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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/) 2021-07-09T16:50:33,024 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/) 2021-07-09T16:50:33,024 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 2021-07-09T16:50:33,024 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 2021-07-09T16:50:33,024 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 2021-07-09T16:50:33,025 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 2021-07-09T16:50:33,025 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 2021-07-09T16:50:33,025 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 2021-07-09T16:50:33,026 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 2021-07-09T16:50:33,026 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 2021-07-09T16:50:33,026 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 2021-07-09T16:50:33,027 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 2021-07-09T16:50:33,027 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 2021-07-09T16:50:33,027 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 2021-07-09T16:50:33,028 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 2021-07-09T16:50:33,028 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 2021-07-09T16:50:33,029 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/) 2021-07-09T16:50:33,030 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/) 2021-07-09T16:50:33,030 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/) 2021-07-09T16:50:33,031 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/) 2021-07-09T16:50:33,031 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 2021-07-09T16:50:33,032 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/) 2021-07-09T16:50:33,032 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/) 2021-07-09T16:50:33,033 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/) 2021-07-09T16:50:33,033 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/) 2021-07-09T16:50:33,033 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 2021-07-09T16:50:33,034 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-09T16:50:33,043 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2021-07-09T16:50:33,068 Collecting mdtraj==0.3.1 2021-07-09T16:50:33,070 Created temporary directory: /tmp/pip-unpack-t8swcheh 2021-07-09T16:50:33,561 Downloading mdtraj-0.3.1.tar.gz (1.7 MB) 2021-07-09T16:50:34,698 Added mdtraj==0.3.1 from https://files.pythonhosted.org/packages/bb/79/e0703632501b528c6d4fb87e672aa68e431579e61ddf15b9178554e45a8e/mdtraj-0.3.1.tar.gz#sha256=86d8b14ea7e8757475f32e346a05e7d8bb0e374d6c7b89a7d7fa9ba7f76acd09 to build tracker '/tmp/pip-req-tracker-_tg3kj10' 2021-07-09T16:50:34,699 Running setup.py (path:/tmp/pip-wheel-s3v9jj44/mdtraj_c90122473a494ae6bb31d5020b05edd5/setup.py) egg_info for package mdtraj 2021-07-09T16:50:34,700 Created temporary directory: /tmp/pip-pip-egg-info-2z8dzlvj 2021-07-09T16:50:34,700 Running command python setup.py egg_info 2021-07-09T16:50:35,876 running egg_info 2021-07-09T16:50:35,878 creating /tmp/pip-pip-egg-info-2z8dzlvj/mdtraj.egg-info 2021-07-09T16:50:35,879 writing /tmp/pip-pip-egg-info-2z8dzlvj/mdtraj.egg-info/PKG-INFO 2021-07-09T16:50:35,882 writing dependency_links to /tmp/pip-pip-egg-info-2z8dzlvj/mdtraj.egg-info/dependency_links.txt 2021-07-09T16:50:35,884 writing requirements to /tmp/pip-pip-egg-info-2z8dzlvj/mdtraj.egg-info/requires.txt 2021-07-09T16:50:35,885 writing top-level names to /tmp/pip-pip-egg-info-2z8dzlvj/mdtraj.egg-info/top_level.txt 2021-07-09T16:50:35,887 writing manifest file '/tmp/pip-pip-egg-info-2z8dzlvj/mdtraj.egg-info/SOURCES.txt' 2021-07-09T16:50:36,047 reading manifest file '/tmp/pip-pip-egg-info-2z8dzlvj/mdtraj.egg-info/SOURCES.txt' 2021-07-09T16:50:36,049 reading manifest template 'MANIFEST.in' 2021-07-09T16:50:36,076 writing manifest file '/tmp/pip-pip-egg-info-2z8dzlvj/mdtraj.egg-info/SOURCES.txt' 2021-07-09T16:50:36,180 Source in /tmp/pip-wheel-s3v9jj44/mdtraj_c90122473a494ae6bb31d5020b05edd5 has version 0.3.1, which satisfies requirement mdtraj==0.3.1 from https://files.pythonhosted.org/packages/bb/79/e0703632501b528c6d4fb87e672aa68e431579e61ddf15b9178554e45a8e/mdtraj-0.3.1.tar.gz#sha256=86d8b14ea7e8757475f32e346a05e7d8bb0e374d6c7b89a7d7fa9ba7f76acd09 2021-07-09T16:50:36,181 Removed mdtraj==0.3.1 from https://files.pythonhosted.org/packages/bb/79/e0703632501b528c6d4fb87e672aa68e431579e61ddf15b9178554e45a8e/mdtraj-0.3.1.tar.gz#sha256=86d8b14ea7e8757475f32e346a05e7d8bb0e374d6c7b89a7d7fa9ba7f76acd09 from build tracker '/tmp/pip-req-tracker-_tg3kj10' 2021-07-09T16:50:36,185 Created temporary directory: /tmp/pip-unpack-4eedrqs0 2021-07-09T16:50:36,186 Building wheels for collected packages: mdtraj 2021-07-09T16:50:36,190 Created temporary directory: /tmp/pip-wheel-ps5p3lr7 2021-07-09T16:50:36,190 Building wheel for mdtraj (setup.py): started 2021-07-09T16:50:36,191 Destination directory: /tmp/pip-wheel-ps5p3lr7 2021-07-09T16:50:36,191 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-s3v9jj44/mdtraj_c90122473a494ae6bb31d5020b05edd5/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-s3v9jj44/mdtraj_c90122473a494ae6bb31d5020b05edd5/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-ps5p3lr7 2021-07-09T16:50:37,424 running bdist_wheel 2021-07-09T16:50:37,428 running build 2021-07-09T16:50:37,428 running build_py 2021-07-09T16:50:37,566 creating build 2021-07-09T16:50:37,566 creating build/lib.linux-armv7l-3.9 2021-07-09T16:50:37,567 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,568 copying MDTraj/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,571 copying MDTraj/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,574 copying MDTraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,576 copying MDTraj/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,578 copying MDTraj/topology.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,581 copying MDTraj/rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,584 copying MDTraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,587 copying MDTraj/compatibility.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,590 copying MDTraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:37,593 creating build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:37,594 copying MDTraj/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:37,596 copying MDTraj/pdb/element.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:37,599 copying MDTraj/pdb/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:37,601 copying MDTraj/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:37,604 copying MDTraj/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:37,609 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:37,610 copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:37,612 copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:37,614 copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:37,617 copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:37,620 copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:37,623 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:37,624 copying MDTraj/utils/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:37,626 copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:37,628 copying MDTraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:37,631 copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:37,633 copying MDTraj/utils/arrays.