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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/) 2021-07-09T16:50:32,762 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/) 2021-07-09T16:50:32,762 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 2021-07-09T16:50:32,762 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 2021-07-09T16:50:32,763 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 2021-07-09T16:50:32,763 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 2021-07-09T16:50:32,763 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 2021-07-09T16:50:32,763 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 2021-07-09T16:50:32,764 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 2021-07-09T16:50:32,764 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 2021-07-09T16:50:32,764 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 2021-07-09T16:50:32,765 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 2021-07-09T16:50:32,765 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 2021-07-09T16:50:32,765 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 2021-07-09T16:50:32,765 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 2021-07-09T16:50:32,766 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 2021-07-09T16:50:32,766 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/) 2021-07-09T16:50:32,767 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/) 2021-07-09T16:50:32,767 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/) 2021-07-09T16:50:32,768 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/) 2021-07-09T16:50:32,768 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 2021-07-09T16:50:32,768 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/) 2021-07-09T16:50:32,769 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/) 2021-07-09T16:50:32,769 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/) 2021-07-09T16:50:32,770 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/) 2021-07-09T16:50:32,770 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 2021-07-09T16:50:32,770 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-09T16:50:32,778 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2021-07-09T16:50:32,796 Collecting mdtraj==0.3 2021-07-09T16:50:32,798 Created temporary directory: /tmp/pip-unpack-vktrct79 2021-07-09T16:50:33,120 Downloading mdtraj-0.3.tar.gz (142 kB) 2021-07-09T16:50:33,344 Added mdtraj==0.3 from https://files.pythonhosted.org/packages/cb/82/93ced2a2e5d37f36330fe3e74081fdd4ce8f933ebd16b4fab14cb5c6c29c/mdtraj-0.3.tar.gz#sha256=4cbd8bbeebacd0fae186244b817edd5dfd7546426fbe7bc2a80002644baa9b8a to build tracker '/tmp/pip-req-tracker-ntms7qpn' 2021-07-09T16:50:33,345 Running setup.py (path:/tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/setup.py) egg_info for package mdtraj 2021-07-09T16:50:33,346 Created temporary directory: /tmp/pip-pip-egg-info-gklp9pq7 2021-07-09T16:50:33,346 Running command python setup.py egg_info 2021-07-09T16:50:34,482 running egg_info 2021-07-09T16:50:34,484 creating /tmp/pip-pip-egg-info-gklp9pq7/mdtraj.egg-info 2021-07-09T16:50:34,485 writing /tmp/pip-pip-egg-info-gklp9pq7/mdtraj.egg-info/PKG-INFO 2021-07-09T16:50:34,488 writing dependency_links to /tmp/pip-pip-egg-info-gklp9pq7/mdtraj.egg-info/dependency_links.txt 2021-07-09T16:50:34,490 writing requirements to /tmp/pip-pip-egg-info-gklp9pq7/mdtraj.egg-info/requires.txt 2021-07-09T16:50:34,491 writing top-level names to /tmp/pip-pip-egg-info-gklp9pq7/mdtraj.egg-info/top_level.txt 2021-07-09T16:50:34,492 writing manifest file '/tmp/pip-pip-egg-info-gklp9pq7/mdtraj.egg-info/SOURCES.txt' 2021-07-09T16:50:34,651 reading manifest file '/tmp/pip-pip-egg-info-gklp9pq7/mdtraj.egg-info/SOURCES.txt' 2021-07-09T16:50:34,656 writing manifest file '/tmp/pip-pip-egg-info-gklp9pq7/mdtraj.egg-info/SOURCES.txt' 2021-07-09T16:50:34,752 Source in /tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241 has version 0.3, which satisfies requirement mdtraj==0.3 from https://files.pythonhosted.org/packages/cb/82/93ced2a2e5d37f36330fe3e74081fdd4ce8f933ebd16b4fab14cb5c6c29c/mdtraj-0.3.tar.gz#sha256=4cbd8bbeebacd0fae186244b817edd5dfd7546426fbe7bc2a80002644baa9b8a 2021-07-09T16:50:34,753 Removed mdtraj==0.3 from https://files.pythonhosted.org/packages/cb/82/93ced2a2e5d37f36330fe3e74081fdd4ce8f933ebd16b4fab14cb5c6c29c/mdtraj-0.3.tar.gz#sha256=4cbd8bbeebacd0fae186244b817edd5dfd7546426fbe7bc2a80002644baa9b8a from build tracker '/tmp/pip-req-tracker-ntms7qpn' 2021-07-09T16:50:34,757 Created temporary directory: /tmp/pip-unpack-6qyfs6tc 2021-07-09T16:50:34,758 Building wheels for collected packages: mdtraj 2021-07-09T16:50:34,762 Created temporary directory: /tmp/pip-wheel-_ovr2moi 2021-07-09T16:50:34,762 Building wheel for mdtraj (setup.py): started 2021-07-09T16:50:34,763 Destination directory: /tmp/pip-wheel-_ovr2moi 2021-07-09T16:50:34,763 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/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-_ovr2moi 2021-07-09T16:50:35,896 running bdist_wheel 2021-07-09T16:50:35,900 running build 2021-07-09T16:50:35,900 running build_py 2021-07-09T16:50:36,036 creating build 2021-07-09T16:50:36,036 creating build/lib.linux-armv7l-3.9 2021-07-09T16:50:36,037 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,038 copying MDTraj/topology.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,040 copying MDTraj/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,043 copying MDTraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,045 copying MDTraj/compatibility.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,047 copying MDTraj/rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,049 copying MDTraj/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,052 copying MDTraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,054 copying MDTraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,056 copying MDTraj/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T16:50:36,059 creating build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:36,060 copying MDTraj/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:36,062 copying MDTraj/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:36,066 copying MDTraj/pdb/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:36,068 copying MDTraj/pdb/element.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:36,070 copying MDTraj/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb 2021-07-09T16:50:36,073 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:36,074 copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:36,077 copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:36,080 copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:36,082 copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:36,084 copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T16:50:36,087 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:36,088 copying MDTraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:36,090 copying MDTraj/utils/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:36,093 copying MDTraj/utils/arrays.