraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,515 copying MDTraj/testing/reference/freesolve_v0.3.tar.bz2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,526 copying MDTraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,568 copying MDTraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,574 copying MDTraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,591 copying MDTraj/testing/reference/alanine-dipeptide-explicit.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,596 copying MDTraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,611 copying MDTraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,616 copying MDTraj/testing/reference/1am7_protein.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,624 copying MDTraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,627 copying MDTraj/testing/reference/native.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,629 copying MDTraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,631 copying MDTraj/testing/reference/nitrogen.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,650 copying MDTraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,658 copying MDTraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,664 copying MDTraj/testing/reference/alanine-dipeptide-implicit.prmtop -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,667 copying MDTraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,672 copying MDTraj/testing/reference/overflow.crd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,705 copying MDTraj/testing/reference/native2.xml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,707 copying MDTraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,711 copying MDTraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,713 copying MDTraj/testing/reference/1am7_uncorrected.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,726 copying MDTraj/testing/reference/imatinib.mol2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,730 copying MDTraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T22:20:12,736 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-09T22:20:12,737 copying MDTraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-09T22:20:12,741 copying MDTraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-09T22:20:12,756 running build_ext 2021-07-09T22:20:12,760 building 'mdtraj.formats.xtc' extension 2021-07-09T22:20:12,761 creating build/temp.linux-armv7l-3.9 2021-07-09T22:20:12,762 creating build/temp.linux-armv7l-3.9/MDTraj 2021-07-09T22:20:12,763 creating build/temp.linux-armv7l-3.9/MDTraj/formats 2021-07-09T22:20:12,764 creating build/temp.linux-armv7l-3.9/MDTraj/formats/xtc 2021-07-09T22:20:12,764 creating build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src 2021-07-09T22:20:12,765 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -IMDTraj/formats/xtc/include/ -IMDTraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src/xdrfile.o 2021-07-09T22:20:12,927 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-09T22:20:12,927 MDTraj/formats/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T22:20:12,927 478 | while (size >= num && num_of_bits < 32) 2021-07-09T22:20:12,927 | ^~ 2021-07-09T22:20:12,928 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-09T22:20:12,928 MDTraj/formats/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T22:20:12,928 524 | while (bytes[num_of_bytes] >= num) 2021-07-09T22:20:12,928 | ^~ 2021-07-09T22:20:12,929 MDTraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-09T22:20:12,929 MDTraj/formats/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T22:20:12,929 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-09T22:20:12,929 | ^~ 2021-07-09T22:20:12,929 MDTraj/formats/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T22:20:12,930 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-09T22:20:12,930 | ^ 2021-07-09T22:20:12,930 MDTraj/formats/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T22:20:12,930 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-09T22:20:12,930 | ^ 2021-07-09T22:20:12,930 MDTraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-09T22:20:12,930 MDTraj/formats/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T22:20:12,931 683 | if (lastbits < num_of_bits) 2021-07-09T22:20:12,931 | ^ 2021-07-09T22:20:12,932 MDTraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-09T22:20:12,932 MDTraj/formats/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T22:20:12,932 797 | if(size3>xfp->buf1size) 2021-07-09T22:20:12,932 | ^ 2021-07-09T22:20:12,934 MDTraj/formats/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T22:20:12,934 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T22:20:12,938 | ^ 2021-07-09T22:20:12,942 MDTraj/formats/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T22:20:12,943 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-09T22:20:12,943 | ^ 2021-07-09T22:20:12,943 MDTraj/formats/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T22:20:12,943 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T22:20:12,949 | ^ 2021-07-09T22:20:12,951 MDTraj/formats/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T22:20:12,951 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-09T22:20:12,956 | ^ 2021-07-09T22:20:12,962 MDTraj/formats/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T22:20:12,962 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-09T22:20:12,962 | ^ 2021-07-09T22:20:12,963 MDTraj/formats/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T22:20:12,963 1611 | maxidx = (LASTIDXn_frames == -1) != 0); 2021-07-09T22:20:16,038 | ^~ 2021-07-09T22:20:16,053 MDTraj/formats/xtc/xtc.c:7931:5: warning: implicit declaration of function ‘read_xtc_nframes’; did you mean ‘read_xtc_natoms’? [-Wimplicit-function-declaration] 2021-07-09T22:20:16,053 7931 | read_xtc_nframes(__pyx_t_4, (&__pyx_v_self->n_frames)); 2021-07-09T22:20:16,053 | ^~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,054 | read_xtc_natoms 2021-07-09T22:20:16,100 MDTraj/formats/xtc/xtc.c: In function ‘PyInit_xtc’: 2021-07-09T22:20:16,105 MDTraj/formats/xtc/xtc.c:10785:36: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-09T22:20:16,105 10785 | __pyx_type_3xtc_XTCTrajectoryFile.tp_print = 0; 2021-07-09T22:20:16,106 | ^ 2021-07-09T22:20:16,118 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T22:20:16,124 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,124 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,125 | ^ 2021-07-09T22:20:16,125 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,125 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,125 