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:37,635 copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:37,639 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:37,639 copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:37,642 copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:37,644 copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:37,646 copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:37,649 copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:37,652 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:37,653 copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:37,655 copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:37,658 copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:37,661 copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:37,663 copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:37,666 copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:37,668 copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:37,672 creating build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,673 copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,675 copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,677 copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,679 copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,682 copying MDTraj/tests/test_compatibility.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,684 copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,687 copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,688 copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,691 copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,694 copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,696 copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,699 copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,701 copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,703 copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:37,712 creating build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T16:50:37,713 copying MDTraj/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T16:50:37,716 copying MDTraj/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/pdb/data 2021-07-09T16:50:37,720 creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,721 copying MDTraj/testing/reference/native.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,724 copying MDTraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,734 copying MDTraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,741 copying MDTraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,760 copying MDTraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,763 copying MDTraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,768 copying MDTraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,790 copying MDTraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,806 copying MDTraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,813 copying MDTraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,818 copying MDTraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,821 copying MDTraj/testing/reference/native2.xml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,824 copying MDTraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,832 copying MDTraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,834 copying MDTraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,843 copying MDTraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,847 copying MDTraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,852 copying MDTraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,858 copying MDTraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,863 copying MDTraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,870 copying MDTraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,873 copying MDTraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,879 copying MDTraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T16:50:37,891 running build_ext 2021-07-09T16:50:37,958 skipping 'MDTraj/xtc/xtc.c' Cython extension (up-to-date) 2021-07-09T16:50:37,958 skipping 'MDTraj/xtc/trr.c' Cython extension (up-to-date) 2021-07-09T16:50:37,958 skipping 'MDTraj/dcd/dcd.c' Cython extension (up-to-date) 2021-07-09T16:50:37,959 skipping 'MDTraj/binpos/binpos.c' Cython extension (up-to-date) 2021-07-09T16:50:37,959 skipping 'MDTraj/rmsd/_rmsd.c' Cython extension (up-to-date) 2021-07-09T16:50:37,960 building 'mdtraj.xtc' extension 2021-07-09T16:50:37,960 creating build/temp.linux-armv7l-3.9 2021-07-09T16:50:37,961 creating build/temp.linux-armv7l-3.9/MDTraj 2021-07-09T16:50:37,961 creating build/temp.linux-armv7l-3.9/MDTraj/xtc 2021-07-09T16:50:37,962 creating build/temp.linux-armv7l-3.9/MDTraj/xtc/src 2021-07-09T16:50:37,963 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 2021-07-09T16:50:38,164 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-09T16:50:38,164 MDTraj/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:38,164 478 | while (size >= num && num_of_bits < 32) 2021-07-09T16:50:38,165 | ^~ 2021-07-09T16:50:38,165 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-09T16:50:38,165 MDTraj/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:38,166 524 | while (bytes[num_of_bytes] >= num) 2021-07-09T16:50:38,166 | ^~ 2021-07-09T16:50:38,166 MDTraj/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-09T16:50:38,166 MDTraj/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:38,167 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-09T16:50:38,167 | ^~ 2021-07-09T16:50:38,167 MDTraj/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:38,168 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-09T16:50:38,168 | ^ 2021-07-09T16:50:38,168 MDTraj/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:38,169 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-09T16:50:38,169 | ^ 2021-07-09T16:50:38,169 MDTraj/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-09T16:50:38,170 MDTraj/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:38,170 683 | if (lastbits < num_of_bits) 2021-07-09T16:50:38,170 | ^ 2021-07-09T16:50:38,171 MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-09T16:50:38,171 MDTraj/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:38,171 797 | if(size3>xfp->buf1size) 2021-07-09T16:50:38,172 | ^ 2021-07-09T16:50:38,173 MDTraj/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:38,173 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T16:50:38,179 | ^ 2021-07-09T16:50:38,185 MDTraj/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:38,185 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-09T16:50:38,185 | ^ 2021-07-09T16:50:38,185 MDTraj/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:38,186 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T16:50:38,194 | ^ 2021-07-09T16:50:38,197 MDTraj/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:38,197 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-09T16:50:38,205 | ^ 2021-07-09T16:50:38,212 MDTraj/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:38,213 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-09T16:50:38,213 | ^ 2021-07-09T16:50:38,213 MDTraj/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:38,214 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)))); 2021-07-09T16:50:41,517 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,517 | | 2021-07-09T16:50:41,517 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:41,518 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T16:50:41,518 MDTraj/xtc/include/xdrfile_xtc.h:32:16: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:41,518 32 | matrix box,rvec *x,float *prec); 2021-07-09T16:50:41,518 | ~~~~~~~^~~ 2021-07-09T16:50:41,521 MDTraj/xtc/xtc.c:3946:657: warning: passing argument 6 of ‘read_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:41,521 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)))); 2021-07-09T16:50:41,521 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,522 | | 2021-07-09T16:50:41,522 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:41,522 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T16:50:41,522 MDTraj/xtc/include/xdrfile_xtc.h:32:26: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:41,522 32 | matrix