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2021-07-09T20:45:20,241 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 2021-07-09T20:45:20,241 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 2021-07-09T20:45:20,241 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 2021-07-09T20:45:20,242 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 2021-07-09T20:45:20,242 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 2021-07-09T20:45:20,242 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 2021-07-09T20:45:20,242 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 2021-07-09T20:45:20,243 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 2021-07-09T20:45:20,243 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 2021-07-09T20:45:20,243 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 2021-07-09T20:45:20,243 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 2021-07-09T20:45:20,244 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 2021-07-09T20:45:20,244 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 2021-07-09T20:45:20,244 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/) 2021-07-09T20:45:20,245 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/) 2021-07-09T20:45:20,245 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/) 2021-07-09T20:45:20,246 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/) 2021-07-09T20:45:20,246 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 2021-07-09T20:45:20,246 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/) 2021-07-09T20:45:20,247 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/) 2021-07-09T20:45:20,247 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/) 2021-07-09T20:45:20,248 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/) 2021-07-09T20:45:20,248 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 2021-07-09T20:45:20,248 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-09T20:45:20,257 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates 2021-07-09T20:45:20,274 Collecting mdtraj==0.7.0 2021-07-09T20:45:20,276 Created temporary directory: /tmp/pip-unpack-3u8mznnp 2021-07-09T20:45:21,372 Downloading mdtraj-0.7.0.zip (2.8 MB) 2021-07-09T20:45:22,443 Added mdtraj==0.7.0 from https://files.pythonhosted.org/packages/bb/31/a472847da32caa824a73c3794f5816005b2a213f6c35df20dc55d1d07be8/mdtraj-0.7.0.zip#sha256=b45210e1d7eabdb9ff30338bcbbbc6d7624720ddd7d76c9ceb88f2baaaa5289f to build tracker '/tmp/pip-req-tracker-rpyu5e7o' 2021-07-09T20:45:22,445 Running setup.py (path:/tmp/pip-wheel-6oq3bl10/mdtraj_d69ada1c4e8b4c299d6cfc9b3667793c/setup.py) egg_info for package mdtraj 2021-07-09T20:45:22,445 Created temporary directory: /tmp/pip-pip-egg-info-k51meduw 2021-07-09T20:45:22,446 Running command python setup.py egg_info 2021-07-09T20:45:24,161 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T20:45:24,161 running egg_info 2021-07-09T20:45:24,163 creating /tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info 2021-07-09T20:45:24,164 writing /tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info/PKG-INFO 2021-07-09T20:45:24,166 writing dependency_links to /tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info/dependency_links.txt 2021-07-09T20:45:24,168 writing entry points to /tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info/entry_points.txt 2021-07-09T20:45:24,169 writing requirements to /tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info/requires.txt 2021-07-09T20:45:24,170 writing top-level names to /tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info/top_level.txt 2021-07-09T20:45:24,172 writing manifest file '/tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info/SOURCES.txt' 2021-07-09T20:45:24,336 reading manifest file '/tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info/SOURCES.txt' 2021-07-09T20:45:24,337 reading manifest template 'MANIFEST.in' 2021-07-09T20:45:24,367 writing manifest file '/tmp/pip-pip-egg-info-k51meduw/mdtraj.egg-info/SOURCES.txt' 2021-07-09T20:45:24,473 Source in /tmp/pip-wheel-6oq3bl10/mdtraj_d69ada1c4e8b4c299d6cfc9b3667793c has version 0.7.0, which satisfies requirement mdtraj==0.7.0 from https://files.pythonhosted.org/packages/bb/31/a472847da32caa824a73c3794f5816005b2a213f6c35df20dc55d1d07be8/mdtraj-0.7.0.zip#sha256=b45210e1d7eabdb9ff30338bcbbbc6d7624720ddd7d76c9ceb88f2baaaa5289f 2021-07-09T20:45:24,474 Removed mdtraj==0.7.0 from https://files.pythonhosted.org/packages/bb/31/a472847da32caa824a73c3794f5816005b2a213f6c35df20dc55d1d07be8/mdtraj-0.7.0.zip#sha256=b45210e1d7eabdb9ff30338bcbbbc6d7624720ddd7d76c9ceb88f2baaaa5289f from build tracker '/tmp/pip-req-tracker-rpyu5e7o' 2021-07-09T20:45:24,478 Created temporary directory: /tmp/pip-unpack-sgy5x1ho 2021-07-09T20:45:24,478 Building wheels for collected packages: mdtraj 2021-07-09T20:45:24,482 Created temporary directory: /tmp/pip-wheel-lfbl1y49 2021-07-09T20:45:24,483 Building wheel for mdtraj (setup.py): started 2021-07-09T20:45:24,483 Destination directory: /tmp/pip-wheel-lfbl1y49 2021-07-09T20:45:24,483 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-6oq3bl10/mdtraj_d69ada1c4e8b4c299d6cfc9b3667793c/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-6oq3bl10/mdtraj_d69ada1c4e8b4c299d6cfc9b3667793c/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-lfbl1y49 2021-07-09T20:45:25,909 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T20:45:26,126 running bdist_wheel 2021-07-09T20:45:26,130 running build 2021-07-09T20:45:26,131 running build_py 2021-07-09T20:45:26,264 creating build 2021-07-09T20:45:26,264 creating build/lib.linux-armv7l-3.9 2021-07-09T20:45:26,265 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,266 creating build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T20:45:26,267 copying scripts/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T20:45:26,269 copying scripts/mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T20:45:26,271 copying scripts/mdinspect.