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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/) 2021-07-09T17:19:45,826 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/) 2021-07-09T17:19:45,827 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 2021-07-09T17:19:45,827 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 2021-07-09T17:19:45,827 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 2021-07-09T17:19:45,828 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 2021-07-09T17:19:45,828 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 2021-07-09T17:19:45,828 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 2021-07-09T17:19:45,829 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 2021-07-09T17:19:45,829 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 2021-07-09T17:19:45,829 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 2021-07-09T17:19:45,830 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 2021-07-09T17:19:45,830 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 2021-07-09T17:19:45,830 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 2021-07-09T17:19:45,831 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 2021-07-09T17:19:45,831 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 2021-07-09T17:19:45,832 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/) 2021-07-09T17:19:45,832 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/) 2021-07-09T17:19:45,833 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/) 2021-07-09T17:19:45,833 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/) 2021-07-09T17:19:45,834 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 2021-07-09T17:19:45,834 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/) 2021-07-09T17:19:45,835 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/) 2021-07-09T17:19:45,836 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/) 2021-07-09T17:19:45,836 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/) 2021-07-09T17:19:45,836 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 2021-07-09T17:19:45,837 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-09T17:19:45,845 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2021-07-09T17:19:45,863 Collecting mdtraj==0.4.0 2021-07-09T17:19:45,865 Created temporary directory: /tmp/pip-unpack-xj3pl58t 2021-07-09T17:19:46,970 Downloading mdtraj-0.4.0.tar.gz (2.2 MB) 2021-07-09T17:19:47,997 Added mdtraj==0.4.0 from https://files.pythonhosted.org/packages/6e/2c/5e68a951b1d038ce32d5e0e128f56ee7ff0ea0ce933e7c05a2b9a2c56b9d/mdtraj-0.4.0.tar.gz#sha256=8eb89b88c3e900e0594ebbaff55c07a59959411a69c7e436933b899e81d7d3e4 to build tracker '/tmp/pip-req-tracker-v_peazbo' 2021-07-09T17:19:47,998 Running setup.py (path:/tmp/pip-wheel-lsdrnpa9/mdtraj_2eb4c1591bc640cfb03fad6db0785533/setup.py) egg_info for package mdtraj 2021-07-09T17:19:47,999 Created temporary directory: /tmp/pip-pip-egg-info-5eds54pi 2021-07-09T17:19:47,999 Running command python setup.py egg_info 2021-07-09T17:19:49,156 running egg_info 2021-07-09T17:19:49,158 creating /tmp/pip-pip-egg-info-5eds54pi/mdtraj.egg-info 2021-07-09T17:19:49,159 writing /tmp/pip-pip-egg-info-5eds54pi/mdtraj.egg-info/PKG-INFO 2021-07-09T17:19:49,162 writing dependency_links to /tmp/pip-pip-egg-info-5eds54pi/mdtraj.egg-info/dependency_links.txt 2021-07-09T17:19:49,164 writing requirements to /tmp/pip-pip-egg-info-5eds54pi/mdtraj.egg-info/requires.txt 2021-07-09T17:19:49,165 writing top-level names to /tmp/pip-pip-egg-info-5eds54pi/mdtraj.egg-info/top_level.txt 2021-07-09T17:19:49,167 writing manifest file '/tmp/pip-pip-egg-info-5eds54pi/mdtraj.egg-info/SOURCES.txt' 2021-07-09T17:19:49,330 reading manifest file '/tmp/pip-pip-egg-info-5eds54pi/mdtraj.egg-info/SOURCES.txt' 2021-07-09T17:19:49,331 reading manifest template 'MANIFEST.in' 2021-07-09T17:19:49,360 writing manifest file '/tmp/pip-pip-egg-info-5eds54pi/mdtraj.egg-info/SOURCES.txt' 2021-07-09T17:19:49,457 Source in /tmp/pip-wheel-lsdrnpa9/mdtraj_2eb4c1591bc640cfb03fad6db0785533 has version 0.4.0, which satisfies requirement mdtraj==0.4.0 from https://files.pythonhosted.org/packages/6e/2c/5e68a951b1d038ce32d5e0e128f56ee7ff0ea0ce933e7c05a2b9a2c56b9d/mdtraj-0.4.0.tar.gz#sha256=8eb89b88c3e900e0594ebbaff55c07a59959411a69c7e436933b899e81d7d3e4 2021-07-09T17:19:49,458 Removed mdtraj==0.4.0 from https://files.pythonhosted.org/packages/6e/2c/5e68a951b1d038ce32d5e0e128f56ee7ff0ea0ce933e7c05a2b9a2c56b9d/mdtraj-0.4.0.tar.gz#sha256=8eb89b88c3e900e0594ebbaff55c07a59959411a69c7e436933b899e81d7d3e4 from build tracker '/tmp/pip-req-tracker-v_peazbo' 2021-07-09T17:19:49,463 Created temporary directory: /tmp/pip-unpack-263pqh8x 2021-07-09T17:19:49,463 Building wheels for collected packages: mdtraj 2021-07-09T17:19:49,468 Created temporary directory: /tmp/pip-wheel-nfj13_m4 2021-07-09T17:19:49,468 Building wheel for mdtraj (setup.py): started 2021-07-09T17:19:49,469 Destination directory: /tmp/pip-wheel-nfj13_m4 2021-07-09T17:19:49,469 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-lsdrnpa9/mdtraj_2eb4c1591bc640cfb03fad6db0785533/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-lsdrnpa9/mdtraj_2eb4c1591bc640cfb03fad6db0785533/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-nfj13_m4 2021-07-09T17:19:50,654 running bdist_wheel 2021-07-09T17:19:50,658 running build 2021-07-09T17:19:50,658 running build_py 2021-07-09T17:19:50,796 creating build 2021-07-09T17:19:50,796 creating build/lib.linux-armv7l-3.9 2021-07-09T17:19:50,797 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,798 copying MDTraj/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,801 copying MDTraj/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,803 copying MDTraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,806 copying MDTraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,807 copying MDTraj/topology.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,810 copying MDTraj/rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,813 copying MDTraj/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,816 copying MDTraj/compatibility.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,818 copying MDTraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,820 copying MDTraj/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T17:19:50,824 creating build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T17:19:50,824 copying MDTraj/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T17:19:50,827 copying MDTraj/pdb/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T17:19:50,829 copying MDTraj/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T17:19:50,831 copying MDTraj/pdb/element.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T17:19:50,833 copying MDTraj/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T17:19:50,837 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T17:19:50,838 copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T17:19:50,841 copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T17:19:50,843 copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T17:19:50,846 copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T17:19:50,847 copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T17:19:50,850 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T17:19:50,851 copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T17:19:50,853 copying MDTraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T17:19:50,855 copying MDTraj/utils/arrays.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T17:19:50,857 copying MDTraj/utils/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T17:19:50,859 copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T17:19:50,861 copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T17:19:50,864 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T17:19:50,865 copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T17:19:50,868 copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T17:19:50,870 copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T17:19:50,872 copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T17:19:50,874 copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T17:19:50,877 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T17:19:50,878 copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T17:19:50,880 copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T17:19:50,882 copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T17:19:50,884 copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T17:19:50,887 copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T17:19:50,888 copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T17:19:50,890 copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T17:19:50,894 creating build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,894 copying MDTraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,896 copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,898 copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,901 copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,902 copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,905 copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,906 copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,908 copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,910 copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,912 copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,915 copying MDTraj/tests/test_compatibility.