box,rvec *x,float *prec); 2021-07-09T16:50:41,522 | ~~~~~~^ 2021-07-09T16:50:41,540 MDTraj/xtc/xtc.c:4031:396: warning: passing argument 5 of ‘read_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:41,540 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)))); 2021-07-09T16:50:41,540 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,541 | | 2021-07-09T16:50:41,541 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:41,541 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T16:50:41,541 MDTraj/xtc/include/xdrfile_xtc.h:32:16: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:41,542 32 | matrix box,rvec *x,float *prec); 2021-07-09T16:50:41,542 | ~~~~~~~^~~ 2021-07-09T16:50:41,544 MDTraj/xtc/xtc.c:4031:657: warning: passing argument 6 of ‘read_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:41,545 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)))); 2021-07-09T16:50:41,545 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,545 | | 2021-07-09T16:50:41,545 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:41,546 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T16:50:41,546 MDTraj/xtc/include/xdrfile_xtc.h:32:26: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:41,546 32 | matrix box,rvec *x,float *prec); 2021-07-09T16:50:41,546 | ~~~~~~^ 2021-07-09T16:50:41,616 MDTraj/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_3xtc_17XTCTrajectoryFile_14_write’: 2021-07-09T16:50:41,619 MDTraj/xtc/xtc.c:5555:372: warning: passing argument 5 of ‘write_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:41,619 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))); 2021-07-09T16:50:41,620 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,620 | | 2021-07-09T16:50:41,620 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:41,620 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T16:50:41,620 MDTraj/xtc/include/xdrfile_xtc.h:37:17: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:41,621 37 | matrix box,rvec *x,float prec); 2021-07-09T16:50:41,621 | ~~~~~~~^~~ 2021-07-09T16:50:41,625 MDTraj/xtc/xtc.c:5555:633: warning: passing argument 6 of ‘write_xtc’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:41,625 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))); 2021-07-09T16:50:41,625 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,625 | | 2021-07-09T16:50:41,625 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:41,626 In file included from MDTraj/xtc/xtc.c:278: 2021-07-09T16:50:41,626 MDTraj/xtc/include/xdrfile_xtc.h:37:27: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:41,626 37 | matrix box,rvec *x,float prec); 2021-07-09T16:50:41,626 | ~~~~~~^ 2021-07-09T16:50:41,688 MDTraj/xtc/xtc.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T16:50:41,693 MDTraj/xtc/xtc.c:8767:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,693 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,693 | ^~ 2021-07-09T16:50:41,697 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,697 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,697 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,698 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:41,698 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:41,698 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,704 MDTraj/xtc/xtc.c:8767:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,704 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,704 | ^~ 2021-07-09T16:50:41,704 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,705 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,705 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,705 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:50:41,705 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:50:41,705 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,711 MDTraj/xtc/xtc.c:8767:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,712 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,712 | ^~ 2021-07-09T16:50:41,712 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,712 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,712 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,713 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:41,713 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:41,713 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,719 MDTraj/xtc/xtc.c:8767:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,719 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,719 | ^~ 2021-07-09T16:50:41,720 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,720 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,720 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,720 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:41,720 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:41,721 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,727 MDTraj/xtc/xtc.c:8767:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,727 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,727 | ^~ 2021-07-09T16:50:41,727 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,727 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,728 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,728 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:50:41,728 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:50:41,728 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,734 MDTraj/xtc/xtc.c:8767:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,734 8767 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,734 | ^~ 2021-07-09T16:50:41,734 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,735 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,735 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,735 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:41,735 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:41,735 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,742 MDTraj/xtc/xtc.c:8780:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,742 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,743 | ^~ 2021-07-09T16:50:41,743 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,743 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,743 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,743 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:41,744 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:41,744 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,749 MDTraj/xtc/xtc.c:8780:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,750 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,750 | ^~ 2021-07-09T16:50:41,750 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,750 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,750 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,751 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:50:41,751 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:50:41,751 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,757 MDTraj/xtc/xtc.c:8780:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,757 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,757 | ^~ 2021-07-09T16:50:41,757 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,757 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,758 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,758 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:41,758 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:41,758 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,764 MDTraj/xtc/xtc.c:8780:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,764 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,764 | ^~ 2021-07-09T16:50:41,765 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,765 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,765 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,765 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:41,765 