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T20:45:26,275 copying MDTraj/openmmxml.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,276 copying MDTraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,279 copying MDTraj/lh5.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,281 copying MDTraj/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,284 copying MDTraj/registry.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,286 copying MDTraj/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,288 copying MDTraj/arc.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,290 copying MDTraj/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,293 copying MDTraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,295 copying MDTraj/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,298 copying MDTraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,300 copying MDTraj/topology.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T20:45:26,304 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,305 copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,307 copying MDTraj/geometry/contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,309 copying MDTraj/geometry/sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,312 copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,314 copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,316 copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,319 copying MDTraj/geometry/hbond.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,321 copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,323 copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,326 copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T20:45:26,329 creating build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,330 copying MDTraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,332 copying MDTraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,335 copying MDTraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,337 copying MDTraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,340 copying MDTraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,342 copying MDTraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,344 copying MDTraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,346 copying MDTraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T20:45:26,350 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T20:45:26,351 copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T20:45:26,353 copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T20:45:26,355 copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T20:45:26,358 copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T20:45:26,360 copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T20:45:26,364 creating build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T20:45:26,365 copying MDTraj/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T20:45:26,369 copying MDTraj/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T20:45:26,371 copying MDTraj/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T20:45:26,374 copying MDTraj/pdb/element.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T20:45:26,378 creating build/lib.linux-armv7l-3.9/mdtraj/pdb/tests 2021-07-09T20:45:26,379 copying MDTraj/pdb/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb/tests 2021-07-09T20:45:26,381 copying MDTraj/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb/tests 2021-07-09T20:45:26,383 copying MDTraj/pdb/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb/tests 2021-07-09T20:45:26,386 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,387 copying MDTraj/utils/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,390 copying MDTraj/utils/six.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,393 copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,395 copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,398 copying MDTraj/utils/ffi.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,400 copying MDTraj/utils/arrays.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,402 copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,404 copying MDTraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T20:45:26,408 creating build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,409 copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,411 copying MDTraj/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,413 copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,416 copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,418 copying MDTraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,420 copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,422 copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,425 copying MDTraj/tests/test_lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,426 copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,429 copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,431 copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,433 copying MDTraj/tests/test_arc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,435 copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,437 copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,439 copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,442 copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,444 copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,446 copying MDTraj/tests/test_topology.