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,916 copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,918 copying MDTraj/tests/test_topology.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,920 copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,922 copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,925 copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T17:19:50,931 creating build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T17:19:50,932 copying MDTraj/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T17:19:50,935 copying MDTraj/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T17:19:50,938 creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,939 copying MDTraj/testing/reference/native2.xml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,942 copying MDTraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,950 copying MDTraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,968 copying MDTraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,973 copying MDTraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,978 copying MDTraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,981 copying MDTraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,985 copying MDTraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,988 copying MDTraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,994 copying MDTraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:50,999 copying MDTraj/testing/reference/native.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,001 copying MDTraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,008 copying MDTraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,014 copying MDTraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,016 copying MDTraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,021 copying MDTraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,024 copying MDTraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,038 copying MDTraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,045 copying MDTraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,049 copying MDTraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,052 copying MDTraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,056 copying MDTraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,069 copying MDTraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,084 copying MDTraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,086 copying MDTraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T17:19:51,111 running build_ext 2021-07-09T17:19:51,174 skipping 'MDTraj/xtc/xtc.c' Cython extension (up-to-date) 2021-07-09T17:19:51,174 skipping 'MDTraj/xtc/trr.c' Cython extension (up-to-date) 2021-07-09T17:19:51,175 skipping 'MDTraj/dcd/dcd.c' Cython extension (up-to-date) 2021-07-09T17:19:51,175 skipping 'MDTraj/binpos/binpos.c' Cython extension (up-to-date) 2021-07-09T17:19:51,176 skipping 'MDTraj/rmsd/_rmsd.c' Cython extension (up-to-date) 2021-07-09T17:19:51,176 building 'mdtraj.xtc' extension 2021-07-09T17:19:51,177 creating build/temp.linux-armv7l-3.9 2021-07-09T17:19:51,177 creating build/temp.linux-armv7l-3.9/MDTraj 2021-07-09T17:19:51,178 creating build/temp.linux-armv7l-3.9/MDTraj/xtc 2021-07-09T17:19:51,178 creating build/temp.linux-armv7l-3.9/MDTraj/xtc/src 2021-07-09T17:19:51,179 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 -IMDTraj/xtc/include/ -IMDTraj/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile.o 2021-07-09T17:19:51,342 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-09T17:19:51,342 MDTraj/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:19:51,343 478 | while (size >= num && num_of_bits < 32) 2021-07-09T17:19:51,343 | ^~ 2021-07-09T17:19:51,344 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-09T17:19:51,344 MDTraj/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:19:51,344 524 | while (bytes[num_of_bytes] >= num) 2021-07-09T17:19:51,344 | ^~ 2021-07-09T17:19:51,346 MDTraj/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-09T17:19:51,347 MDTraj/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:19:51,347 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-09T17:19:51,347 | ^~ 2021-07-09T17:19:51,347 MDTraj/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:19:51,348 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-09T17:19:51,348 | ^ 2021-07-09T17:19:51,348 MDTraj/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:19:51,349 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-09T17:19:51,349 | ^ 2021-07-09T17:19:51,349 MDTraj/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-09T17:19:51,350 MDTraj/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:19:51,350 683 | if (lastbits < num_of_bits) 2021-07-09T17:19:51,350 | ^ 2021-07-09T17:19:51,352 MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-09T17:19:51,353 MDTraj/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:19:51,353 797 | if(size3>xfp->buf1size) 2021-07-09T17:19:51,353 | ^ 2021-07-09T17:19:51,355 MDTraj/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:19:51,355 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T17:19:51,362 | ^ 2021-07-09T17:19:51,367 MDTraj/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:19:51,367 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-09T17:19:51,367 | ^ 2021-07-09T17:19:51,368 MDTraj/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:19:51,368 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T17:19:51,377 | ^ 2021-07-09T17:19:51,379 MDTraj/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:19:51,379 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-09T17:19:51,388 | ^ 2021-07-09T17:19:51,394 MDTraj/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:19:51,394 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-09T17:19:51,394 | ^ 2021-07-09T17:19:51,396 MDTraj/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:19:51,396 1611 | maxidx = (LASTIDXfh, __pyx_v_self->n_atoms, ((int *)(&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_step.diminfo[0].strides)))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_time.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_xyz.diminfo[0].strides, __pyx_t_22, __pyx_pybuffernd_xyz.diminfo[1].strides, __pyx_t_23, __pyx_pybuffernd_xyz.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_prec.rcbuffer->pybuffer.buf, __pyx_t_24, __pyx_pybuffernd_prec.diminfo[0].strides)))); 2021-07-09T17:19:54,451 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,451 | | 2021-07-09T17:19:54,451 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:19:54,451 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T17:19:54,451 MDTraj/xtc/include/xdrfile_xtc.h:32:16: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:19:54,451 32 | matrix box,rvec *x,float *prec); 2021-07-09T17:19:54,452 | ~~~~~~~^~~ 2021-07-09T17:19:54,453 MDTraj/xtc/xtc.c:3946:657: warning: passing argument 6 of ‘read_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:19:54,453 3946 | __pyx_v_status = read_xtc(__pyx_v_self->fh, __pyx_v_self->n_atoms, ((int *)(&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_step.diminfo[0].strides)))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_time.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_20, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_xyz.diminfo[0].strides, __pyx_t_22, __pyx_pybuffernd_xyz.diminfo[1].strides, __pyx_t_23, __pyx_pybuffernd_xyz.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_prec.rcbuffer->pybuffer.buf, __pyx_t_24, __pyx_pybuffernd_prec.diminfo[0].strides)))); 2021-07-09T17:19:54,453 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,454 | | 2021-07-09T17:19:54,454 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:19:54,454 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T17:19:54,454 MDTraj/xtc/include/xdrfile_xtc.h:32:26: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:19:54,454 32 | matrix box,rvec *x,float *prec); 2021-07-09T17:19:54,454 | ~~~~~~^ 2021-07-09T17:19:54,470 MDTraj/xtc/xtc.c:4031:396: warning: passing argument 5 of ‘read_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:19:54,470 4031 | __pyx_v_status = read_xtc(__pyx_v_self->fh, __pyx_v_self->n_atoms, ((int *)(&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_step.diminfo[0].strides)))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_26, __pyx_pybuffernd_time.