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:41,765 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,771 MDTraj/xtc/xtc.c:8780:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,771 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,771 | ^~ 2021-07-09T16:50:41,772 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,772 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,772 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,772 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:50:41,772 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:50:41,772 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:41,778 MDTraj/xtc/xtc.c:8780:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:41,778 8780 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:41,779 | ^~ 2021-07-09T16:50:41,779 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:41,779 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:41,779 from MDTraj/xtc/xtc.c:4: 2021-07-09T16:50:41,779 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:41,779 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:41,780 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:42,032 At top level: 2021-07-09T16:50:42,036 MDTraj/xtc/xtc.c:6614:13: warning: ‘__pyx_pw_5numpy_7ndarray_3__releasebuffer__’ defined but not used [-Wunused-function] 2021-07-09T16:50:42,036 6614 | static void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-09T16:50:42,037 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:42,040 MDTraj/xtc/xtc.c:5798:12: warning: ‘__pyx_pw_5numpy_7ndarray_1__getbuffer__’ defined but not used [-Wunused-function] 2021-07-09T16:50:42,041 5798 | static int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-09T16:50:42,041 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:43,902 MDTraj/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_3xtc_17XTCTrajectoryFile_14_write’: 2021-07-09T16:50:43,902 MDTraj/xtc/xtc.c:187:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T16:50:43,903 187 | #define PyInt_FromLong PyLong_FromLong 2021-07-09T16:50:43,903 | ^~~~~~~~~~~~~~~ 2021-07-09T16:50:43,905 MDTraj/xtc/xtc.c:5337:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T16:50:43,906 5337 | int __pyx_v_status; 2021-07-09T16:50:43,906 | ^~~~~~~~~~~~~~ 2021-07-09T16:50:50,498 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 2021-07-09T16:50:50,738 building 'mdtraj.trr' extension 2021-07-09T16:50:50,739 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 2021-07-09T16:50:50,891 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-09T16:50:50,892 MDTraj/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:50,892 478 | while (size >= num && num_of_bits < 32) 2021-07-09T16:50:50,892 | ^~ 2021-07-09T16:50:50,892 MDTraj/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-09T16:50:50,892 MDTraj/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:50,893 524 | while (bytes[num_of_bytes] >= num) 2021-07-09T16:50:50,893 | ^~ 2021-07-09T16:50:50,893 MDTraj/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-09T16:50:50,894 MDTraj/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:50,894 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-09T16:50:50,894 | ^~ 2021-07-09T16:50:50,894 MDTraj/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:50,894 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-09T16:50:50,894 | ^ 2021-07-09T16:50:50,894 MDTraj/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:50,895 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-09T16:50:50,895 | ^ 2021-07-09T16:50:50,895 MDTraj/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-09T16:50:50,895 MDTraj/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:50,895 683 | if (lastbits < num_of_bits) 2021-07-09T16:50:50,895 | ^ 2021-07-09T16:50:50,896 MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-09T16:50:50,897 MDTraj/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:50,897 797 | if(size3>xfp->buf1size) 2021-07-09T16:50:50,897 | ^ 2021-07-09T16:50:50,898 MDTraj/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:50,898 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T16:50:50,902 | ^ 2021-07-09T16:50:50,906 MDTraj/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:50,907 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-09T16:50:50,907 | ^ 2021-07-09T16:50:50,907 MDTraj/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:50,907 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T16:50:50,913 | ^ 2021-07-09T16:50:50,915 MDTraj/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:50,915 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-09T16:50:50,921 | ^ 2021-07-09T16:50:50,927 MDTraj/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:50:50,927 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-09T16:50:50,927 | ^ 2021-07-09T16:50:50,927 MDTraj/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:50:50,928 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); 2021-07-09T16:50:54,947 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:54,947 | | 2021-07-09T16:50:54,947 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:54,948 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T16:50:54,949 MDTraj/xtc/include/xdrfile_trr.h:33:16: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:54,949 33 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T16:50:54,949 | ~~~~~~~^~~ 2021-07-09T16:50:54,951 MDTraj/xtc/trr.c:3827:816: warning: passing argument 7 of ‘read_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:54,951 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); 2021-07-09T16:50:54,951 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:54,951 | | 2021-07-09T16:50:54,952 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:54,952 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T16:50:54,952 MDTraj/xtc/include/xdrfile_trr.h:33:26: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:54,952 33 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T16:50:54,952 | ~~~~~~^ 2021-07-09T16:50:54,968 MDTraj/xtc/trr.c:3912:555: warning: passing argument 6 of ‘read_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:54,968 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); 2021-07-09T16:50:54,968 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:54,968 | | 2021-07-09T16:50:54,968 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:54,969 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T16:50:54,969 MDTraj/xtc/include/xdrfile_trr.h:33:16: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:54,969 33 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T16:50:54,969 | ~~~~~~~^~~ 2021-07-09T16:50:54,970 MDTraj/xtc/trr.c:3912:816: warning: passing argument 7 of ‘read_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:54,970 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); 2021-07-09T16:50:54,971 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:54,971 | | 2021-07-09T16:50:54,971 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:54,971 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T16:50:54,971 MDTraj/xtc/include/xdrfile_trr.h:33:26: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:54,972 33 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T16:50:54,972 | ~~~~~~^ 2021-07-09T16:50:55,040 MDTraj/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_3trr_17TRRTrajectoryFile_14_write’: 2021-07-09T16:50:55,043 MDTraj/xtc/trr.c:5564:528: warning: passing argument 6 of ‘write_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:55,043 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); 2021-07-09T16:50:55,044 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,044 | | 2021-07-09T16:50:55,044 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:55,044 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T16:50:55,044 MDTraj/xtc/include/xdrfile_trr.h:37:17: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:55,044 37 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T16:50:55,044 | ~~~~~~~^~~ 2021-07-09T16:50:55,047 MDTraj/xtc/trr.c:5564:789: warning: passing argument 7 of ‘write_trr’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-09T16:50:55,047 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); 2021-07-09T16:50:55,047 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,047 | | 2021-07-09T16:50:55,048 | __pyx_t_5numpy_float32_t * {aka float *} 2021-07-09T16:50:55,048 In file included from MDTraj/xtc/trr.c:278: 2021-07-09T16:50:55,048 MDTraj/xtc/include/xdrfile_trr.h:37:27: note: expected ‘float (*)[3]’ but argument is of type ‘__pyx_t_5numpy_float32_t *’ {aka ‘float *’} 2021-07-09T16:50:55,048 37 | matrix box,rvec *x,rvec *v,rvec *f); 2021-07-09T16:50:55,048 | ~~~~~~^ 2021-07-09T16:50:55,106 MDTraj/xtc/trr.