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:36,095 copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:36,097 copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:36,100 copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T16:50:36,103 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:36,103 copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:36,105 copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:36,107 copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:36,110 copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:36,112 copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T16:50:36,115 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:36,115 copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:36,117 copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:36,120 copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:36,122 copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:36,124 copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:36,127 copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:36,129 copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T16:50:36,132 creating build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,133 copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,135 copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,138 copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,140 copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,143 copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,146 copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,148 copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,151 copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,153 copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,155 copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,158 copying MDTraj/tests/test_compatibility.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,160 copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,162 copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,164 copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T16:50:36,174 running build_ext 2021-07-09T16:50:36,243 cythoning MDTraj/xtc/xtc.pyx to MDTraj/xtc/xtc.c 2021-07-09T16:50:37,080 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/MDTraj/xtc/xtc.pyx 2021-07-09T16:50:37,081 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T16:50:38,622 Error compiling Cython file: 2021-07-09T16:50:38,623 ------------------------------------------------------------ 2021-07-09T16:50:38,623 ... 2021-07-09T16:50:38,623 cimport cython 2021-07-09T16:50:38,623 import numpy as np 2021-07-09T16:50:38,623 cimport numpy as np 2021-07-09T16:50:38,623 np.import_array() 2021-07-09T16:50:38,623 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:38,624 cimport xdrlib 2021-07-09T16:50:38,624 ^ 2021-07-09T16:50:38,624 ------------------------------------------------------------ 2021-07-09T16:50:38,624 MDTraj/xtc/xtc.pyx:29:8: 'xdrlib.pxd' not found 2021-07-09T16:50:38,624 Error compiling Cython file: 2021-07-09T16:50:38,624 ------------------------------------------------------------ 2021-07-09T16:50:38,625 ... 2021-07-09T16:50:38,625 See Also 2021-07-09T16:50:38,625 -------- 2021-07-09T16:50:38,625 mdtraj.load_xtc : High-level wrapper that returns a ``md.Trajectory`` 2021-07-09T16:50:38,625 """ 2021-07-09T16:50:38,625 cdef xdrlib.XDRFILE* fh 2021-07-09T16:50:38,625 ^ 2021-07-09T16:50:38,626 ------------------------------------------------------------ 2021-07-09T16:50:38,626 MDTraj/xtc/xtc.pyx:109:9: 'XDRFILE' is not a type identifier 2021-07-09T16:50:38,786 Error compiling Cython file: 2021-07-09T16:50:38,787 ------------------------------------------------------------ 2021-07-09T16:50:38,787 ... 2021-07-09T16:50:38,787 if mode == b'r': 2021-07-09T16:50:38,787 self.n_atoms = 0 2021-07-09T16:50:38,787 if not os.path.exists(filename): 2021-07-09T16:50:38,787 raise IOError("The file '%s' doesn't exist" % filename) 2021-07-09T16:50:38,787 xdrlib.read_xtc_natoms(filename, &self.n_atoms) 2021-07-09T16:50:38,788 ^ 2021-07-09T16:50:38,788 ------------------------------------------------------------ 2021-07-09T16:50:38,788 MDTraj/xtc/xtc.pyx:131:18: cimported module has no attribute 'read_xtc_natoms' 2021-07-09T16:50:38,788 Error compiling Cython file: 2021-07-09T16:50:38,788 ------------------------------------------------------------ 2021-07-09T16:50:38,788 ... 2021-07-09T16:50:38,789 xdrlib.read_xtc_natoms(filename, &self.n_atoms) 2021-07-09T16:50:38,789 if self.n_atoms <= 0: 2021-07-09T16:50:38,789 raise IOError('Malformed XTC file. Number of atoms <= 0. ' 2021-07-09T16:50:38,789 'Are you sure this is a valid GROMACS xtc file?') 2021-07-09T16:50:38,789 self.fh = xdrlib.xdrfile_open(filename, b'r') 2021-07-09T16:50:38,789 ^ 2021-07-09T16:50:38,789 ------------------------------------------------------------ 2021-07-09T16:50:38,790 MDTraj/xtc/xtc.pyx:136:28: cimported module has no attribute 'xdrfile_open' 2021-07-09T16:50:38,792 Error compiling Cython file: 2021-07-09T16:50:38,792 ------------------------------------------------------------ 2021-07-09T16:50:38,792 ... 2021-07-09T16:50:38,792 elif mode == b'w': 2021-07-09T16:50:38,792 if force_overwrite and os.path.exists(filename): 2021-07-09T16:50:38,792 os.unlink(filename) 2021-07-09T16:50:38,793 self.fh = xdrlib.xdrfile_open(filename, 'w') 2021-07-09T16:50:38,793 ^ 2021-07-09T16:50:38,793 ------------------------------------------------------------ 2021-07-09T16:50:38,793 MDTraj/xtc/xtc.pyx:149:28: cimported module has no attribute 'xdrfile_open' 2021-07-09T16:50:38,800 Error compiling Cython file: 2021-07-09T16:50:38,800 ------------------------------------------------------------ 2021-07-09T16:50:38,800 ... 2021-07-09T16:50:38,801 def close(self): 2021-07-09T16:50:38,801 "Close the XTC file handle" 2021-07-09T16:50:38,801 if self.is_open: 2021-07-09T16:50:38,801 xdrlib.xdrfile_close(self.fh) 2021-07-09T16:50:38,801 ^ 2021-07-09T16:50:38,801 ------------------------------------------------------------ 2021-07-09T16:50:38,802 MDTraj/xtc/xtc.pyx:184:18: cimported module has no attribute 'xdrfile_close' 2021-07-09T16:50:38,820 Error compiling Cython file: 2021-07-09T16:50:38,820 ------------------------------------------------------------ 2021-07-09T16:50:38,820 ... 2021-07-09T16:50:38,820 cdef np.ndarray[dtype=np.float32_t, ndim=2] framebuffer = np.zeros((self.n_atoms, 3), dtype=np.float32) 2021-07-09T16:50:38,821 while (i < n_frames) and (status != _EXDRENDOFFILE): 2021-07-09T16:50:38,821 if atom_indices is None: 2021-07-09T16:50:38,821 status = xdrlib.read_xtc(self.fh, self.n_atoms, &step[i], 2021-07-09T16:50:38,821 ^ 2021-07-09T16:50:38,821 ------------------------------------------------------------ 2021-07-09T16:50:38,821 MDTraj/xtc/xtc.pyx:291:31: cimported module has no attribute 'read_xtc' 2021-07-09T16:50:38,822 Error compiling Cython file: 2021-07-09T16:50:38,822 ------------------------------------------------------------ 2021-07-09T16:50:38,822 ... 2021-07-09T16:50:38,822 while (i < n_frames) and (status != _EXDRENDOFFILE): 2021-07-09T16:50:38,822 if atom_indices is None: 2021-07-09T16:50:38,822 status = xdrlib.read_xtc(self.fh, self.n_atoms, &step[i], 2021-07-09T16:50:38,822 &time[i], &box[i,0,0], &xyz[i,0,0], &prec[i]) 2021-07-09T16:50:38,822 else: 2021-07-09T16:50:38,823 status = xdrlib.read_xtc(self.fh, self.n_atoms, &step[i], 2021-07-09T16:50:38,823 ^ 2021-07-09T16:50:38,823 ------------------------------------------------------------ 2021-07-09T16:50:38,823 MDTraj/xtc/xtc.pyx:294:31: cimported module has no attribute 'read_xtc' 2021-07-09T16:50:38,842 Error compiling Cython file: 2021-07-09T16:50:38,843 ------------------------------------------------------------ 2021-07-09T16:50:38,843 ... 