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_27, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_28, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_29, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_framebuffer.rcbuffer->pybuffer.buf, __pyx_t_31, __pyx_pybuffernd_framebuffer.diminfo[0].strides, __pyx_t_32, __pyx_pybuffernd_framebuffer.diminfo[1].strides))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_prec.rcbuffer->pybuffer.buf, __pyx_t_30, __pyx_pybuffernd_prec.diminfo[0].strides)))); 2021-07-09T17:19:54,470 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,470 | | 2021-07-09T17:19:54,470 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:19:54,471 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T17:19:54,471 MDTraj/xtc/include/xdrfile_xtc.h:32:16: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:19:54,471 32 | matrix box,rvec *x,float *prec); 2021-07-09T17:19:54,471 | ~~~~~~~^~~ 2021-07-09T17:19:54,472 MDTraj/xtc/xtc.c:4031:657: warning: passing argument 6 of ‘read_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:19:54,472 4031 | __pyx_v_status = read_xtc(__pyx_v_self->fh, __pyx_v_self->n_atoms, ((int *)(&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_step.diminfo[0].strides)))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_26, __pyx_pybuffernd_time.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_27, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_28, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_29, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_framebuffer.rcbuffer->pybuffer.buf, __pyx_t_31, __pyx_pybuffernd_framebuffer.diminfo[0].strides, __pyx_t_32, __pyx_pybuffernd_framebuffer.diminfo[1].strides))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_prec.rcbuffer->pybuffer.buf, __pyx_t_30, __pyx_pybuffernd_prec.diminfo[0].strides)))); 2021-07-09T17:19:54,473 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,473 | | 2021-07-09T17:19:54,473 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:19:54,473 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T17:19:54,473 MDTraj/xtc/include/xdrfile_xtc.h:32:26: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:19:54,474 32 | matrix box,rvec *x,float *prec); 2021-07-09T17:19:54,474 | ~~~~~~^ 2021-07-09T17:19:54,537 MDTraj/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_3xtc_17XTCTrajectoryFile_14_write’: 2021-07-09T17:19:54,540 MDTraj/xtc/xtc.c:5555:372: warning: passing argument 5 of ‘write_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:19:54,541 5555 | __pyx_v_status = write_xtc(__pyx_v_self->fh, __pyx_v_n_atoms, (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_step.diminfo[0].strides)), (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_time.diminfo[0].strides)), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_12, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_xyz.diminfo[0].strides, __pyx_t_14, __pyx_pybuffernd_xyz.diminfo[1].strides, __pyx_t_15, __pyx_pybuffernd_xyz.diminfo[2].strides))), (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_prec.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_prec.diminfo[0].strides))); 2021-07-09T17:19:54,541 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,541 | | 2021-07-09T17:19:54,541 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:19:54,541 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T17:19:54,541 MDTraj/xtc/include/xdrfile_xtc.h:37:17: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:19:54,542 37 | matrix box,rvec *x,float prec); 2021-07-09T17:19:54,542 | ~~~~~~~^~~ 2021-07-09T17:19:54,544 MDTraj/xtc/xtc.c:5555:633: warning: passing argument 6 of ‘write_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:19:54,544 5555 | __pyx_v_status = write_xtc(__pyx_v_self->fh, __pyx_v_n_atoms, (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_step.diminfo[0].strides)), (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_time.diminfo[0].strides)), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_11, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_12, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_xyz.diminfo[0].strides, __pyx_t_14, __pyx_pybuffernd_xyz.diminfo[1].strides, __pyx_t_15, __pyx_pybuffernd_xyz.diminfo[2].strides))), (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_prec.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_prec.diminfo[0].strides))); 2021-07-09T17:19:54,544 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,545 | | 2021-07-09T17:19:54,545 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:19:54,545 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T17:19:54,545 MDTraj/xtc/include/xdrfile_xtc.h:37:27: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:19:54,545 37 | matrix box,rvec *x,float prec); 2021-07-09T17:19:54,546 | ~~~~~~^ 2021-07-09T17:19:54,602 MDTraj/xtc/xtc.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T17:19:54,607 MDTraj/xtc/xtc.c:8767:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,607 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,607 | ^~ 2021-07-09T17:19:54,607 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,608 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,608 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,608 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:19:54,608 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:19:54,608 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,613 MDTraj/xtc/xtc.c:8767:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,613 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,613 | ^~ 2021-07-09T17:19:54,613 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,614 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,614 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,614 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:19:54,614 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:19:54,614 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,618 MDTraj/xtc/xtc.c:8767:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,619 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,619 | ^~ 2021-07-09T17:19:54,619 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,619 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,619 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,619 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:19:54,619 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:19:54,620 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,624 MDTraj/xtc/xtc.c:8767:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,624 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,624 | ^~ 2021-07-09T17:19:54,624 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,625 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,625 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,625 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:19:54,625 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:19:54,625 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,629 MDTraj/xtc/xtc.c:8767:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,630 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,630 | ^~ 2021-07-09T17:19:54,630 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,630 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,630 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,630 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:19:54,630 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:19:54,631 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,635 MDTraj/xtc/xtc.c:8767:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,635 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,635 | ^~ 2021-07-09T17:19:54,636 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,636 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,636 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,636 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:19:54,636 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:19:54,636 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,642 MDTraj/xtc/xtc.c:8780:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,642 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,642 | ^~ 2021-07-09T17:19:54,642 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,642 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,643 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,643 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:19:54,643 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:19:54,643 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,647 MDTraj/xtc/xtc.c:8780:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,647 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,648 | ^~ 2021-07-09T17:19:54,648 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,648 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,648 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,648 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:19:54,648 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:19:54,648 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,653 MDTraj/xtc/xtc.c:8780:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,653 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,653 | ^~ 2021-07-09T17:19:54,653 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,653 