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T16:50:55,110 MDTraj/xtc/trr.c:8775:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,111 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,111 | ^~ 2021-07-09T16:50:55,113 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,113 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,113 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,113 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:55,113 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:55,113 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,118 MDTraj/xtc/trr.c:8775:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,118 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,119 | ^~ 2021-07-09T16:50:55,119 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,119 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,119 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,119 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:50:55,119 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:50:55,119 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,124 MDTraj/xtc/trr.c:8775:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,124 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,124 | ^~ 2021-07-09T16:50:55,125 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,125 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,125 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,125 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:55,125 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:55,125 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,130 MDTraj/xtc/trr.c:8775:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,130 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,130 | ^~ 2021-07-09T16:50:55,131 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,131 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,131 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,131 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:55,131 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:55,131 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,136 MDTraj/xtc/trr.c:8775:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,136 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,136 | ^~ 2021-07-09T16:50:55,136 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,137 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,137 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,137 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:50:55,137 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:50:55,137 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,142 MDTraj/xtc/trr.c:8775:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,142 8775 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,143 | ^~ 2021-07-09T16:50:55,143 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,143 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,143 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,143 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:55,143 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:55,143 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,149 MDTraj/xtc/trr.c:8788:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,149 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,150 | ^~ 2021-07-09T16:50:55,150 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,150 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,150 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,150 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:55,150 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:55,150 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,155 MDTraj/xtc/trr.c:8788:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,155 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,155 | ^~ 2021-07-09T16:50:55,155 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,156 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,156 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,156 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:50:55,156 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:50:55,156 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,161 MDTraj/xtc/trr.c:8788:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,161 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,161 | ^~ 2021-07-09T16:50:55,161 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,161 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,161 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,162 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:55,162 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:55,162 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,166 MDTraj/xtc/trr.c:8788:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,167 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,167 | ^~ 2021-07-09T16:50:55,167 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,167 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,167 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,167 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:55,167 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:55,168 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,172 MDTraj/xtc/trr.c:8788:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,172 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,172 | ^~ 2021-07-09T16:50:55,173 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,173 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,173 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,173 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:50:55,173 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:50:55,173 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,178 MDTraj/xtc/trr.c:8788:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:50:55,178 8788 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:50:55,178 | ^~ 2021-07-09T16:50:55,179 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:50:55,179 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:50:55,179 from MDTraj/xtc/trr.c:4: 2021-07-09T16:50:55,179 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:50:55,179 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:50:55,179 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,437 At top level: 2021-07-09T16:50:55,441 MDTraj/xtc/trr.c:6623:13: warning: ‘__pyx_pw_5numpy_7ndarray_3__releasebuffer__’ defined but not used [-Wunused-function] 2021-07-09T16:50:55,442 6623 | static void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-09T16:50:55,442 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:55,446 MDTraj/xtc/trr.c:5807:12: warning: ‘__pyx_pw_5numpy_7ndarray_1__getbuffer__’ defined but not used [-Wunused-function] 2021-07-09T16:50:55,446 5807 | static int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-09T16:50:55,446 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:50:57,022 