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,125 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,125 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,125 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,132 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,132 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,132 | ^ 2021-07-09T22:20:16,132 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,132 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,133 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,133 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T22:20:16,133 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T22:20:16,133 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,139 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,139 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,139 | ^ 2021-07-09T22:20:16,140 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,140 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,140 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,140 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,140 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,140 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,146 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,146 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,146 | ^ 2021-07-09T22:20:16,147 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,147 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,147 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,147 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,147 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,147 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,153 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,153 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,154 | ^ 2021-07-09T22:20:16,154 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,154 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,154 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,154 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T22:20:16,154 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T22:20:16,154 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,160 MDTraj/formats/xtc/xtc.c:11242:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,161 11242 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,161 | ^ 2021-07-09T22:20:16,161 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,161 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,161 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,161 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,161 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,161 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,169 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,169 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,170 | ^ 2021-07-09T22:20:16,170 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,170 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,170 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,170 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,170 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,170 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,176 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,177 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,177 | ^ 2021-07-09T22:20:16,177 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,177 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,177 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,177 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T22:20:16,177 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T22:20:16,177 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,184 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,184 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,184 | ^ 2021-07-09T22:20:16,184 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,184 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,184 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,184 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,184 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,185 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,191 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,191 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,191 | ^ 2021-07-09T22:20:16,191 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,191 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,192 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,192 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,192 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,192 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,198 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,198 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,198 | ^ 2021-07-09T22:20:16,198 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,199 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,199 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,199 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T22:20:16,199 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T22:20:16,199 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,205 MDTraj/formats/xtc/xtc.c:11258:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,205 11258 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T22:20:16,206 | ^ 2021-07-09T22:20:16,206 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,206 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,206 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,206 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,206 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,206 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,243 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_ExceptionSave’: 2021-07-09T22:20:16,254 MDTraj/formats/xtc/xtc.c:11628:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T22:20:16,254 11628 | *type = tstate->exc_type; 2021-07-09T22:20:16,254 | ^~~~~~~~ 2021-07-09T22:20:16,254 | curexc_type 2021-07-09T22:20:16,265 MDTraj/formats/xtc/xtc.c:11629:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T22:20:16,265 11629 | *value = tstate->exc_value; 2021-07-09T22:20:16,265 | ^~~~~~~~~ 2021-07-09T22:20:16,265 | curexc_value 2021-07-09T22:20:16,275 MDTraj/formats/xtc/xtc.c:11630:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T22:20:16,276 11630 | *tb = tstate->exc_traceback; 2021-07-09T22:20:16,276 | ^~~~~~~~~~~~~ 2021-07-09T22:20:16,276 | curexc_traceback 2021-07-09T22:20:16,276 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_ExceptionReset’: 2021-07-09T22:20:16,287 