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T20:45:26,449 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T20:45:26,450 copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T20:45:26,452 copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T20:45:26,455 copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T20:45:26,457 copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T20:45:26,459 copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T20:45:26,468 creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,469 copying MDTraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,480 copying MDTraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,487 copying MDTraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,493 copying MDTraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,495 copying MDTraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,497 copying MDTraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,502 copying MDTraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,504 copying MDTraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,509 copying MDTraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,525 copying MDTraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,528 copying MDTraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,543 copying MDTraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,549 copying MDTraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,551 copying MDTraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,553 copying MDTraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,558 copying MDTraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,563 copying MDTraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,590 copying MDTraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,592 copying MDTraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,612 copying MDTraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,615 copying MDTraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,620 copying MDTraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,622 copying MDTraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,630 copying MDTraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,635 copying MDTraj/testing/reference/native.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,637 copying MDTraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,681 copying MDTraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,689 copying MDTraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,696 copying MDTraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,699 copying MDTraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,702 copying MDTraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,704 copying MDTraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,711 copying MDTraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,732 copying MDTraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,738 copying MDTraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,748 copying MDTraj/testing/reference/native2.xml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T20:45:26,752 creating build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T20:45:26,753 copying MDTraj/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T20:45:26,756 copying MDTraj/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T20:45:26,770 running build_ext 2021-07-09T20:45:26,833 skipping 'MDTraj/xtc/xtc.c' Cython extension (up-to-date) 2021-07-09T20:45:26,834 skipping 'MDTraj/xtc/trr.c' Cython extension (up-to-date) 2021-07-09T20:45:26,834 skipping 'MDTraj/dcd/dcd.c' Cython extension (up-to-date) 2021-07-09T20:45:26,835 skipping 'MDTraj/binpos/binpos.c' Cython extension (up-to-date) 2021-07-09T20:45:26,836 skipping 'MDTraj/rmsd/_rmsd.c' Cython extension (up-to-date) 2021-07-09T20:45:26,836 building 'mdtraj.xtc' extension 2021-07-09T20:45:26,837 creating build/temp.linux-armv7l-3.9 2021-07-09T20:45:26,838 creating build/temp.linux-armv7l-3.9/MDTraj 2021-07-09T20:45:26,838 creating build/temp.linux-armv7l-3.9/MDTraj/xtc 2021-07-09T20:45:26,839 creating build/temp.linux-armv7l-3.9/MDTraj/xtc/src 2021-07-09T20:45:26,840 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 2021-07-09T20:45:27,002 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-09T20:45:27,002 MDTraj/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T20:45:27,002 478 | while (size >= num && num_of_bits < 32) 2021-07-09T20:45:27,003 | ^~ 2021-07-09T20:45:27,003 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-09T20:45:27,003 MDTraj/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T20:45:27,003 524 | while (bytes[num_of_bytes] >= num) 2021-07-09T20:45:27,003 | ^~ 2021-07-09T20:45:27,004 MDTraj/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-09T20:45:27,004 MDTraj/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T20:45:27,004 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-09T20:45:27,004 | ^~ 2021-07-09T20:45:27,004 