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,653 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,654 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:19:54,654 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:19:54,654 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,658 MDTraj/xtc/xtc.c:8780:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,658 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,659 | ^~ 2021-07-09T17:19:54,659 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,659 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,659 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,659 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:19:54,659 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:19:54,659 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,664 MDTraj/xtc/xtc.c:8780:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,664 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,664 | ^~ 2021-07-09T17:19:54,664 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,664 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,664 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,665 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:19:54,665 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:19:54,665 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,669 MDTraj/xtc/xtc.c:8780:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:19:54,669 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:19:54,670 | ^~ 2021-07-09T17:19:54,670 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:19:54,670 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:19:54,670 from MDTraj/xtc/xtc.c:4: 2021-07-09T17:19:54,670 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:19:54,670 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:19:54,671 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,914 At top level: 2021-07-09T17:19:54,918 MDTraj/xtc/xtc.c:6614:13: warning: ‘__pyx_pw_5numpy_7ndarray_3__releasebuffer__’ defined but not used [-Wunused-function] 2021-07-09T17:19:54,918 6614 | static void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-09T17:19:54,918 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:54,922 MDTraj/xtc/xtc.c:5798:12: warning: ‘__pyx_pw_5numpy_7ndarray_1__getbuffer__’ defined but not used [-Wunused-function] 2021-07-09T17:19:54,922 5798 | static int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-09T17:19:54,922 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:19:56,666 MDTraj/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_3xtc_17XTCTrajectoryFile_14_write’: 2021-07-09T17:19:56,667 MDTraj/xtc/xtc.c:187:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T17:19:56,667 187 | #define PyInt_FromLong PyLong_FromLong 2021-07-09T17:19:56,667 | ^~~~~~~~~~~~~~~ 2021-07-09T17:19:56,670 MDTraj/xtc/xtc.c:5337:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T17:19:56,670 5337 | int __pyx_v_status; 2021-07-09T17:19:56,670 | ^~~~~~~~~~~~~~ 2021-07-09T17:20:03,012 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/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-3.9/MDTraj/xtc/xtc.o -o build/lib.linux-armv7l-3.9/mdtraj/xtc.cpython-39-arm-linux-gnueabihf.so 2021-07-09T17:20:03,160 building 'mdtraj.trr' extension 2021-07-09T17:20:03,160 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/xtc/include/ -IMDTraj/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile.o 2021-07-09T17:20:03,309 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-09T17:20:03,309 MDTraj/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:20:03,309 478 | while (size >= num && num_of_bits < 32) 2021-07-09T17:20:03,310 | ^~ 2021-07-09T17:20:03,310 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-09T17:20:03,310 MDTraj/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:03,310 524 | while (bytes[num_of_bytes] >= num) 2021-07-09T17:20:03,310 | ^~ 2021-07-09T17:20:03,311 MDTraj/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-09T17:20:03,311 MDTraj/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:20:03,311 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-09T17:20:03,311 | ^~ 2021-07-09T17:20:03,312 MDTraj/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:20:03,312 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-09T17:20:03,312 | ^ 2021-07-09T17:20:03,312 MDTraj/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:20:03,312 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-09T17:20:03,312 | ^ 2021-07-09T17:20:03,313 MDTraj/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-09T17:20:03,313 MDTraj/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:03,313 683 | if (lastbits < num_of_bits) 2021-07-09T17:20:03,313 | ^ 2021-07-09T17:20:03,314 MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-09T17:20:03,314 MDTraj/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:03,314 797 | if(size3>xfp->buf1size) 2021-07-09T17:20:03,315 | ^ 2021-07-09T17:20:03,316 MDTraj/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:03,316 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T17:20:03,320 | ^ 2021-07-09T17:20:03,324 MDTraj/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:20:03,324 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-09T17:20:03,325 | ^ 2021-07-09T17:20:03,325 MDTraj/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:03,325 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T17:20:03,331 | ^ 2021-07-09T17:20:03,333 MDTraj/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:03,333 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-09T17:20:03,339 | ^ 2021-07-09T17:20:03,345 MDTraj/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:20:03,345 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-09T17:20:03,345 | ^ 2021-07-09T17:20:03,346 MDTraj/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:03,346 1611 | maxidx = (LASTIDXfh, __pyx_v_self->n_atoms, ((int *)(&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_step.diminfo[0].strides)))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_time.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_lambd.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_lambd.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_20, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_21, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz.rcbuffer->pybuffer.buf, __pyx_t_22, __pyx_pybuffernd_xyz.diminfo[0].strides, __pyx_t_23, __pyx_pybuffernd_xyz.diminfo[1].strides, __pyx_t_24, __pyx_pybuffernd_xyz.diminfo[2].strides))), NULL, NULL); 2021-07-09T17:20:06,864 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:06,864 | | 2021-07-09T17:20:06,864 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:20:06,864 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T17:20:06,864 MDTraj/xtc/include/xdrfile_trr.h:33:16: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:20:06,865 33 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T17:20:06,865 | ~~~~~~~^~~ 2021-07-09T17:20:06,867 MDTraj/xtc/trr.c:3827:816: warning: passing argument 7 of ‘read_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:20:06,867 3827 | __pyx_v_status = read_trr(__pyx_v_self->fh, __pyx_v_self->n_atoms, ((int *)(&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_step.diminfo[0].strides)))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_time.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_lambd.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_lambd.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_20, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_21, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz.rcbuffer->pybuffer.buf, __pyx_t_22, __pyx_pybuffernd_xyz.diminfo[0].strides, __pyx_t_23, __pyx_pybuffernd_xyz.diminfo[1].strides, __pyx_t_24, __pyx_pybuffernd_xyz.diminfo[2].strides))), NULL, NULL); 2021-07-09T17:20:06,867 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:06,867 | | 2021-07-09T17:20:06,867 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:20:06,868 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T17:20:06,868 MDTraj/xtc/include/xdrfile_trr.h:33:26: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:20:06,868 33 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T17:20:06,868 | ~~~~~~^ 2021-07-09T17:20:06,888 MDTraj/xtc/trr.c:3912:555: warning: passing argument 6 of ‘read_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:20:06,888 3912 | __pyx_v_status = read_trr(__pyx_v_self->fh, __pyx_v_self->n_atoms, ((int *)(&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_step.diminfo[0].strides)))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_26, __pyx_pybuffernd_time.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_lambd.rcbuffer->pybuffer.buf, __pyx_t_27, __pyx_pybuffernd_lambd.