MDTraj/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_3trr_17TRRTrajectoryFile_14_write’: 2021-07-09T16:50:57,022 MDTraj/xtc/trr.c:187:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T16:50:57,022 187 | #define PyInt_FromLong PyLong_FromLong 2021-07-09T16:50:57,022 | ^~~~~~~~~~~~~~~ 2021-07-09T16:50:57,026 MDTraj/xtc/trr.c:5338:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T16:50:57,026 5338 | int __pyx_v_status; 2021-07-09T16:50:57,026 | ^~~~~~~~~~~~~~ 2021-07-09T16:51:03,712 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 2021-07-09T16:51:03,981 building 'mdtraj.dcd' extension 2021-07-09T16:51:03,982 creating build/temp.linux-armv7l-3.9/MDTraj/dcd 2021-07-09T16:51:03,984 creating build/temp.linux-armv7l-3.9/MDTraj/dcd/src 2021-07-09T16:51:03,984 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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 2021-07-09T16:51:04,570 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-09T16:51:04,570 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-09T16:51:04,571 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-09T16:51:04,571 from MDTraj/dcd/dcd.c:275: 2021-07-09T16:51:04,571 /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] 2021-07-09T16:51:04,571 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-09T16:51:04,571 | ^~~~~~~ 2021-07-09T16:51:04,801 MDTraj/dcd/dcd.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T16:51:04,804 MDTraj/dcd/dcd.c:7213:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,804 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,805 | ^~ 2021-07-09T16:51:04,805 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,805 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,805 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,805 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:04,805 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:04,805 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,809 MDTraj/dcd/dcd.c:7213:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,810 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,810 | ^~ 2021-07-09T16:51:04,810 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,810 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,810 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,810 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:51:04,810 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:51:04,810 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,814 MDTraj/dcd/dcd.c:7213:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,814 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,814 | ^~ 2021-07-09T16:51:04,815 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,815 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,815 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,815 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:04,815 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:04,815 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,818 MDTraj/dcd/dcd.c:7213:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,819 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,819 | ^~ 2021-07-09T16:51:04,819 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,819 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,819 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,819 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:04,820 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:04,820 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,823 MDTraj/dcd/dcd.c:7213:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,823 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,823 | ^~ 2021-07-09T16:51:04,823 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,824 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,824 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,824 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:51:04,824 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:51:04,824 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,827 MDTraj/dcd/dcd.c:7213:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,828 7213 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,828 | ^~ 2021-07-09T16:51:04,828 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,828 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,828 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,828 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:04,828 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:04,828 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,833 MDTraj/dcd/dcd.c:7226:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,833 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,833 | ^~ 2021-07-09T16:51:04,833 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,833 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,834 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,834 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:04,834 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:04,834 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,837 MDTraj/dcd/dcd.c:7226:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,837 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,838 | ^~ 2021-07-09T16:51:04,838 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,838 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,838 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,838 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:51:04,838 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:51:04,838 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,842 MDTraj/dcd/dcd.c:7226:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,842 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,842 | ^~ 2021-07-09T16:51:04,842 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,842 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,843 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,843 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:04,843 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:04,843 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,846 MDTraj/dcd/dcd.c:7226:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,846 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,847 | ^~ 2021-07-09T16:51:04,847 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,847 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,847 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,847 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:04,847 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:04,847 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,851 MDTraj/dcd/dcd.c:7226:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,851 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,851 | ^~ 2021-07-09T16:51:04,851 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,852 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,852 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,852 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:51:04,852 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:51:04,852 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:04,855 MDTraj/dcd/dcd.c:7226:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:04,855 7226 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:04,856 | ^~ 2021-07-09T16:51:04,856 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:04,856 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:04,856 from MDTraj/dcd/dcd.c:4: 2021-07-09T16:51:04,856 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:04,856 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:04,857 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:05,050 At top level: 2021-07-09T16:51:05,053 MDTraj/dcd/dcd.c:5200:13: warning: ‘__pyx_pw_5numpy_7ndarray_3__releasebuffer__’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,053 