2021-07-09T16:50:38,843 # all same shape 2021-07-09T16:50:38,843 assert n_frames == len(box) == len(step) == len(time) == len(prec) 2021-07-09T16:50:38,843 for i in range(n_frames): 2021-07-09T16:50:38,843 status = xdrlib.write_xtc(self.fh, n_atoms, step[i], time[i], &box[i, 0, 0], &xyz[i, 0, 0], prec[i]) 2021-07-09T16:50:38,843 ^ 2021-07-09T16:50:38,844 ------------------------------------------------------------ 2021-07-09T16:50:38,844 MDTraj/xtc/xtc.pyx:387:27: cimported module has no attribute 'write_xtc' 2021-07-09T16:50:38,994 cythoning MDTraj/xtc/trr.pyx to MDTraj/xtc/trr.c 2021-07-09T16:50:39,003 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/MDTraj/xtc/trr.pyx 2021-07-09T16:50:39,003 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T16:50:40,476 Error compiling Cython file: 2021-07-09T16:50:40,476 ------------------------------------------------------------ 2021-07-09T16:50:40,476 ... 2021-07-09T16:50:40,476 cimport cython 2021-07-09T16:50:40,476 import numpy as np 2021-07-09T16:50:40,476 cimport numpy as np 2021-07-09T16:50:40,477 np.import_array() 2021-07-09T16:50:40,477 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:40,477 cimport trrlib 2021-07-09T16:50:40,477 ^ 2021-07-09T16:50:40,477 ------------------------------------------------------------ 2021-07-09T16:50:40,477 MDTraj/xtc/trr.pyx:45:8: 'trrlib.pxd' not found 2021-07-09T16:50:40,478 Error compiling Cython file: 2021-07-09T16:50:40,478 ------------------------------------------------------------ 2021-07-09T16:50:40,478 ... 2021-07-09T16:50:40,478 See Also 2021-07-09T16:50:40,478 -------- 2021-07-09T16:50:40,478 mdtraj.load_trr : High-level wrapper that returns a ``md.Trajectory`` 2021-07-09T16:50:40,478 """ 2021-07-09T16:50:40,479 cdef trrlib.XDRFILE* fh 2021-07-09T16:50:40,479 ^ 2021-07-09T16:50:40,479 ------------------------------------------------------------ 2021-07-09T16:50:40,479 MDTraj/xtc/trr.pyx:123:9: 'XDRFILE' is not a type identifier 2021-07-09T16:50:40,633 Error compiling Cython file: 2021-07-09T16:50:40,633 ------------------------------------------------------------ 2021-07-09T16:50:40,633 ... 2021-07-09T16:50:40,634 if mode == b'r': 2021-07-09T16:50:40,634 self.n_atoms = 0 2021-07-09T16:50:40,634 if not os.path.exists(filename): 2021-07-09T16:50:40,634 raise IOError("The file '%s' doesn't exist" % filename) 2021-07-09T16:50:40,634 trrlib.read_trr_natoms(filename, &self.n_atoms) 2021-07-09T16:50:40,634 ^ 2021-07-09T16:50:40,634 ------------------------------------------------------------ 2021-07-09T16:50:40,635 MDTraj/xtc/trr.pyx:145:18: cimported module has no attribute 'read_trr_natoms' 2021-07-09T16:50:40,635 Error compiling Cython file: 2021-07-09T16:50:40,635 ------------------------------------------------------------ 2021-07-09T16:50:40,635 ... 2021-07-09T16:50:40,635 trrlib.read_trr_natoms(filename, &self.n_atoms) 2021-07-09T16:50:40,635 if self.n_atoms <= 0: 2021-07-09T16:50:40,635 raise IOError('Malformed TRR file. Number of atoms <= 0. ' 2021-07-09T16:50:40,635 'Are you sure this is a valid GROMACS TRR file?') 2021-07-09T16:50:40,636 self.fh = trrlib.xdrfile_open(filename, b'r') 2021-07-09T16:50:40,636 ^ 2021-07-09T16:50:40,636 ------------------------------------------------------------ 2021-07-09T16:50:40,636 MDTraj/xtc/trr.pyx:150:28: cimported module has no attribute 'xdrfile_open' 2021-07-09T16:50:40,637 Error compiling Cython file: 2021-07-09T16:50:40,637 ------------------------------------------------------------ 2021-07-09T16:50:40,638 ... 2021-07-09T16:50:40,638 elif mode == b'w': 2021-07-09T16:50:40,638 if force_overwrite and os.path.exists(filename): 2021-07-09T16:50:40,638 os.unlink(filename) 2021-07-09T16:50:40,638 self.fh = trrlib.xdrfile_open(filename, 'w') 2021-07-09T16:50:40,638 ^ 2021-07-09T16:50:40,638 ------------------------------------------------------------ 2021-07-09T16:50:40,639 MDTraj/xtc/trr.pyx:163:28: cimported module has no attribute 'xdrfile_open' 2021-07-09T16:50:40,643 Error compiling Cython file: 2021-07-09T16:50:40,643 ------------------------------------------------------------ 2021-07-09T16:50:40,643 ... 2021-07-09T16:50:40,643 self.close() 2021-07-09T16:50:40,644 def close(self): 2021-07-09T16:50:40,644 """Close the TRR file""" 2021-07-09T16:50:40,644 if self.is_open: 2021-07-09T16:50:40,644 trrlib.xdrfile_close(self.fh) 2021-07-09T16:50:40,644 ^ 2021-07-09T16:50:40,644 ------------------------------------------------------------ 2021-07-09T16:50:40,644 MDTraj/xtc/trr.pyx:188:18: cimported module has no attribute 'xdrfile_close' 2021-07-09T16:50:40,662 Error compiling Cython file: 2021-07-09T16:50:40,662 ------------------------------------------------------------ 2021-07-09T16:50:40,662 ... 2021-07-09T16:50:40,663 while (i < n_frames) and (status != _EXDRENDOFFILE): 2021-07-09T16:50:40,663 if atom_indices is None: 2021-07-09T16:50:40,663 status = trrlib.read_trr(self.fh, self.n_atoms, &step[i], &time[i], &lambd[i], 2021-07-09T16:50:40,663 ^ 2021-07-09T16:50:40,663 ------------------------------------------------------------ 2021-07-09T16:50:40,663 MDTraj/xtc/trr.pyx:302:31: cimported module has no attribute 'read_trr' 2021-07-09T16:50:40,664 Error compiling Cython file: 2021-07-09T16:50:40,664 ------------------------------------------------------------ 2021-07-09T16:50:40,664 ... 2021-07-09T16:50:40,664 while (i < n_frames) and (status != _EXDRENDOFFILE): 2021-07-09T16:50:40,664 if atom_indices is None: 2021-07-09T16:50:40,664 status = trrlib.read_trr(self.fh, self.n_atoms, &step[i], &time[i], &lambd[i], 2021-07-09T16:50:40,664 &box[i,0,0], &xyz[i,0,0], NULL, NULL) 2021-07-09T16:50:40,665 else: 2021-07-09T16:50:40,665 status = trrlib.read_trr(self.fh, self.n_atoms, &step[i], &time[i], &lambd[i], 2021-07-09T16:50:40,665 ^ 2021-07-09T16:50:40,665 ------------------------------------------------------------ 2021-07-09T16:50:40,665 MDTraj/xtc/trr.pyx:305:31: cimported module has no attribute 'read_trr' 2021-07-09T16:50:40,685 Error compiling Cython file: 2021-07-09T16:50:40,685 ------------------------------------------------------------ 2021-07-09T16:50:40,685 ... 2021-07-09T16:50:40,686 # all same length 2021-07-09T16:50:40,686 assert n_frames == len(box) == len(step) == len(time) == len(lambd) 2021-07-09T16:50:40,686 for i in range(n_frames): 2021-07-09T16:50:40,686 status = trrlib.write_trr(self.fh, n_atoms, step[i], time[i], lambd[i], 2021-07-09T16:50:40,686 ^ 2021-07-09T16:50:40,686 ------------------------------------------------------------ 2021-07-09T16:50:40,687 MDTraj/xtc/trr.pyx:401:27: cimported module has no attribute 'write_trr' 2021-07-09T16:50:40,838 cythoning MDTraj/dcd/dcd.pyx to MDTraj/dcd/dcd.c 2021-07-09T16:50:40,846 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/MDTraj/dcd/dcd.pyx 2021-07-09T16:50:40,847 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T16:50:41,021 warning: MDTraj/dcd/dcd.pyx:303:8: Unreachable code 2021-07-09T16:50:42,373 Error compiling Cython file: 2021-07-09T16:50:42,373 ------------------------------------------------------------ 2021-07-09T16:50:42,373 ... 2021-07-09T16:50:42,373 import numpy as np 2021-07-09T16:50:42,373 cimport numpy as np 2021-07-09T16:50:42,374 np.import_array() 2021-07-09T16:50:42,374 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,374 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,374 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,374 ^ 2021-07-09T16:50:42,374 ------------------------------------------------------------ 2021-07-09T16:50:42,374 MDTraj/dcd/dcd.pyx:29:0: 'dcdlib.pxd' not found 2021-07-09T16:50:42,379 Error compiling Cython file: 2021-07-09T16:50:42,379 ------------------------------------------------------------ 2021-07-09T16:50:42,379 ... 