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_28, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_29, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_framebuffer.rcbuffer->pybuffer.buf, __pyx_t_32, __pyx_pybuffernd_framebuffer.diminfo[0].strides, __pyx_t_33, __pyx_pybuffernd_framebuffer.diminfo[1].strides))), NULL, NULL); 2021-07-09T17:20:06,888 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:06,888 | | 2021-07-09T17:20:06,888 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:20:06,888 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T17:20:06,889 MDTraj/xtc/include/xdrfile_trr.h:33:16: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:20:06,889 33 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T17:20:06,889 | ~~~~~~~^~~ 2021-07-09T17:20:06,891 MDTraj/xtc/trr.c:3912:816: warning: passing argument 7 of ‘read_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:20:06,891 3912 | __pyx_v_status = read_trr(__pyx_v_self->fh, __pyx_v_self->n_atoms, ((int *)(&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_step.diminfo[0].strides)))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_26, __pyx_pybuffernd_time.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_lambd.rcbuffer->pybuffer.buf, __pyx_t_27, __pyx_pybuffernd_lambd.diminfo[0].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_28, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_29, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_30, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_framebuffer.rcbuffer->pybuffer.buf, __pyx_t_32, __pyx_pybuffernd_framebuffer.diminfo[0].strides, __pyx_t_33, __pyx_pybuffernd_framebuffer.diminfo[1].strides))), NULL, NULL); 2021-07-09T17:20:06,891 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:06,891 | | 2021-07-09T17:20:06,891 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:20:06,892 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T17:20:06,892 MDTraj/xtc/include/xdrfile_trr.h:33:26: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:20:06,892 33 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T17:20:06,892 | ~~~~~~^ 2021-07-09T17:20:06,965 MDTraj/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_3trr_17TRRTrajectoryFile_14_write’: 2021-07-09T17:20:06,969 MDTraj/xtc/trr.c:5564:528: warning: passing argument 6 of ‘write_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:20:06,969 5564 | __pyx_v_status = write_trr(__pyx_v_self->fh, __pyx_v_n_atoms, (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_step.diminfo[0].strides)), (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_time.diminfo[0].strides)), (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_lambd.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_lambd.diminfo[0].strides)), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_13, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_xyz.diminfo[0].strides, __pyx_t_15, __pyx_pybuffernd_xyz.diminfo[1].strides, __pyx_t_16, __pyx_pybuffernd_xyz.diminfo[2].strides))), NULL, NULL); 2021-07-09T17:20:06,970 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:06,970 | | 2021-07-09T17:20:06,970 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:20:06,970 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T17:20:06,970 MDTraj/xtc/include/xdrfile_trr.h:37:17: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:20:06,970 37 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T17:20:06,970 | ~~~~~~~^~~ 2021-07-09T17:20:06,974 MDTraj/xtc/trr.c:5564:789: warning: passing argument 7 of ‘write_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T17:20:06,974 5564 | __pyx_v_status = write_trr(__pyx_v_self->fh, __pyx_v_n_atoms, (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_step.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_step.diminfo[0].strides)), (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_time.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_time.diminfo[0].strides)), (*__Pyx_BufPtrCContig1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_lambd.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_lambd.diminfo[0].strides)), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_box.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_box.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_box.diminfo[1].strides, __pyx_t_13, __pyx_pybuffernd_box.diminfo[2].strides))), (&(*__Pyx_BufPtrCContig3d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_xyz.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_xyz.diminfo[0].strides, __pyx_t_15, __pyx_pybuffernd_xyz.diminfo[1].strides, __pyx_t_16, __pyx_pybuffernd_xyz.diminfo[2].strides))), NULL, NULL); 2021-07-09T17:20:06,974 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:06,975 | | 2021-07-09T17:20:06,975 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T17:20:06,975 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T17:20:06,975 MDTraj/xtc/include/xdrfile_trr.h:37:27: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T17:20:06,975 37 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T17:20:06,976 | ~~~~~~^ 2021-07-09T17:20:07,036 MDTraj/xtc/trr.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T17:20:07,042 MDTraj/xtc/trr.c:8775:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,042 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,042 | ^~ 2021-07-09T17:20:07,042 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,042 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,043 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,043 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:07,043 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:07,043 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,050 MDTraj/xtc/trr.c:8775:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,050 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,050 | ^~ 2021-07-09T17:20:07,050 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,050 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,050 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,050 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:07,051 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:07,051 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,057 MDTraj/xtc/trr.c:8775:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,057 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,057 | ^~ 2021-07-09T17:20:07,057 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,058 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,058 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,058 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:07,058 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:07,058 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,064 MDTraj/xtc/trr.c:8775:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,064 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,065 | ^~ 2021-07-09T17:20:07,065 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,065 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,065 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,065 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:07,065 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:07,065 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,071 MDTraj/xtc/trr.c:8775:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,072 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,072 | ^~ 2021-07-09T17:20:07,072 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,072 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,072 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,072 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:07,072 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:07,073 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,079 MDTraj/xtc/trr.c:8775:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,079 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,079 | ^~ 2021-07-09T17:20:07,079 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,080 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,080 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,080 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:07,080 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:07,080 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,088 MDTraj/xtc/trr.c:8788:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,088 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,088 | ^~ 2021-07-09T17:20:07,088 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,088 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,088 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,089 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:07,089 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:07,089 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,095 MDTraj/xtc/trr.c:8788:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,095 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,095 | ^~ 2021-07-09T17:20:07,095 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,096 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,096 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,096 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:07,096 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:07,096 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,102 