5200 | static void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-09T16:51:05,053 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:05,055 MDTraj/dcd/dcd.c:4384:12: warning: ‘__pyx_pw_5numpy_7ndarray_1__getbuffer__’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,055 4384 | static int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-09T16:51:05,056 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:05,056 In file included from MDTraj/dcd/include/dcdplugin.h:1, 2021-07-09T16:51:05,056 from MDTraj/dcd/dcd.c:277: 2021-07-09T16:51:05,056 MDTraj/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,056 473 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-09T16:51:05,057 | ^~~~~~~~~~~~~ 2021-07-09T16:51:05,057 MDTraj/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,057 469 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-09T16:51:05,057 | ^~~~~~~~~~~~~~ 2021-07-09T16:51:05,057 MDTraj/dcd/include/fastio.h:465:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,057 465 | static int fio_write_int32(fio_fd fd, int i) { 2021-07-09T16:51:05,057 | ^~~~~~~~~~~~~~~ 2021-07-09T16:51:05,058 MDTraj/dcd/include/fastio.h:456:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,058 456 | static fio_size_t fio_ftell(fio_fd fd) { 2021-07-09T16:51:05,058 | ^~~~~~~~~ 2021-07-09T16:51:05,058 MDTraj/dcd/include/fastio.h:449:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,058 449 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { 2021-07-09T16:51:05,058 | ^~~~~~~~~ 2021-07-09T16:51:05,058 MDTraj/dcd/include/fastio.h:414:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,059 414 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { 2021-07-09T16:51:05,059 | ^~~~~~~~~ 2021-07-09T16:51:05,059 MDTraj/dcd/include/fastio.h:393:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,059 393 | static int fio_fclose(fio_fd fd) { 2021-07-09T16:51:05,060 | ^~~~~~~~~~ 2021-07-09T16:51:05,060 MDTraj/dcd/include/fastio.h:365:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2021-07-09T16:51:05,060 365 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2021-07-09T16:51:05,061 | ^~~~~~~~ 2021-07-09T16:51:10,503 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 2021-07-09T16:51:10,744 MDTraj/dcd/src/dcdplugin.c: In function ‘read_dcdheader’: 2021-07-09T16:51:10,745 MDTraj/dcd/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:51:10,745 129 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { 2021-07-09T16:51:10,746 | ^~ 2021-07-09T16:51:10,746 MDTraj/dcd/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:51:10,746 146 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { 2021-07-09T16:51:10,747 | ^~ 2021-07-09T16:51:10,747 MDTraj/dcd/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:51:10,748 164 | if (input_integer[0] != dcdcordmagic) { 2021-07-09T16:51:10,748 | ^~ 2021-07-09T16:51:10,751 MDTraj/dcd/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:51:10,752 341 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { 2021-07-09T16:51:10,752 | ^~ 2021-07-09T16:51:10,753 MDTraj/dcd/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T16:51:10,753 358 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { 2021-07-09T16:51:10,753 | ^~ 2021-07-09T16:51:10,757 MDTraj/dcd/src/dcdplugin.c: In function ‘read_dcdstep’: 2021-07-09T16:51:10,758 MDTraj/dcd/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:51:10,758 540 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-09T16:51:10,758 | ^~ 2021-07-09T16:51:10,759 MDTraj/dcd/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T16:51:10,759 544 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-09T16:51:10,759 | ^~ 2021-07-09T16:51:10,784 In file included from MDTraj/dcd/src/dcdplugin.c:55: 2021-07-09T16:51:10,784 At top level: 2021-07-09T16:51:10,785 MDTraj/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2021-07-09T16:51:10,785 96 | static void swap2_aligned(void *v, long ndata) { 2021-07-09T16:51:10,785 | ^~~~~~~~~~~~~ 2021-07-09T16:51:10,786 MDTraj/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2021-07-09T16:51:10,786 32 | static void swap2_unaligned(void *v, long ndata) { 2021-07-09T16:51:10,786 | ^~~~~~~~~~~~~~~ 2021-07-09T16:51:10,786 In file included from MDTraj/dcd/src/dcdplugin.c:46: 2021-07-09T16:51:10,787 MDTraj/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-09T16:51:10,787 473 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-09T16:51:10,787 | ^~~~~~~~~~~~~ 2021-07-09T16:51:10,787 MDTraj/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-09T16:51:10,787 469 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-09T16:51:10,787 | ^~~~~~~~~~~~~~ 2021-07-09T16:51:12,026 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 2021-07-09T16:51:12,209 building 'mdtraj.binpos' extension 2021-07-09T16:51:12,210 creating build/temp.linux-armv7l-3.9/MDTraj/binpos 2021-07-09T16:51:12,211 creating build/temp.linux-armv7l-3.9/MDTraj/binpos/src 2021-07-09T16:51:12,212 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 2021-07-09T16:51:12,663 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-09T16:51:12,664 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-09T16:51:12,664 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-09T16:51:12,664 from MDTraj/binpos/binpos.c:275: 2021-07-09T16:51:12,664 /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] 2021-07-09T16:51:12,664 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-09T16:51:12,665 | ^~~~~~~ 2021-07-09T16:51:12,844 MDTraj/binpos/binpos.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-09T16:51:12,847 MDTraj/binpos/binpos.c:6451:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,848 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,848 | ^~ 2021-07-09T16:51:12,848 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,848 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,848 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,848 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:12,848 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:12,848 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,852 MDTraj/binpos/binpos.c:6451:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,852 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,852 | ^~ 2021-07-09T16:51:12,852 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,852 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,853 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,853 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:51:12,853 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:51:12,853 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,856 MDTraj/binpos/binpos.c:6451:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,856 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,856 | ^~ 2021-07-09T16:51:12,856 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,857 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,857 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,857 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:12,857 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:12,857 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,860 MDTraj/binpos/binpos.c:6451:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,860 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,860 | ^~ 2021-07-09T16:51:12,860 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,860 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,860 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,860 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:12,861 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:12,861 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,863 MDTraj/binpos/binpos.c:6451:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,864 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,864 | ^~ 2021-07-09T16:51:12,864 