MDTraj/formats/xtc/xtc.c:11642:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T22:20:16,287 11642 | tmp_type = tstate->exc_type; 2021-07-09T22:20:16,287 | ^~~~~~~~ 2021-07-09T22:20:16,287 | curexc_type 2021-07-09T22:20:16,297 MDTraj/formats/xtc/xtc.c:11643:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T22:20:16,298 11643 | tmp_value = tstate->exc_value; 2021-07-09T22:20:16,298 | ^~~~~~~~~ 2021-07-09T22:20:16,298 | curexc_value 2021-07-09T22:20:16,308 MDTraj/formats/xtc/xtc.c:11644:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T22:20:16,308 11644 | tmp_tb = tstate->exc_traceback; 2021-07-09T22:20:16,309 | ^~~~~~~~~~~~~ 2021-07-09T22:20:16,309 | curexc_traceback 2021-07-09T22:20:16,319 MDTraj/formats/xtc/xtc.c:11645:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T22:20:16,319 11645 | tstate->exc_type = type; 2021-07-09T22:20:16,319 | ^~~~~~~~ 2021-07-09T22:20:16,319 | curexc_type 2021-07-09T22:20:16,330 MDTraj/formats/xtc/xtc.c:11646:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T22:20:16,330 11646 | tstate->exc_value = value; 2021-07-09T22:20:16,330 | ^~~~~~~~~ 2021-07-09T22:20:16,330 | curexc_value 2021-07-09T22:20:16,341 MDTraj/formats/xtc/xtc.c:11647:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T22:20:16,341 11647 | tstate->exc_traceback = tb; 2021-07-09T22:20:16,341 | ^~~~~~~~~~~~~ 2021-07-09T22:20:16,341 | curexc_traceback 2021-07-09T22:20:16,344 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_GetException’: 2021-07-09T22:20:16,355 MDTraj/formats/xtc/xtc.c:11690:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T22:20:16,355 11690 | tmp_type = tstate->exc_type; 2021-07-09T22:20:16,355 | ^~~~~~~~ 2021-07-09T22:20:16,355 | curexc_type 2021-07-09T22:20:16,365 MDTraj/formats/xtc/xtc.c:11691:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T22:20:16,366 11691 | tmp_value = tstate->exc_value; 2021-07-09T22:20:16,366 | ^~~~~~~~~ 2021-07-09T22:20:16,366 | curexc_value 2021-07-09T22:20:16,376 MDTraj/formats/xtc/xtc.c:11692:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T22:20:16,377 11692 | tmp_tb = tstate->exc_traceback; 2021-07-09T22:20:16,377 | ^~~~~~~~~~~~~ 2021-07-09T22:20:16,377 | curexc_traceback 2021-07-09T22:20:16,387 MDTraj/formats/xtc/xtc.c:11693:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T22:20:16,387 11693 | tstate->exc_type = local_type; 2021-07-09T22:20:16,388 | ^~~~~~~~ 2021-07-09T22:20:16,388 | curexc_type 2021-07-09T22:20:16,398 MDTraj/formats/xtc/xtc.c:11694:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T22:20:16,398 11694 | tstate->exc_value = local_value; 2021-07-09T22:20:16,398 | ^~~~~~~~~ 2021-07-09T22:20:16,398 | curexc_value 2021-07-09T22:20:16,409 MDTraj/formats/xtc/xtc.c:11695:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T22:20:16,409 11695 | tstate->exc_traceback = local_tb; 2021-07-09T22:20:16,409 | ^~~~~~~~~~~~~ 2021-07-09T22:20:16,409 | curexc_traceback 2021-07-09T22:20:16,589 MDTraj/formats/xtc/xtc.c: In function ‘__Pyx_PyObject_AsStringAndSize’: 2021-07-09T22:20:16,596 MDTraj/formats/xtc/xtc.c:13710:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,597 13710 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-09T22:20:16,597 | ^ 2021-07-09T22:20:16,597 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,597 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,597 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,597 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,597 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,598 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,605 MDTraj/formats/xtc/xtc.c:13710:13: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,605 13710 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-09T22:20:16,605 | ^ 2021-07-09T22:20:16,605 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,606 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,606 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,606 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T22:20:16,606 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T22:20:16,606 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,614 MDTraj/formats/xtc/xtc.c:13710:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T22:20:16,614 13710 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-09T22:20:16,614 | ^ 2021-07-09T22:20:16,614 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T22:20:16,614 from /usr/include/python3.9/Python.h:97, 2021-07-09T22:20:16,614 from MDTraj/formats/xtc/xtc.c:16: 2021-07-09T22:20:16,614 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T22:20:16,615 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T22:20:16,615 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,621 MDTraj/formats/xtc/xtc.c:13711:20: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-09T22:20:16,621 13711 | return PyUnicode_AsUTF8(o); 2021-07-09T22:20:16,621 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:20:16,757 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T22:20:16,901 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-09T22:20:16,901 ERROR: Failed building wheel for mdtraj 2021-07-09T22:20:16,902 Running setup.py clean for mdtraj 2021-07-09T22:20:16,902 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-z66gcxb7/mdtraj_4e9889fb1b124d0286ea22bb963f6a76/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 2021-07-09T22:20:18,334 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T22:20:18,354 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2021-07-09T22:20:18,380 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2021-07-09T22:20:19,188 running clean 2021-07-09T22:20:19,191 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T22:20:19,196 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T22:20:19,274 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T22:20:19,275 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T22:20:19,275 removing 'build' 2021-07-09T22:20:19,416 Failed to build mdtraj 2021-07-09T22:20:19,417 ERROR: Failed to build one or more wheels 2021-07-09T22:20:19,417 Exception information: 2021-07-09T22:20:19,417 Traceback (most recent call last): 2021-07-09T22:20:19,417 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T22:20:19,417 status = self.run(options, args) 2021-07-09T22:20:19,417 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T22:20:19,417 return func(self, options, args) 2021-07-09T22:20:19,417 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T22:20:19,417 raise CommandError( 2021-07-09T22:20:19,417 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T22:20:19,420 Removed build tracker: '/tmp/pip-req-tracker-yfjvr3vd'