MDTraj/xtc/trr.c:8788:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,102 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,103 | ^~ 2021-07-09T17:20:07,103 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,103 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,103 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,103 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:07,103 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:07,103 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,110 MDTraj/xtc/trr.c:8788:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,110 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,110 | ^~ 2021-07-09T17:20:07,110 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,110 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,110 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,110 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:07,111 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:07,111 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,117 MDTraj/xtc/trr.c:8788:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,117 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,117 | ^~ 2021-07-09T17:20:07,117 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,117 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,118 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,118 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:07,118 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:07,118 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,124 MDTraj/xtc/trr.c:8788:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:07,124 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:07,125 | ^~ 2021-07-09T17:20:07,125 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:07,125 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:07,125 from MDTraj/xtc/trr.c:4: 2021-07-09T17:20:07,125 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:07,125 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:07,126 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,408 At top level: 2021-07-09T17:20:07,413 MDTraj/xtc/trr.c:6623:13: warning: ‘__pyx_pw_5numpy_7ndarray_3__releasebuffer__’ defined but not used [-Wunused-function] 2021-07-09T17:20:07,413 6623 | static void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-09T17:20:07,413 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:07,418 MDTraj/xtc/trr.c:5807:12: warning: ‘__pyx_pw_5numpy_7ndarray_1__getbuffer__’ defined but not used [-Wunused-function] 2021-07-09T17:20:07,418 5807 | static int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-09T17:20:07,418 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:08,989 MDTraj/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_3trr_17TRRTrajectoryFile_14_write’: 2021-07-09T17:20:08,990 MDTraj/xtc/trr.c:187:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T17:20:08,990 187 | #define PyInt_FromLong PyLong_FromLong 2021-07-09T17:20:08,990 | ^~~~~~~~~~~~~~~ 2021-07-09T17:20:08,994 MDTraj/xtc/trr.c:5338:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T17:20:08,994 5338 | int __pyx_v_status; 2021-07-09T17:20:08,994 | ^~~~~~~~~~~~~~ 2021-07-09T17:20:15,356 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/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-3.9/MDTraj/xtc/trr.o -o build/lib.linux-armv7l-3.9/mdtraj/trr.cpython-39-arm-linux-gnueabihf.so 2021-07-09T17:20:15,502 building 'mdtraj.dcd' extension 2021-07-09T17:20:15,502 creating build/temp.linux-armv7l-3.9/MDTraj/dcd 2021-07-09T17:20:15,503 creating build/temp.linux-armv7l-3.9/MDTraj/dcd/src 2021-07-09T17:20:15,504 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/dcd/include/ -IMDTraj/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/dcd/dcd.c -o build/temp.linux-armv7l-3.9/MDTraj/dcd/dcd.o 2021-07-09T17:20:15,900 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-09T17:20:15,900 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-09T17:20:15,901 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-09T17:20:15,901 from MDTraj/dcd/dcd.c:275: 2021-07-09T17:20:15,901 /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] 2021-07-09T17:20:15,901 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-09T17:20:15,901 | ^~~~~~~ 2021-07-09T17:20:16,134 MDTraj/dcd/dcd.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T17:20:16,139 MDTraj/dcd/dcd.c:7213:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,140 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,140 | ^~ 2021-07-09T17:20:16,141 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,141 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,141 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,141 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:16,141 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:16,141 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,147 MDTraj/dcd/dcd.c:7213:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,148 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,148 | ^~ 2021-07-09T17:20:16,148 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,148 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,148 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,149 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:16,149 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:16,149 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,155 MDTraj/dcd/dcd.c:7213:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,155 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,155 | ^~ 2021-07-09T17:20:16,155 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,156 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,156 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,156 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:16,156 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:16,156 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,162 MDTraj/dcd/dcd.c:7213:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,162 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,162 | ^~ 2021-07-09T17:20:16,162 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,163 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,163 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,163 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:16,163 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:16,163 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,169 MDTraj/dcd/dcd.c:7213:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,169 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,169 | ^~ 2021-07-09T17:20:16,170 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,170 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,170 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,170 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:16,170 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:16,170 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,176 MDTraj/dcd/dcd.c:7213:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,176 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,177 | ^~ 2021-07-09T17:20:16,177 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,177 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,177 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,177 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:16,177 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:16,177 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,185 MDTraj/dcd/dcd.c:7226:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,185 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,185 | ^~ 2021-07-09T17:20:16,185 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,186 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,186 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,186 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:16,186 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:16,186 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,191 MDTraj/dcd/dcd.c:7226:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,191 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,191 | ^~ 2021-07-09T17:20:16,191 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,191 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,191 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,191 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:16,192 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:16,192 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,196 MDTraj/dcd/dcd.c:7226:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,197 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,197 | ^~ 2021-07-09T17:20:16,197 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,197 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,197 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,198 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:16,198 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:16,198 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,202 