MDTraj/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T20:45:27,005 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-09T20:45:27,005 | ^ 2021-07-09T20:45:27,005 MDTraj/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T20:45:27,005 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-09T20:45:27,005 | ^ 2021-07-09T20:45:27,005 MDTraj/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-09T20:45:27,005 MDTraj/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T20:45:27,006 683 | if (lastbits < num_of_bits) 2021-07-09T20:45:27,006 | ^ 2021-07-09T20:45:27,007 MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-09T20:45:27,007 MDTraj/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T20:45:27,007 797 | if(size3>xfp->buf1size) 2021-07-09T20:45:27,007 | ^ 2021-07-09T20:45:27,009 MDTraj/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T20:45:27,009 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T20:45:27,013 | ^ 2021-07-09T20:45:27,017 MDTraj/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T20:45:27,018 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-09T20:45:27,018 | ^ 2021-07-09T20:45:27,018 MDTraj/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T20:45:27,018 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T20:45:27,024 | ^ 2021-07-09T20:45:27,026 MDTraj/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T20:45:27,026 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-09T20:45:27,032 | ^ 2021-07-09T20:45:27,037 MDTraj/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T20:45:27,038 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-09T20:45:27,038 | ^ 2021-07-09T20:45:27,038 MDTraj/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T20:45:27,038 1611 | maxidx = (LASTIDXn_frames == -1) != 0); 2021-07-09T20:45:30,111 | ^~ 2021-07-09T20:45:30,126 MDTraj/xtc/xtc.c:7610:5: warning: implicit declaration of function ‘read_xtc_nframes’; did you mean ‘read_xtc_natoms’? [-Wimplicit-function-declaration] 2021-07-09T20:45:30,126 7610 | read_xtc_nframes(__pyx_t_4, (&__pyx_v_self->n_frames)); 2021-07-09T20:45:30,126 | ^~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,126 | read_xtc_natoms 2021-07-09T20:45:30,191 MDTraj/xtc/xtc.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T20:45:30,197 MDTraj/xtc/xtc.c:10875:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,197 10875 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,197 | ^ 2021-07-09T20:45:30,198 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,198 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,199 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,199 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,199 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,199 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,206 MDTraj/xtc/xtc.c:10875:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,206 10875 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,206 | ^ 2021-07-09T20:45:30,207 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,207 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,207 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,207 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T20:45:30,207 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T20:45:30,207 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,214 MDTraj/xtc/xtc.c:10875:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,214 10875 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,215 | ^ 2021-07-09T20:45:30,215 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,215 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,215 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,215 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,215 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,215 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,222 MDTraj/xtc/xtc.c:10875:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,223 10875 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,223 | ^ 2021-07-09T20:45:30,223 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,223 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,223 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,223 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,223 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,224 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,231 MDTraj/xtc/xtc.c:10875:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,231 10875 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,231 | ^ 2021-07-09T20:45:30,231 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,231 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,231 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,231 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T20:45:30,232 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T20:45:30,232 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,239 MDTraj/xtc/xtc.c:10875:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,239 10875 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,239 | ^ 2021-07-09T20:45:30,239 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,239 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,240 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,240 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,240 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,240 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,248 MDTraj/xtc/xtc.c:10891:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,249 