2021-07-09T16:50:42,379 import numpy as np 2021-07-09T16:50:42,379 cimport numpy as np 2021-07-09T16:50:42,379 np.import_array() 2021-07-09T16:50:42,380 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,380 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,380 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,380 ^ 2021-07-09T16:50:42,380 ------------------------------------------------------------ 2021-07-09T16:50:42,380 MDTraj/dcd/dcd.pyx:29:0: 'dcdlib/molfile_timestep_t.pxd' not found 2021-07-09T16:50:42,382 Error compiling Cython file: 2021-07-09T16:50:42,383 ------------------------------------------------------------ 2021-07-09T16:50:42,383 ... 2021-07-09T16:50:42,383 import numpy as np 2021-07-09T16:50:42,383 cimport numpy as np 2021-07-09T16:50:42,383 np.import_array() 2021-07-09T16:50:42,383 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,383 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,384 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,384 ^ 2021-07-09T16:50:42,384 ------------------------------------------------------------ 2021-07-09T16:50:42,384 MDTraj/dcd/dcd.pyx:29:0: 'dcdlib/dcdhandle.pxd' not found 2021-07-09T16:50:42,387 Error compiling Cython file: 2021-07-09T16:50:42,387 ------------------------------------------------------------ 2021-07-09T16:50:42,387 ... 2021-07-09T16:50:42,387 cimport numpy as np 2021-07-09T16:50:42,387 np.import_array() 2021-07-09T16:50:42,388 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,388 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,388 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,388 from dcdlib cimport open_dcd_read, close_file_read, read_next_timestep 2021-07-09T16:50:42,388 ^ 2021-07-09T16:50:42,388 ------------------------------------------------------------ 2021-07-09T16:50:42,389 MDTraj/dcd/dcd.pyx:30:0: 'dcdlib/open_dcd_read.pxd' not found 2021-07-09T16:50:42,391 Error compiling Cython file: 2021-07-09T16:50:42,391 ------------------------------------------------------------ 2021-07-09T16:50:42,391 ... 2021-07-09T16:50:42,391 cimport numpy as np 2021-07-09T16:50:42,391 np.import_array() 2021-07-09T16:50:42,391 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,391 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,392 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,392 from dcdlib cimport open_dcd_read, close_file_read, read_next_timestep 2021-07-09T16:50:42,392 ^ 2021-07-09T16:50:42,392 ------------------------------------------------------------ 2021-07-09T16:50:42,392 MDTraj/dcd/dcd.pyx:30:0: 'dcdlib/close_file_read.pxd' not found 2021-07-09T16:50:42,395 Error compiling Cython file: 2021-07-09T16:50:42,395 ------------------------------------------------------------ 2021-07-09T16:50:42,395 ... 2021-07-09T16:50:42,395 cimport numpy as np 2021-07-09T16:50:42,396 np.import_array() 2021-07-09T16:50:42,396 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,396 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,396 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,396 from dcdlib cimport open_dcd_read, close_file_read, read_next_timestep 2021-07-09T16:50:42,396 ^ 2021-07-09T16:50:42,396 ------------------------------------------------------------ 2021-07-09T16:50:42,397 MDTraj/dcd/dcd.pyx:30:0: 'dcdlib/read_next_timestep.pxd' not found 2021-07-09T16:50:42,399 Error compiling Cython file: 2021-07-09T16:50:42,399 ------------------------------------------------------------ 2021-07-09T16:50:42,400 ... 2021-07-09T16:50:42,400 np.import_array() 2021-07-09T16:50:42,400 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,400 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,400 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,400 from dcdlib cimport open_dcd_read, close_file_read, read_next_timestep 2021-07-09T16:50:42,400 from dcdlib cimport open_dcd_write, close_file_write, write_timestep 2021-07-09T16:50:42,401 ^ 2021-07-09T16:50:42,401 ------------------------------------------------------------ 2021-07-09T16:50:42,401 MDTraj/dcd/dcd.pyx:31:0: 'dcdlib/open_dcd_write.pxd' not found 2021-07-09T16:50:42,403 Error compiling Cython file: 2021-07-09T16:50:42,403 ------------------------------------------------------------ 2021-07-09T16:50:42,403 ... 2021-07-09T16:50:42,404 np.import_array() 2021-07-09T16:50:42,404 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,404 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,404 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,404 from dcdlib cimport open_dcd_read, close_file_read, read_next_timestep 2021-07-09T16:50:42,404 from dcdlib cimport open_dcd_write, close_file_write, write_timestep 2021-07-09T16:50:42,405 ^ 2021-07-09T16:50:42,405 ------------------------------------------------------------ 2021-07-09T16:50:42,405 MDTraj/dcd/dcd.pyx:31:0: 'dcdlib/close_file_write.pxd' not found 2021-07-09T16:50:42,407 Error compiling Cython file: 2021-07-09T16:50:42,407 ------------------------------------------------------------ 2021-07-09T16:50:42,407 ... 2021-07-09T16:50:42,408 np.import_array() 2021-07-09T16:50:42,408 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:42,408 from libc.stdlib cimport malloc, free 2021-07-09T16:50:42,408 from dcdlib cimport molfile_timestep_t, dcdhandle 2021-07-09T16:50:42,408 from dcdlib cimport open_dcd_read, close_file_read, read_next_timestep 2021-07-09T16:50:42,408 from dcdlib cimport open_dcd_write, close_file_write, write_timestep 2021-07-09T16:50:42,408 ^ 2021-07-09T16:50:42,409 ------------------------------------------------------------ 2021-07-09T16:50:42,409 MDTraj/dcd/dcd.pyx:31:0: 'dcdlib/write_timestep.pxd' not found 2021-07-09T16:50:42,409 Error compiling Cython file: 2021-07-09T16:50:42,409 ------------------------------------------------------------ 2021-07-09T16:50:42,409 ... 2021-07-09T16:50:42,410 """ 2021-07-09T16:50:42,410 # n_atoms and n_frames hold the number of atoms and the number of frames 2021-07-09T16:50:42,410 # in the file, as read off the header of the DCD file during read mode 2021-07-09T16:50:42,410 cdef int frame_counter, n_atoms, n_frames 2021-07-09T16:50:42,410 cdef dcdhandle* fh 2021-07-09T16:50:42,410 ^ 2021-07-09T16:50:42,411 ------------------------------------------------------------ 2021-07-09T16:50:42,411 MDTraj/dcd/dcd.pyx:111:9: 'dcdhandle' is not a type identifier 2021-07-09T16:50:42,411 Error compiling Cython file: 2021-07-09T16:50:42,411 ------------------------------------------------------------ 2021-07-09T16:50:42,411 ... 2021-07-09T16:50:42,412 cdef int frame_counter, n_atoms, n_frames 2021-07-09T16:50:42,412 cdef dcdhandle* fh 2021-07-09T16:50:42,412 cdef char* mode 2021-07-09T16:50:42,412 cdef char* filename 2021-07-09T16:50:42,412 cdef int is_open, _needs_write_initialization 2021-07-09T16:50:42,412 cdef molfile_timestep_t* timestep 2021-07-09T16:50:42,412 ^ 2021-07-09T16:50:42,413 ------------------------------------------------------------ 2021-07-09T16:50:42,413 MDTraj/dcd/dcd.pyx:115:9: 'molfile_timestep_t' is not a type identifier 2021-07-09T16:50:42,528 Error compiling Cython file: 2021-07-09T16:50:42,528 ------------------------------------------------------------ 2021-07-09T16:50:42,528 ... 2021-07-09T16:50:42,528 """ 2021-07-09T16:50:42,529 self.distance_unit = 'angstroms' 2021-07-09T16:50:42,529 self.is_open = False 2021-07-09T16:50:42,529 if mode == b'r': 2021-07-09T16:50:42,529 self.fh = open_dcd_read(filename, "dcd", &self.n_atoms, &self.n_frames) 2021-07-09T16:50:42,529 ^ 2021-07-09T16:50:42,529 ------------------------------------------------------------ 2021-07-09T16:50:42,529 MDTraj/dcd/dcd.pyx:125:22: 'open_dcd_read' is not a constant, variable or function identifier 2021-07-09T16:50:42,530 Error compiling Cython file: 2021-07-09T16:50:42,530 ------------------------------------------------------------ 2021-07-09T16:50:42,530 ... 