MDTraj/dcd/dcd.c:7226:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,202 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,203 | ^~ 2021-07-09T17:20:16,203 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,203 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,203 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,203 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:16,203 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:16,203 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,208 MDTraj/dcd/dcd.c:7226:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,208 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,208 | ^~ 2021-07-09T17:20:16,209 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,209 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,209 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,209 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:16,209 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:16,209 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,214 MDTraj/dcd/dcd.c:7226:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:16,214 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:16,214 | ^~ 2021-07-09T17:20:16,214 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:16,214 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:16,215 from MDTraj/dcd/dcd.c:4: 2021-07-09T17:20:16,215 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:16,215 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:16,215 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,443 At top level: 2021-07-09T17:20:16,447 MDTraj/dcd/dcd.c:5200:13: warning: ‘__pyx_pw_5numpy_7ndarray_3__releasebuffer__’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,447 5200 | static void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-09T17:20:16,447 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,450 MDTraj/dcd/dcd.c:4384:12: warning: ‘__pyx_pw_5numpy_7ndarray_1__getbuffer__’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,450 4384 | static int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-09T17:20:16,451 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:16,451 In file included from MDTraj/dcd/include/dcdplugin.h:1, 2021-07-09T17:20:16,451 from MDTraj/dcd/dcd.c:277: 2021-07-09T17:20:16,451 MDTraj/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,451 473 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-09T17:20:16,452 | ^~~~~~~~~~~~~ 2021-07-09T17:20:16,452 MDTraj/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,452 469 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-09T17:20:16,452 | ^~~~~~~~~~~~~~ 2021-07-09T17:20:16,452 MDTraj/dcd/include/fastio.h:465:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,453 465 | static int fio_write_int32(fio_fd fd, int i) { 2021-07-09T17:20:16,453 | ^~~~~~~~~~~~~~~ 2021-07-09T17:20:16,453 MDTraj/dcd/include/fastio.h:456:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,453 456 | static fio_size_t fio_ftell(fio_fd fd) { 2021-07-09T17:20:16,453 | ^~~~~~~~~ 2021-07-09T17:20:16,453 MDTraj/dcd/include/fastio.h:449:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,454 449 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { 2021-07-09T17:20:16,454 | ^~~~~~~~~ 2021-07-09T17:20:16,454 MDTraj/dcd/include/fastio.h:414:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,454 414 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { 2021-07-09T17:20:16,454 | ^~~~~~~~~ 2021-07-09T17:20:16,455 MDTraj/dcd/include/fastio.h:393:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,455 393 | static int fio_fclose(fio_fd fd) { 2021-07-09T17:20:16,456 | ^~~~~~~~~~ 2021-07-09T17:20:16,456 MDTraj/dcd/include/fastio.h:365:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2021-07-09T17:20:16,457 365 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2021-07-09T17:20:16,457 | ^~~~~~~~ 2021-07-09T17:20:21,576 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/dcd/include/ -IMDTraj/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-3.9/MDTraj/dcd/src/dcdplugin.o 2021-07-09T17:20:21,807 MDTraj/dcd/src/dcdplugin.c: In function ‘read_dcdheader’: 2021-07-09T17:20:21,808 MDTraj/dcd/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:21,808 129 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { 2021-07-09T17:20:21,809 | ^~ 2021-07-09T17:20:21,809 MDTraj/dcd/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:21,809 146 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { 2021-07-09T17:20:21,809 | ^~ 2021-07-09T17:20:21,809 MDTraj/dcd/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:21,810 164 | if (input_integer[0] != dcdcordmagic) { 2021-07-09T17:20:21,810 | ^~ 2021-07-09T17:20:21,812 MDTraj/dcd/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:21,813 341 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { 2021-07-09T17:20:21,813 | ^~ 2021-07-09T17:20:21,813 MDTraj/dcd/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T17:20:21,813 358 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { 2021-07-09T17:20:21,813 | ^~ 2021-07-09T17:20:21,817 MDTraj/dcd/src/dcdplugin.c: In function ‘read_dcdstep’: 2021-07-09T17:20:21,817 MDTraj/dcd/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:20:21,818 540 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-09T17:20:21,818 | ^~ 2021-07-09T17:20:21,818 MDTraj/dcd/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T17:20:21,818 544 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-09T17:20:21,818 | ^~ 2021-07-09T17:20:21,844 In file included from MDTraj/dcd/src/dcdplugin.c:55: 2021-07-09T17:20:21,845 At top level: 2021-07-09T17:20:21,845 MDTraj/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2021-07-09T17:20:21,845 96 | static void swap2_aligned(void *v, long ndata) { 2021-07-09T17:20:21,845 | ^~~~~~~~~~~~~ 2021-07-09T17:20:21,845 MDTraj/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2021-07-09T17:20:21,846 32 | static void swap2_unaligned(void *v, long ndata) { 2021-07-09T17:20:21,846 | ^~~~~~~~~~~~~~~ 2021-07-09T17:20:21,846 In file included from MDTraj/dcd/src/dcdplugin.c:46: 2021-07-09T17:20:21,846 MDTraj/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-09T17:20:21,847 473 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-09T17:20:21,847 | ^~~~~~~~~~~~~ 2021-07-09T17:20:21,847 MDTraj/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-09T17:20:21,847 469 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-09T17:20:21,847 | ^~~~~~~~~~~~~~ 2021-07-09T17:20:23,058 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/dcd/dcd.o build/temp.linux-armv7l-3.9/MDTraj/dcd/src/dcdplugin.o -lm -o build/lib.linux-armv7l-3.9/mdtraj/dcd.cpython-39-arm-linux-gnueabihf.so 2021-07-09T17:20:23,213 building 'mdtraj.binpos' extension 2021-07-09T17:20:23,214 creating build/temp.linux-armv7l-3.9/MDTraj/binpos 2021-07-09T17:20:23,215 creating build/temp.linux-armv7l-3.9/MDTraj/binpos/src 2021-07-09T17:20:23,216 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/binpos/include/ -IMDTraj/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/binpos/binpos.c -o build/temp.linux-armv7l-3.9/MDTraj/binpos/binpos.o 2021-07-09T17:20:23,624 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-09T17:20:23,624 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-09T17:20:23,624 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-09T17:20:23,624 from MDTraj/binpos/binpos.c:275: 2021-07-09T17:20:23,624 /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] 2021-07-09T17:20:23,625 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-09T17:20:23,625 | ^~~~~~~ 2021-07-09T17:20:23,778 MDTraj/binpos/binpos.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T17:20:23,781 MDTraj/binpos/binpos.c:6451:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,781 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,781 | ^~ 2021-07-09T17:20:23,781 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,782 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,782 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,782 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:23,782 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:23,782 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,785 MDTraj/binpos/binpos.c:6451:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,786 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,786 | ^~ 2021-07-09T17:20:23,786 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,786 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,786 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,786 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:23,786 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:23,787 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,789 MDTraj/binpos/binpos.c:6451:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,789 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,790 | ^~ 2021-07-09T17:20:23,790 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,790 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,790 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,790 