10891 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,249 | ^ 2021-07-09T20:45:30,249 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,249 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,249 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,249 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,250 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,250 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,257 MDTraj/xtc/xtc.c:10891:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,257 10891 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,257 | ^ 2021-07-09T20:45:30,257 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,257 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,258 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,258 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T20:45:30,258 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T20:45:30,258 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,265 MDTraj/xtc/xtc.c:10891:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,265 10891 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,265 | ^ 2021-07-09T20:45:30,265 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,266 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,266 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,266 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,266 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,266 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,273 MDTraj/xtc/xtc.c:10891:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,273 10891 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,274 | ^ 2021-07-09T20:45:30,274 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,274 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,274 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,274 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,274 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,274 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,281 MDTraj/xtc/xtc.c:10891:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,282 10891 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,282 | ^ 2021-07-09T20:45:30,282 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,282 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,282 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,282 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T20:45:30,282 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T20:45:30,282 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,289 MDTraj/xtc/xtc.c:10891:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,290 10891 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-09T20:45:30,290 | ^ 2021-07-09T20:45:30,290 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,290 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,290 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,290 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,291 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,291 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,311 MDTraj/xtc/xtc.c: In function ‘__Pyx_Raise’: 2021-07-09T20:45:30,317 MDTraj/xtc/xtc.c:11093:9: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,318 11093 | owned_instance = PyEval_CallObject(type, args); 2021-07-09T20:45:30,318 | ^~~~~~~~~~~~~~ 2021-07-09T20:45:30,318 In file included from /usr/include/python3.9/Python.h:145, 2021-07-09T20:45:30,319 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,319 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-09T20:45:30,319 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-09T20:45:30,319 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,333 MDTraj/xtc/xtc.c: In function ‘__Pyx_GetException’: 2021-07-09T20:45:30,344 MDTraj/xtc/xtc.c:11254:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T20:45:30,344 11254 | tmp_type = tstate->exc_type; 2021-07-09T20:45:30,344 | ^~~~~~~~ 2021-07-09T20:45:30,344 | curexc_type 2021-07-09T20:45:30,355 MDTraj/xtc/xtc.c:11255:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T20:45:30,355 11255 | tmp_value = tstate->exc_value; 2021-07-09T20:45:30,355 | ^~~~~~~~~ 2021-07-09T20:45:30,355 | curexc_value 2021-07-09T20:45:30,366 MDTraj/xtc/xtc.c:11256:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T20:45:30,366 11256 | tmp_tb = tstate->exc_traceback; 2021-07-09T20:45:30,366 | ^~~~~~~~~~~~~ 2021-07-09T20:45:30,367 | curexc_traceback 2021-07-09T20:45:30,377 MDTraj/xtc/xtc.c:11257:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T20:45:30,378 11257 | tstate->exc_type = local_type; 2021-07-09T20:45:30,378 | ^~~~~~~~ 2021-07-09T20:45:30,378 | curexc_type 2021-07-09T20:45:30,388 MDTraj/xtc/xtc.c:11258:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T20:45:30,389 11258 | tstate->exc_value = local_value; 2021-07-09T20:45:30,389 | ^~~~~~~~~ 2021-07-09T20:45:30,389 | curexc_value 2021-07-09T20:45:30,400 MDTraj/xtc/xtc.c:11259:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T20:45:30,400 11259 | tstate->exc_traceback = local_tb; 2021-07-09T20:45:30,400 | ^~~~~~~~~~~~~ 2021-07-09T20:45:30,400 | curexc_traceback 2021-07-09T20:45:30,490 MDTraj/xtc/xtc.c: In function ‘__Pyx_ExceptionSave’: 2021-07-09T20:45:30,502 MDTraj/xtc/xtc.c:12095:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T20:45:30,502 12095 | *type = tstate->exc_type; 2021-07-09T20:45:30,502 | ^~~~~~~~ 2021-07-09T20:45:30,502 | curexc_type 2021-07-09T20:45:30,513 