2021-07-09T16:50:42,530 """ 2021-07-09T16:50:42,530 self.distance_unit = 'angstroms' 2021-07-09T16:50:42,530 self.is_open = False 2021-07-09T16:50:42,531 if mode == b'r': 2021-07-09T16:50:42,531 self.fh = open_dcd_read(filename, "dcd", &self.n_atoms, &self.n_frames) 2021-07-09T16:50:42,531 ^ 2021-07-09T16:50:42,531 ------------------------------------------------------------ 2021-07-09T16:50:42,531 MDTraj/dcd/dcd.pyx:125:53: Cannot convert 'int *' to Python object 2021-07-09T16:50:42,531 Error compiling Cython file: 2021-07-09T16:50:42,531 ------------------------------------------------------------ 2021-07-09T16:50:42,532 ... 2021-07-09T16:50:42,532 """ 2021-07-09T16:50:42,532 self.distance_unit = 'angstroms' 2021-07-09T16:50:42,532 self.is_open = False 2021-07-09T16:50:42,532 if mode == b'r': 2021-07-09T16:50:42,532 self.fh = open_dcd_read(filename, "dcd", &self.n_atoms, &self.n_frames) 2021-07-09T16:50:42,532 ^ 2021-07-09T16:50:42,532 ------------------------------------------------------------ 2021-07-09T16:50:42,533 MDTraj/dcd/dcd.pyx:125:68: Cannot convert 'int *' to Python object 2021-07-09T16:50:42,533 Error compiling Cython file: 2021-07-09T16:50:42,533 ------------------------------------------------------------ 2021-07-09T16:50:42,533 ... 2021-07-09T16:50:42,533 else: 2021-07-09T16:50:42,533 raise ValueError("most must be one of ['r', 'w']") 2021-07-09T16:50:42,534 # alloc the molfile_timestep, which is the struct that the library is 2021-07-09T16:50:42,534 # going to deposit its data into each timestep 2021-07-09T16:50:42,534 self.timestep = malloc(sizeof(molfile_timestep_t)) 2021-07-09T16:50:42,534 ^ 2021-07-09T16:50:42,534 ------------------------------------------------------------ 2021-07-09T16:50:42,534 MDTraj/dcd/dcd.pyx:143:25: 'molfile_timestep_t' is not a type identifier 2021-07-09T16:50:42,534 Error compiling Cython file: 2021-07-09T16:50:42,535 ------------------------------------------------------------ 2021-07-09T16:50:42,535 ... 2021-07-09T16:50:42,535 else: 2021-07-09T16:50:42,535 raise ValueError("most must be one of ['r', 'w']") 2021-07-09T16:50:42,535 # alloc the molfile_timestep, which is the struct that the library is 2021-07-09T16:50:42,535 # going to deposit its data into each timestep 2021-07-09T16:50:42,535 self.timestep = malloc(sizeof(molfile_timestep_t)) 2021-07-09T16:50:42,536 ^ 2021-07-09T16:50:42,536 ------------------------------------------------------------ 2021-07-09T16:50:42,536 MDTraj/dcd/dcd.pyx:143:78: 'molfile_timestep_t' is not a constant, variable or function identifier 2021-07-09T16:50:42,536 Error compiling Cython file: 2021-07-09T16:50:42,536 ------------------------------------------------------------ 2021-07-09T16:50:42,536 ... 2021-07-09T16:50:42,537 is delayed until the first call to write() 2021-07-09T16:50:42,537 """ 2021-07-09T16:50:42,537 assert not self.is_open and self._needs_write_initialization 2021-07-09T16:50:42,537 self.n_atoms = n_atoms 2021-07-09T16:50:42,537 self.fh = open_dcd_write(self.filename, "dcd", self.n_atoms) 2021-07-09T16:50:42,537 ^ 2021-07-09T16:50:42,537 ------------------------------------------------------------ 2021-07-09T16:50:42,538 MDTraj/dcd/dcd.pyx:162:18: 'open_dcd_write' is not a constant, variable or function identifier 2021-07-09T16:50:42,538 Error compiling Cython file: 2021-07-09T16:50:42,538 ------------------------------------------------------------ 2021-07-09T16:50:42,538 ... 2021-07-09T16:50:42,539 def close(self): 2021-07-09T16:50:42,539 "Close the DCD file handle" 2021-07-09T16:50:42,539 if self.is_open and self.fh is not NULL: 2021-07-09T16:50:42,539 if self.mode == b'r': 2021-07-09T16:50:42,539 close_file_read(self.fh) 2021-07-09T16:50:42,539 ^ 2021-07-09T16:50:42,539 ------------------------------------------------------------ 2021-07-09T16:50:42,540 MDTraj/dcd/dcd.pyx:173:16: 'close_file_read' is not a constant, variable or function identifier 2021-07-09T16:50:42,540 Error compiling Cython file: 2021-07-09T16:50:42,540 ------------------------------------------------------------ 2021-07-09T16:50:42,540 ... 2021-07-09T16:50:42,540 "Close the DCD file handle" 2021-07-09T16:50:42,540 if self.is_open and self.fh is not NULL: 2021-07-09T16:50:42,540 if self.mode == b'r': 2021-07-09T16:50:42,541 close_file_read(self.fh) 2021-07-09T16:50:42,541 else: 2021-07-09T16:50:42,541 close_file_write(self.fh) 2021-07-09T16:50:42,541 ^ 2021-07-09T16:50:42,541 ------------------------------------------------------------ 2021-07-09T16:50:42,541 MDTraj/dcd/dcd.pyx:175:16: 'close_file_write' is not a constant, variable or function identifier 2021-07-09T16:50:42,549 Error compiling Cython file: 2021-07-09T16:50:42,549 ------------------------------------------------------------ 2021-07-09T16:50:42,549 ... 2021-07-09T16:50:42,549 cdef int i, j 2021-07-09T16:50:42,549 cdef int status = _DCD_SUCCESS 2021-07-09T16:50:42,549 for i in range(_n_frames): 2021-07-09T16:50:42,549 if atom_indices is None: 2021-07-09T16:50:42,550 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:42,550 ^ 2021-07-09T16:50:42,550 ------------------------------------------------------------ 2021-07-09T16:50:42,550 MDTraj/dcd/dcd.pyx:264:39: Cannot convert 'float32_t *' to Python object 2021-07-09T16:50:42,550 Error compiling Cython file: 2021-07-09T16:50:42,550 ------------------------------------------------------------ 2021-07-09T16:50:42,550 ... 2021-07-09T16:50:42,551 cdef int status = _DCD_SUCCESS 2021-07-09T16:50:42,551 for i in range(_n_frames): 2021-07-09T16:50:42,551 if atom_indices is None: 2021-07-09T16:50:42,551 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:42,551 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:42,551 ^ 2021-07-09T16:50:42,551 ------------------------------------------------------------ 2021-07-09T16:50:42,552 MDTraj/dcd/dcd.pyx:265:25: 'read_next_timestep' is not a constant, variable or function identifier 2021-07-09T16:50:42,552 Error compiling Cython file: 2021-07-09T16:50:42,552 ------------------------------------------------------------ 2021-07-09T16:50:42,552 ... 2021-07-09T16:50:42,552 for i in range(_n_frames): 2021-07-09T16:50:42,552 if atom_indices is None: 2021-07-09T16:50:42,552 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:42,553 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:42,553 else: 2021-07-09T16:50:42,553 self.timestep.coords = &framebuffer[0,0] 2021-07-09T16:50:42,553 ^ 2021-07-09T16:50:42,553 ------------------------------------------------------------ 2021-07-09T16:50:42,553 MDTraj/dcd/dcd.pyx:267:39: Cannot convert 'float32_t *' to Python object 2021-07-09T16:50:42,553 Error compiling Cython file: 2021-07-09T16:50:42,554 ------------------------------------------------------------ 2021-07-09T16:50:42,554 ... 2021-07-09T16:50:42,554 if atom_indices is None: 2021-07-09T16:50:42,554 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:42,554 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:42,554 else: 2021-07-09T16:50:42,554 self.timestep.coords = &framebuffer[0,0] 2021-07-09T16:50:42,554 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:42,554 ^ 2021-07-09T16:50:42,555 ------------------------------------------------------------ 2021-07-09T16:50:42,555 MDTraj/dcd/dcd.pyx:268:25: 'read_next_timestep' is not a constant, variable or function identifier 2021-07-09T16:50:42,555 Error compiling Cython file: 2021-07-09T16:50:42,555 ------------------------------------------------------------ 2021-07-09T16:50:42,555 ... 