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:23,790 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:23,790 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,793 MDTraj/binpos/binpos.c:6451:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,793 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,793 | ^~ 2021-07-09T17:20:23,793 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,794 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,794 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,794 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:23,794 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:23,794 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,797 MDTraj/binpos/binpos.c:6451:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,797 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,797 | ^~ 2021-07-09T17:20:23,797 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,797 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,798 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,798 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:23,798 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:23,798 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,801 MDTraj/binpos/binpos.c:6451:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,801 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,801 | ^~ 2021-07-09T17:20:23,801 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,801 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,801 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,802 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:23,802 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:23,802 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,805 MDTraj/binpos/binpos.c:6464:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,806 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,806 | ^~ 2021-07-09T17:20:23,806 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,806 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,806 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,806 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:23,806 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:23,807 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,809 MDTraj/binpos/binpos.c:6464:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,809 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,810 | ^~ 2021-07-09T17:20:23,810 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,810 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,810 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,810 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:23,810 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:23,810 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,813 MDTraj/binpos/binpos.c:6464:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,813 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,813 | ^~ 2021-07-09T17:20:23,814 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,814 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,814 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,814 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:23,814 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:23,814 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,817 MDTraj/binpos/binpos.c:6464:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,817 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,817 | ^~ 2021-07-09T17:20:23,817 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,818 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,818 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,818 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:23,818 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:23,818 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,821 MDTraj/binpos/binpos.c:6464:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,821 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,821 | ^~ 2021-07-09T17:20:23,821 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,821 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,821 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,822 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T17:20:23,822 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T17:20:23,822 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,825 MDTraj/binpos/binpos.c:6464:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T17:20:23,825 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T17:20:23,825 | ^~ 2021-07-09T17:20:23,825 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T17:20:23,825 from /usr/include/python3.9/Python.h:97, 2021-07-09T17:20:23,826 from MDTraj/binpos/binpos.c:4: 2021-07-09T17:20:23,826 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T17:20:23,826 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T17:20:23,826 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:23,998 At top level: 2021-07-09T17:20:24,001 MDTraj/binpos/binpos.c:4523:13: warning: ‘__pyx_pw_5numpy_7ndarray_3__releasebuffer__’ defined but not used [-Wunused-function] 2021-07-09T17:20:24,001 4523 | static void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-09T17:20:24,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:24,003 MDTraj/binpos/binpos.c:3707:12: warning: ‘__pyx_pw_5numpy_7ndarray_1__getbuffer__’ defined but not used [-Wunused-function] 2021-07-09T17:20:24,003 3707 | static int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-09T17:20:24,003 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:25,593 MDTraj/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_6binpos_20BINPOSTrajectoryFile_7_read’: 2021-07-09T17:20:25,595 MDTraj/binpos/binpos.c:2927:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T17:20:25,595 2927 | if (__pyx_t_1) { 2021-07-09T17:20:25,595 | ^ 2021-07-09T17:20:25,596 MDTraj/binpos/binpos.c:2444:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T17:20:25,596 2444 | int __pyx_v_status; 2021-07-09T17:20:25,596 | ^~~~~~~~~~~~~~ 2021-07-09T17:20:25,596 MDTraj/binpos/binpos.c:211:48: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T17:20:25,597 211 | #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) 2021-07-09T17:20:25,597 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T17:20:25,598 MDTraj/binpos/binpos.c:2441:7: note: ‘__pyx_v_i’ was declared here 2021-07-09T17:20:25,598 2441 | int __pyx_v_i; 2021-07-09T17:20:25,598 | ^~~~~~~~~ 2021-07-09T17:20:28,758 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/binpos/include/ -IMDTraj/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/binpos/src/binposplugin.c -o build/temp.linux-armv7l-3.9/MDTraj/binpos/src/binposplugin.o 2021-07-09T17:20:29,180 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/binpos/binpos.o build/temp.linux-armv7l-3.9/MDTraj/binpos/src/binposplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/binpos.cpython-39-arm-linux-gnueabihf.so 2021-07-09T17:20:29,341 building 'mdtraj._rmsd' extension 2021-07-09T17:20:29,342 creating build/temp.linux-armv7l-3.9/MDTraj/rmsd 2021-07-09T17:20:29,342 creating build/temp.linux-armv7l-3.9/MDTraj/rmsd/src 2021-07-09T17:20:29,343 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 -std=c99 -O2 -msse2 -msse3 -fopenmp 2021-07-09T17:20:29,362 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’ 2021-07-09T17:20:29,363 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse3’ 2021-07-09T17:20:29,365 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T17:20:29,509 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-09T17:20:29,510 ERROR: Failed building wheel for mdtraj 2021-07-09T17:20:29,511 Running setup.py clean for mdtraj 2021-07-09T17:20:29,512 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-lsdrnpa9/mdtraj_2eb4c1591bc640cfb03fad6db0785533/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-lsdrnpa9/mdtraj_2eb4c1591bc640cfb03fad6db0785533/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 2021-07-09T17:20:30,685 running clean 2021-07-09T17:20:30,687 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T17:20:30,699 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T17:20:30,737 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T17:20:30,737 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T17:20:30,738 removing 'build' 2021-07-09T17:20:30,838 Failed to build mdtraj 2021-07-09T17:20:30,839 ERROR: Failed to build one or more wheels 2021-07-09T17:20:30,840 Exception information: 2021-07-09T17:20:30,840 Traceback (most recent call last): 2021-07-09T17:20:30,840 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T17:20:30,840 status = self.run(options, args) 2021-07-09T17:20:30,840 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T17:20:30,840 return func(self, options, args) 2021-07-09T17:20:30,840 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T17:20:30,840 raise CommandError( 2021-07-09T17:20:30,840 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T17:20:30,843 Removed build tracker: '/tmp/pip-req-tracker-v_peazbo'