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,864 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,864 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,864 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:51:12,864 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:51:12,865 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,867 MDTraj/binpos/binpos.c:6451:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,867 6451 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,868 | ^~ 2021-07-09T16:51:12,868 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,868 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,868 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,868 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:12,868 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:12,868 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,872 MDTraj/binpos/binpos.c:6464:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,872 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,872 | ^~ 2021-07-09T16:51:12,873 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,873 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,873 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,873 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:12,873 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:12,873 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,876 MDTraj/binpos/binpos.c:6464:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,876 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,876 | ^~ 2021-07-09T16:51:12,876 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,877 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,877 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,877 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:51:12,877 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:51:12,877 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,880 MDTraj/binpos/binpos.c:6464:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,880 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,880 | ^~ 2021-07-09T16:51:12,880 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,880 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,880 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,881 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:12,881 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:12,881 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,884 MDTraj/binpos/binpos.c:6464:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,884 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,884 | ^~ 2021-07-09T16:51:12,884 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,884 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,884 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,885 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:12,885 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:12,885 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,887 MDTraj/binpos/binpos.c:6464:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,888 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,888 | ^~ 2021-07-09T16:51:12,888 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,888 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,888 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,888 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-09T16:51:12,888 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-09T16:51:12,889 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:12,891 MDTraj/binpos/binpos.c:6464:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-09T16:51:12,892 6464 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-09T16:51:12,892 | ^~ 2021-07-09T16:51:12,892 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-09T16:51:12,892 from /usr/include/python3.9/Python.h:97, 2021-07-09T16:51:12,892 from MDTraj/binpos/binpos.c:4: 2021-07-09T16:51:12,892 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-09T16:51:12,892 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-09T16:51:12,893 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:13,110 At top level: 2021-07-09T16:51:13,113 MDTraj/binpos/binpos.c:4523:13: warning: ‘__pyx_pw_5numpy_7ndarray_3__releasebuffer__’ defined but not used [-Wunused-function] 2021-07-09T16:51:13,113 4523 | static void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-09T16:51:13,114 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:13,115 MDTraj/binpos/binpos.c:3707:12: warning: ‘__pyx_pw_5numpy_7ndarray_1__getbuffer__’ defined but not used [-Wunused-function] 2021-07-09T16:51:13,116 3707 | static int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-09T16:51:13,116 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:14,751 MDTraj/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_6binpos_20BINPOSTrajectoryFile_7_read’: 2021-07-09T16:51:14,753 MDTraj/binpos/binpos.c:2927:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T16:51:14,753 2927 | if (__pyx_t_1) { 2021-07-09T16:51:14,753 | ^ 2021-07-09T16:51:14,754 MDTraj/binpos/binpos.c:2444:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T16:51:14,754 2444 | int __pyx_v_status; 2021-07-09T16:51:14,754 | ^~~~~~~~~~~~~~ 2021-07-09T16:51:14,755 MDTraj/binpos/binpos.c:211:48: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T16:51:14,755 211 | #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) 2021-07-09T16:51:14,755 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T16:51:14,756 MDTraj/binpos/binpos.c:2441:7: note: ‘__pyx_v_i’ was declared here 2021-07-09T16:51:14,756 2441 | int __pyx_v_i; 2021-07-09T16:51:14,756 | ^~~~~~~~~ 2021-07-09T16:51:17,809 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 2021-07-09T16:51:18,193 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 2021-07-09T16:51:18,329 building 'mdtraj._rmsd' extension 2021-07-09T16:51:18,330 creating build/temp.linux-armv7l-3.9/MDTraj/rmsd 2021-07-09T16:51:18,331 creating build/temp.linux-armv7l-3.9/MDTraj/rmsd/src 2021-07-09T16:51:18,331 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 2021-07-09T16:51:18,347 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’ 2021-07-09T16:51:18,348 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse3’ 2021-07-09T16:51:18,350 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T16:51:18,478 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-09T16:51:18,479 ERROR: Failed building wheel for mdtraj 2021-07-09T16:51:18,480 Running setup.py clean for mdtraj 2021-07-09T16:51:18,480 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-s3v9jj44/mdtraj_c90122473a494ae6bb31d5020b05edd5/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-s3v9jj44/mdtraj_c90122473a494ae6bb31d5020b05edd5/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 2021-07-09T16:51:19,678 running clean 2021-07-09T16:51:19,680 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T16:51:19,692 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T16:51:19,726 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T16:51:19,726 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T16:51:19,726 removing 'build' 2021-07-09T16:51:19,817 Failed to build mdtraj 2021-07-09T16:51:19,817 ERROR: Failed to build one or more wheels 2021-07-09T16:51:19,818 Exception information: 2021-07-09T16:51:19,818 Traceback (most recent call last): 2021-07-09T16:51:19,818 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T16:51:19,818 status = self.run(options, args) 2021-07-09T16:51:19,818 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T16:51:19,818 return func(self, options, args) 2021-07-09T16:51:19,818 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T16:51:19,818 raise CommandError( 2021-07-09T16:51:19,818 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T16:51:19,821 Removed build tracker: '/tmp/pip-req-tracker-_tg3kj10'