2021-07-09T16:50:42,555 if status != _DCD_SUCCESS: 2021-07-09T16:50:42,555 # if the frame was not successfully read, then we're done 2021-07-09T16:50:42,556 break 2021-07-09T16:50:42,556 for j in range(_stride - 1): 2021-07-09T16:50:42,556 status = read_next_timestep(self.fh, self.n_atoms, NULL) 2021-07-09T16:50:42,556 ^ 2021-07-09T16:50:42,556 ------------------------------------------------------------ 2021-07-09T16:50:42,556 MDTraj/dcd/dcd.pyx:284:25: 'read_next_timestep' is not a constant, variable or function identifier 2021-07-09T16:50:42,557 Error compiling Cython file: 2021-07-09T16:50:42,557 ------------------------------------------------------------ 2021-07-09T16:50:42,557 ... 2021-07-09T16:50:42,557 if status != _DCD_SUCCESS: 2021-07-09T16:50:42,557 # if the frame was not successfully read, then we're done 2021-07-09T16:50:42,557 break 2021-07-09T16:50:42,557 for j in range(_stride - 1): 2021-07-09T16:50:42,557 status = read_next_timestep(self.fh, self.n_atoms, NULL) 2021-07-09T16:50:42,558 ^ 2021-07-09T16:50:42,558 ------------------------------------------------------------ 2021-07-09T16:50:42,558 MDTraj/dcd/dcd.pyx:284:67: Cannot convert 'void *' to Python object 2021-07-09T16:50:42,570 Error compiling Cython file: 2021-07-09T16:50:42,570 ------------------------------------------------------------ 2021-07-09T16:50:42,570 ... 2021-07-09T16:50:42,570 cdef int i, status 2021-07-09T16:50:42,570 cdef int n_frames = len(xyz) 2021-07-09T16:50:42,570 for i in range(n_frames): 2021-07-09T16:50:42,571 self.timestep.coords = &xyz[i, 0, 0] 2021-07-09T16:50:42,571 ^ 2021-07-09T16:50:42,571 ------------------------------------------------------------ 2021-07-09T16:50:42,571 MDTraj/dcd/dcd.pyx:368:35: Cannot convert 'float32_t *' to Python object 2021-07-09T16:50:42,571 Error compiling Cython file: 2021-07-09T16:50:42,571 ------------------------------------------------------------ 2021-07-09T16:50:42,572 ... 2021-07-09T16:50:42,572 self.timestep.C = cell_lengths[i, 2] 2021-07-09T16:50:42,572 self.timestep.alpha = cell_angles[i, 0] 2021-07-09T16:50:42,572 self.timestep.beta = cell_angles[i, 1] 2021-07-09T16:50:42,572 self.timestep.gamma = cell_angles[i, 2] 2021-07-09T16:50:42,572 status = write_timestep(self.fh, self.timestep) 2021-07-09T16:50:42,572 ^ 2021-07-09T16:50:42,572 ------------------------------------------------------------ 2021-07-09T16:50:42,573 MDTraj/dcd/dcd.pyx:376:21: 'write_timestep' is not a constant, variable or function identifier 2021-07-09T16:50:42,698 cythoning MDTraj/binpos/binpos.pyx to MDTraj/binpos/binpos.c 2021-07-09T16:50:42,707 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/MDTraj/binpos/binpos.pyx 2021-07-09T16:50:42,708 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T16:50:44,090 Error compiling Cython file: 2021-07-09T16:50:44,090 ------------------------------------------------------------ 2021-07-09T16:50:44,090 ... 2021-07-09T16:50:44,090 import numpy as np 2021-07-09T16:50:44,091 cimport numpy as np 2021-07-09T16:50:44,091 np.import_array() 2021-07-09T16:50:44,091 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:44,091 from libc.stdlib cimport malloc, free 2021-07-09T16:50:44,091 from binposlib cimport molfile_timestep_t 2021-07-09T16:50:44,091 ^ 2021-07-09T16:50:44,091 ------------------------------------------------------------ 2021-07-09T16:50:44,092 MDTraj/binpos/binpos.pyx:30:0: 'binposlib.pxd' not found 2021-07-09T16:50:44,098 Error compiling Cython file: 2021-07-09T16:50:44,098 ------------------------------------------------------------ 2021-07-09T16:50:44,098 ... 2021-07-09T16:50:44,098 import numpy as np 2021-07-09T16:50:44,098 cimport numpy as np 2021-07-09T16:50:44,099 np.import_array() 2021-07-09T16:50:44,099 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:44,099 from libc.stdlib cimport malloc, free 2021-07-09T16:50:44,099 from binposlib cimport molfile_timestep_t 2021-07-09T16:50:44,099 ^ 2021-07-09T16:50:44,099 ------------------------------------------------------------ 2021-07-09T16:50:44,100 MDTraj/binpos/binpos.pyx:30:0: 'binposlib/molfile_timestep_t.pxd' not found 2021-07-09T16:50:44,103 Error compiling Cython file: 2021-07-09T16:50:44,103 ------------------------------------------------------------ 2021-07-09T16:50:44,104 ... 2021-07-09T16:50:44,104 cimport numpy as np 2021-07-09T16:50:44,104 np.import_array() 2021-07-09T16:50:44,104 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:44,104 from libc.stdlib cimport malloc, free 2021-07-09T16:50:44,104 from binposlib cimport molfile_timestep_t 2021-07-09T16:50:44,104 from binposlib cimport open_binpos_read, close_file_read, read_next_timestep 2021-07-09T16:50:44,105 ^ 2021-07-09T16:50:44,105 ------------------------------------------------------------ 2021-07-09T16:50:44,105 MDTraj/binpos/binpos.pyx:31:0: 'binposlib/open_binpos_read.pxd' not found 2021-07-09T16:50:44,108 Error compiling Cython file: 2021-07-09T16:50:44,108 ------------------------------------------------------------ 2021-07-09T16:50:44,109 ... 2021-07-09T16:50:44,109 cimport numpy as np 2021-07-09T16:50:44,109 np.import_array() 2021-07-09T16:50:44,109 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:44,109 from libc.stdlib cimport malloc, free 2021-07-09T16:50:44,109 from binposlib cimport molfile_timestep_t 2021-07-09T16:50:44,109 from binposlib cimport open_binpos_read, close_file_read, read_next_timestep 2021-07-09T16:50:44,110 ^ 2021-07-09T16:50:44,110 ------------------------------------------------------------ 2021-07-09T16:50:44,110 MDTraj/binpos/binpos.pyx:31:0: 'binposlib/close_file_read.pxd' not found 2021-07-09T16:50:44,114 Error compiling Cython file: 2021-07-09T16:50:44,114 ------------------------------------------------------------ 2021-07-09T16:50:44,114 ... 2021-07-09T16:50:44,114 cimport numpy as np 2021-07-09T16:50:44,114 np.import_array() 2021-07-09T16:50:44,114 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:44,114 from libc.stdlib cimport malloc, free 2021-07-09T16:50:44,115 from binposlib cimport molfile_timestep_t 2021-07-09T16:50:44,115 from binposlib cimport open_binpos_read, close_file_read, read_next_timestep 2021-07-09T16:50:44,115 ^ 2021-07-09T16:50:44,115 ------------------------------------------------------------ 2021-07-09T16:50:44,115 MDTraj/binpos/binpos.pyx:31:0: 'binposlib/read_next_timestep.pxd' not found 2021-07-09T16:50:44,120 Error compiling Cython file: 2021-07-09T16:50:44,121 ------------------------------------------------------------ 2021-07-09T16:50:44,121 ... 2021-07-09T16:50:44,121 np.import_array() 2021-07-09T16:50:44,121 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:44,121 from libc.stdlib cimport malloc, free 2021-07-09T16:50:44,121 from binposlib cimport molfile_timestep_t 2021-07-09T16:50:44,122 from binposlib cimport open_binpos_read, close_file_read, read_next_timestep 2021-07-09T16:50:44,122 from binposlib cimport open_binpos_write, close_file_write, write_timestep 2021-07-09T16:50:44,122 ^ 2021-07-09T16:50:44,122 ------------------------------------------------------------ 2021-07-09T16:50:44,122 MDTraj/binpos/binpos.pyx:32:0: 'binposlib/open_binpos_write.pxd' not found 2021-07-09T16:50:44,126 Error compiling Cython file: 2021-07-09T16:50:44,126 ------------------------------------------------------------ 2021-07-09T16:50:44,126 ... 