MDTraj/xtc/xtc.c:12096:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T20:45:30,513 12096 | *value = tstate->exc_value; 2021-07-09T20:45:30,513 | ^~~~~~~~~ 2021-07-09T20:45:30,513 | curexc_value 2021-07-09T20:45:30,524 MDTraj/xtc/xtc.c:12097:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T20:45:30,524 12097 | *tb = tstate->exc_traceback; 2021-07-09T20:45:30,525 | ^~~~~~~~~~~~~ 2021-07-09T20:45:30,525 | curexc_traceback 2021-07-09T20:45:30,525 MDTraj/xtc/xtc.c: In function ‘__Pyx_ExceptionReset’: 2021-07-09T20:45:30,536 MDTraj/xtc/xtc.c:12109:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T20:45:30,536 12109 | tmp_type = tstate->exc_type; 2021-07-09T20:45:30,536 | ^~~~~~~~ 2021-07-09T20:45:30,536 | curexc_type 2021-07-09T20:45:30,547 MDTraj/xtc/xtc.c:12110:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T20:45:30,547 12110 | tmp_value = tstate->exc_value; 2021-07-09T20:45:30,547 | ^~~~~~~~~ 2021-07-09T20:45:30,547 | curexc_value 2021-07-09T20:45:30,558 MDTraj/xtc/xtc.c:12111:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T20:45:30,559 12111 | tmp_tb = tstate->exc_traceback; 2021-07-09T20:45:30,559 | ^~~~~~~~~~~~~ 2021-07-09T20:45:30,559 | curexc_traceback 2021-07-09T20:45:30,570 MDTraj/xtc/xtc.c:12112:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-09T20:45:30,570 12112 | tstate->exc_type = type; 2021-07-09T20:45:30,570 | ^~~~~~~~ 2021-07-09T20:45:30,570 | curexc_type 2021-07-09T20:45:30,581 MDTraj/xtc/xtc.c:12113:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-09T20:45:30,581 12113 | tstate->exc_value = value; 2021-07-09T20:45:30,581 | ^~~~~~~~~ 2021-07-09T20:45:30,581 | curexc_value 2021-07-09T20:45:30,592 MDTraj/xtc/xtc.c:12114:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-09T20:45:30,592 12114 | tstate->exc_traceback = tb; 2021-07-09T20:45:30,593 | ^~~~~~~~~~~~~ 2021-07-09T20:45:30,593 | curexc_traceback 2021-07-09T20:45:30,671 MDTraj/xtc/xtc.c: In function ‘__Pyx_PyObject_AsStringAndSize’: 2021-07-09T20:45:30,678 MDTraj/xtc/xtc.c:13399:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,678 13399 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-09T20:45:30,678 | ^ 2021-07-09T20:45:30,678 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,679 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,679 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,679 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,679 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,679 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,687 MDTraj/xtc/xtc.c:13399:13: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,687 13399 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-09T20:45:30,687 | ^ 2021-07-09T20:45:30,687 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,688 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,688 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,688 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T20:45:30,688 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T20:45:30,688 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,696 MDTraj/xtc/xtc.c:13399:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T20:45:30,696 13399 | *length = PyUnicode_GET_DATA_SIZE(o); 2021-07-09T20:45:30,696 | ^ 2021-07-09T20:45:30,696 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T20:45:30,696 from /usr/include/python3.9/Python.h:97, 2021-07-09T20:45:30,696 from MDTraj/xtc/xtc.c:16: 2021-07-09T20:45:30,696 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T20:45:30,697 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T20:45:30,697 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,703 MDTraj/xtc/xtc.c:13400:20: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-09T20:45:30,703 13400 | return PyUnicode_AsUTF8(o); 2021-07-09T20:45:30,703 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:45:30,834 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T20:45:30,951 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-09T20:45:30,952 ERROR: Failed building wheel for mdtraj 2021-07-09T20:45:30,953 Running setup.py clean for mdtraj 2021-07-09T20:45:30,953 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-6oq3bl10/mdtraj_d69ada1c4e8b4c299d6cfc9b3667793c/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-6oq3bl10/mdtraj_d69ada1c4e8b4c299d6cfc9b3667793c/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 2021-07-09T20:45:32,376 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T20:45:32,579 running clean 2021-07-09T20:45:32,582 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T20:45:32,586 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T20:45:32,637 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T20:45:32,638 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T20:45:32,638 removing 'build' 2021-07-09T20:45:32,741 Failed to build mdtraj 2021-07-09T20:45:32,741 ERROR: Failed to build one or more wheels 2021-07-09T20:45:32,742 Exception information: 2021-07-09T20:45:32,742 Traceback (most recent call last): 2021-07-09T20:45:32,742 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T20:45:32,742 status = self.run(options, args) 2021-07-09T20:45:32,742 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T20:45:32,742 return func(self, options, args) 2021-07-09T20:45:32,742 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T20:45:32,742 raise CommandError( 2021-07-09T20:45:32,742 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T20:45:32,745 Removed build tracker: '/tmp/pip-req-tracker-rpyu5e7o'