2021-07-09T16:50:44,126 np.import_array() 2021-07-09T16:50:44,126 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:44,127 from libc.stdlib cimport malloc, free 2021-07-09T16:50:44,127 from binposlib cimport molfile_timestep_t 2021-07-09T16:50:44,127 from binposlib cimport open_binpos_read, close_file_read, read_next_timestep 2021-07-09T16:50:44,127 from binposlib cimport open_binpos_write, close_file_write, write_timestep 2021-07-09T16:50:44,127 ^ 2021-07-09T16:50:44,128 ------------------------------------------------------------ 2021-07-09T16:50:44,128 MDTraj/binpos/binpos.pyx:32:0: 'binposlib/close_file_write.pxd' not found 2021-07-09T16:50:44,131 Error compiling Cython file: 2021-07-09T16:50:44,131 ------------------------------------------------------------ 2021-07-09T16:50:44,131 ... 2021-07-09T16:50:44,132 np.import_array() 2021-07-09T16:50:44,132 from mdtraj.utils.arrays import ensure_type 2021-07-09T16:50:44,132 from libc.stdlib cimport malloc, free 2021-07-09T16:50:44,132 from binposlib cimport molfile_timestep_t 2021-07-09T16:50:44,132 from binposlib cimport open_binpos_read, close_file_read, read_next_timestep 2021-07-09T16:50:44,132 from binposlib cimport open_binpos_write, close_file_write, write_timestep 2021-07-09T16:50:44,133 ^ 2021-07-09T16:50:44,133 ------------------------------------------------------------ 2021-07-09T16:50:44,133 MDTraj/binpos/binpos.pyx:32:0: 'binposlib/write_timestep.pxd' not found 2021-07-09T16:50:44,133 Error compiling Cython file: 2021-07-09T16:50:44,134 ------------------------------------------------------------ 2021-07-09T16:50:44,134 ... 2021-07-09T16:50:44,134 cdef char* filename 2021-07-09T16:50:44,134 cdef int write_initialized 2021-07-09T16:50:44,134 cdef readonly char* distance_unit 2021-07-09T16:50:44,134 cdef void* fh 2021-07-09T16:50:44,135 cdef molfile_timestep_t* timestep 2021-07-09T16:50:44,135 ^ 2021-07-09T16:50:44,135 ------------------------------------------------------------ 2021-07-09T16:50:44,135 MDTraj/binpos/binpos.pyx:104:9: 'molfile_timestep_t' is not a type identifier 2021-07-09T16:50:44,232 Error compiling Cython file: 2021-07-09T16:50:44,232 ------------------------------------------------------------ 2021-07-09T16:50:44,233 ... 2021-07-09T16:50:44,233 if mode == b'r': 2021-07-09T16:50:44,233 self.n_atoms = 0 2021-07-09T16:50:44,233 if not os.path.exists(filename): 2021-07-09T16:50:44,233 raise IOError("The file '%s' doesn't exist" % filename) 2021-07-09T16:50:44,233 self.fh = open_binpos_read(filename, "binpos", &self.n_atoms) 2021-07-09T16:50:44,233 ^ 2021-07-09T16:50:44,234 ------------------------------------------------------------ 2021-07-09T16:50:44,234 MDTraj/binpos/binpos.pyx:117:22: 'open_binpos_read' is not a constant, variable or function identifier 2021-07-09T16:50:44,234 Error compiling Cython file: 2021-07-09T16:50:44,234 ------------------------------------------------------------ 2021-07-09T16:50:44,234 ... 2021-07-09T16:50:44,235 if mode == b'r': 2021-07-09T16:50:44,235 self.n_atoms = 0 2021-07-09T16:50:44,235 if not os.path.exists(filename): 2021-07-09T16:50:44,235 raise IOError("The file '%s' doesn't exist" % filename) 2021-07-09T16:50:44,235 self.fh = open_binpos_read(filename, "binpos", &self.n_atoms) 2021-07-09T16:50:44,235 ^ 2021-07-09T16:50:44,235 ------------------------------------------------------------ 2021-07-09T16:50:44,235 MDTraj/binpos/binpos.pyx:117:59: Cannot convert 'int *' to Python object 2021-07-09T16:50:44,236 Error compiling Cython file: 2021-07-09T16:50:44,236 ------------------------------------------------------------ 2021-07-09T16:50:44,236 ... 2021-07-09T16:50:44,236 if mode == b'r': 2021-07-09T16:50:44,236 self.n_atoms = 0 2021-07-09T16:50:44,236 if not os.path.exists(filename): 2021-07-09T16:50:44,236 raise IOError("The file '%s' doesn't exist" % filename) 2021-07-09T16:50:44,237 self.fh = open_binpos_read(filename, "binpos", &self.n_atoms) 2021-07-09T16:50:44,237 ^ 2021-07-09T16:50:44,237 ------------------------------------------------------------ 2021-07-09T16:50:44,237 MDTraj/binpos/binpos.pyx:117:38: Cannot convert Python object to 'void *' 2021-07-09T16:50:44,237 Error compiling Cython file: 2021-07-09T16:50:44,237 ------------------------------------------------------------ 2021-07-09T16:50:44,237 ... 2021-07-09T16:50:44,238 if mode == b'r': 2021-07-09T16:50:44,238 self.n_atoms = 0 2021-07-09T16:50:44,238 if not os.path.exists(filename): 2021-07-09T16:50:44,238 raise IOError("The file '%s' doesn't exist" % filename) 2021-07-09T16:50:44,238 self.fh = open_binpos_read(filename, "binpos", &self.n_atoms) 2021-07-09T16:50:44,238 ^ 2021-07-09T16:50:44,238 ------------------------------------------------------------ 2021-07-09T16:50:44,239 MDTraj/binpos/binpos.pyx:117:38: Storing unsafe C derivative of temporary Python reference 2021-07-09T16:50:44,239 Error compiling Cython file: 2021-07-09T16:50:44,239 ------------------------------------------------------------ 2021-07-09T16:50:44,239 ... 2021-07-09T16:50:44,239 elif mode == b'w': 2021-07-09T16:50:44,239 self.write_initialized = False 2021-07-09T16:50:44,239 else: 2021-07-09T16:50:44,240 raise ValueError('mode must be one of "r" or "w". you supplied "%s"' % mode) 2021-07-09T16:50:44,240 self.timestep = malloc(sizeof(molfile_timestep_t)) 2021-07-09T16:50:44,240 ^ 2021-07-09T16:50:44,240 ------------------------------------------------------------ 2021-07-09T16:50:44,240 MDTraj/binpos/binpos.pyx:138:25: 'molfile_timestep_t' is not a type identifier 2021-07-09T16:50:44,240 Error compiling Cython file: 2021-07-09T16:50:44,241 ------------------------------------------------------------ 2021-07-09T16:50:44,241 ... 2021-07-09T16:50:44,241 elif mode == b'w': 2021-07-09T16:50:44,241 self.write_initialized = False 2021-07-09T16:50:44,241 else: 2021-07-09T16:50:44,241 raise ValueError('mode must be one of "r" or "w". you supplied "%s"' % mode) 2021-07-09T16:50:44,241 self.timestep = malloc(sizeof(molfile_timestep_t)) 2021-07-09T16:50:44,241 ^ 2021-07-09T16:50:44,242 ------------------------------------------------------------ 2021-07-09T16:50:44,242 MDTraj/binpos/binpos.pyx:138:78: 'molfile_timestep_t' is not a constant, variable or function identifier 2021-07-09T16:50:44,242 Error compiling Cython file: 2021-07-09T16:50:44,242 ------------------------------------------------------------ 2021-07-09T16:50:44,242 ... 2021-07-09T16:50:44,243 self.filename = filename 2021-07-09T16:50:44,243 self.mode = mode 2021-07-09T16:50:44,243 def _initialize_write(self, n_atoms): 2021-07-09T16:50:44,243 self.fh = open_binpos_write(self.filename, "binpos", n_atoms) 2021-07-09T16:50:44,243 ^ 2021-07-09T16:50:44,243 ------------------------------------------------------------ 2021-07-09T16:50:44,243 MDTraj/binpos/binpos.pyx:149:18: 'open_binpos_write' is not a constant, variable or function identifier 2021-07-09T16:50:44,244 Error compiling Cython file: 2021-07-09T16:50:44,244 ------------------------------------------------------------ 2021-07-09T16:50:44,244 ... 2021-07-09T16:50:44,244 self.filename = filename 2021-07-09T16:50:44,244 self.mode = mode 2021-07-09T16:50:44,244 def _initialize_write(self, n_atoms): 2021-07-09T16:50:44,245 self.fh = open_binpos_write(self.filename, "binpos", n_atoms) 2021-07-09T16:50:44,245 ^ 2021-07-09T16:50:44,245 ------------------------------------------------------------ 2021-07-09T16:50:44,245 MDTraj/binpos/binpos.pyx:149:35: Cannot convert Python object to 'void *' 2021-07-09T16:50:44,245 Error compiling Cython file: 2021-07-09T16:50:44,245 ------------------------------------------------------------ 2021-07-09T16:50:44,245 ... 2021-07-09T16:50:44,246 self.filename = filename 2021-07-09T16:50:44,246 self.mode = mode 2021-07-09T16:50:44,246 def _initialize_write(self, n_atoms): 2021-07-09T16:50:44,246 self.fh = open_binpos_write(self.filename, "binpos", n_atoms) 2021-07-09T16:50:44,246 ^ 2021-07-09T16:50:44,246 ------------------------------------------------------------ 2021-07-09T16:50:44,247 MDTraj/binpos/binpos.pyx:149:35: Storing unsafe C derivative of temporary Python reference 2021-07-09T16:50:44,253 Error compiling Cython file: 2021-07-09T16:50:44,254 ------------------------------------------------------------ 2021-07-09T16:50:44,254 ... 2021-07-09T16:50:44,254 cdef np.ndarray[dtype=np.float32_t, ndim=3] xyz = np.zeros((n_frames, n_atoms_to_read, 3), dtype=np.float32) 2021-07-09T16:50:44,254 for i in range(n_frames): 2021-07-09T16:50:44,254 if atom_indices is None: 2021-07-09T16:50:44,254 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:44,254 ^ 2021-07-09T16:50:44,255 ------------------------------------------------------------ 2021-07-09T16:50:44,255 MDTraj/binpos/binpos.pyx:221:39: Cannot convert 'float32_t *' to Python object 2021-07-09T16:50:44,255 Error compiling Cython file: 2021-07-09T16:50:44,255 ------------------------------------------------------------ 2021-07-09T16:50:44,255 ... 2021-07-09T16:50:44,255 cdef np.ndarray[dtype=np.float32_t, ndim=3] xyz = np.zeros((n_frames, n_atoms_to_read, 3), dtype=np.float32) 2021-07-09T16:50:44,256 for i in range(n_frames): 2021-07-09T16:50:44,256 if atom_indices is None: 2021-07-09T16:50:44,256 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:44,256 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:44,256 ^ 2021-07-09T16:50:44,256 ------------------------------------------------------------ 2021-07-09T16:50:44,256 MDTraj/binpos/binpos.pyx:222:25: 'read_next_timestep' is not a constant, variable or function identifier 2021-07-09T16:50:44,257 Error compiling Cython file: 2021-07-09T16:50:44,257 ------------------------------------------------------------ 2021-07-09T16:50:44,257 ... 2021-07-09T16:50:44,257 cdef np.ndarray[dtype=np.float32_t, ndim=3] xyz = np.zeros((n_frames, n_atoms_to_read, 3), dtype=np.float32) 2021-07-09T16:50:44,257 for i in range(n_frames): 2021-07-09T16:50:44,257 if atom_indices is None: 2021-07-09T16:50:44,257 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:44,257 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:44,258 ^ 2021-07-09T16:50:44,258 ------------------------------------------------------------ 2021-07-09T16:50:44,258 MDTraj/binpos/binpos.pyx:222:48: Cannot convert 'void *' to Python object 2021-07-09T16:50:44,258 Error compiling Cython file: 2021-07-09T16:50:44,258 ------------------------------------------------------------ 2021-07-09T16:50:44,258 ... 2021-07-09T16:50:44,258 for i in range(n_frames): 2021-07-09T16:50:44,259 if atom_indices is None: 2021-07-09T16:50:44,259 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:44,259 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:44,259 else: 2021-07-09T16:50:44,259 self.timestep.coords = &framebuffer[0, 0] 2021-07-09T16:50:44,259 ^ 2021-07-09T16:50:44,259 ------------------------------------------------------------ 2021-07-09T16:50:44,259 MDTraj/binpos/binpos.pyx:224:39: Cannot convert 'float32_t *' to Python object 2021-07-09T16:50:44,260 Error compiling Cython file: 2021-07-09T16:50:44,260 ------------------------------------------------------------ 2021-07-09T16:50:44,260 ... 2021-07-09T16:50:44,260 if atom_indices is None: 2021-07-09T16:50:44,260 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:44,260 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:44,260 else: 2021-07-09T16:50:44,260 self.timestep.coords = &framebuffer[0, 0] 2021-07-09T16:50:44,261 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:44,261 ^ 2021-07-09T16:50:44,261 ------------------------------------------------------------ 2021-07-09T16:50:44,261 MDTraj/binpos/binpos.pyx:225:25: 'read_next_timestep' is not a constant, variable or function identifier 2021-07-09T16:50:44,261 Error compiling Cython file: 2021-07-09T16:50:44,261 ------------------------------------------------------------ 2021-07-09T16:50:44,261 ... 2021-07-09T16:50:44,262 if atom_indices is None: 2021-07-09T16:50:44,262 self.timestep.coords = &xyz[i,0,0] 2021-07-09T16:50:44,262 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:44,262 else: 2021-07-09T16:50:44,262 self.timestep.coords = &framebuffer[0, 0] 2021-07-09T16:50:44,262 status = read_next_timestep(self.fh, self.n_atoms, self.timestep) 2021-07-09T16:50:44,262 ^ 2021-07-09T16:50:44,262 ------------------------------------------------------------ 2021-07-09T16:50:44,263 MDTraj/binpos/binpos.pyx:225:48: Cannot convert 'void *' to Python object 2021-07-09T16:50:44,263 Error compiling Cython file: 2021-07-09T16:50:44,263 ------------------------------------------------------------ 2021-07-09T16:50:44,264 ... 2021-07-09T16:50:44,264 def _write(self, np.ndarray[dtype=np.float32_t, ndim=3] xyz not None): 2021-07-09T16:50:44,264 cdef int i, status 2021-07-09T16:50:44,264 cdef int n_frames = len(xyz) 2021-07-09T16:50:44,264 for i in range(n_frames): 2021-07-09T16:50:44,264 self.timestep.coords = &xyz[i, 0, 0] 2021-07-09T16:50:44,264 ^ 2021-07-09T16:50:44,265 ------------------------------------------------------------ 2021-07-09T16:50:44,265 MDTraj/binpos/binpos.pyx:265:35: Cannot convert 'float32_t *' to Python object 2021-07-09T16:50:44,265 Error compiling Cython file: 2021-07-09T16:50:44,265 ------------------------------------------------------------ 2021-07-09T16:50:44,265 ... 2021-07-09T16:50:44,265 cdef int i, status 2021-07-09T16:50:44,265 cdef int n_frames = len(xyz) 2021-07-09T16:50:44,266 for i in range(n_frames): 2021-07-09T16:50:44,266 self.timestep.coords = &xyz[i, 0, 0] 2021-07-09T16:50:44,266 status = write_timestep(self.fh, self.timestep) 2021-07-09T16:50:44,266 ^ 2021-07-09T16:50:44,266 ------------------------------------------------------------ 2021-07-09T16:50:44,266 MDTraj/binpos/binpos.pyx:266:21: 'write_timestep' is not a constant, variable or function identifier 2021-07-09T16:50:44,267 Error compiling Cython file: 2021-07-09T16:50:44,267 ------------------------------------------------------------ 2021-07-09T16:50:44,267 ... 2021-07-09T16:50:44,267 cdef int i, status 2021-07-09T16:50:44,267 cdef int n_frames = len(xyz) 2021-07-09T16:50:44,267 for i in range(n_frames): 2021-07-09T16:50:44,267 self.timestep.coords = &xyz[i, 0, 0] 2021-07-09T16:50:44,268 status = write_timestep(self.fh, self.timestep) 2021-07-09T16:50:44,268 ^ 2021-07-09T16:50:44,268 ------------------------------------------------------------ 2021-07-09T16:50:44,268 MDTraj/binpos/binpos.pyx:266:40: Cannot convert 'void *' to Python object 2021-07-09T16:50:44,268 Error compiling Cython file: 2021-07-09T16:50:44,268 ------------------------------------------------------------ 2021-07-09T16:50:44,268 ... 2021-07-09T16:50:44,269 def close(self): 2021-07-09T16:50:44,269 """Close the BINPOS file""" 2021-07-09T16:50:44,269 if self.is_open: 2021-07-09T16:50:44,269 if self.mode == b'r': 2021-07-09T16:50:44,269 close_file_read(self.fh) 2021-07-09T16:50:44,269 ^ 2021-07-09T16:50:44,269 ------------------------------------------------------------ 2021-07-09T16:50:44,270 MDTraj/binpos/binpos.pyx:275:16: 'close_file_read' is not a constant, variable or function identifier 2021-07-09T16:50:44,270 Error compiling Cython file: 2021-07-09T16:50:44,270 ------------------------------------------------------------ 2021-07-09T16:50:44,270 ... 2021-07-09T16:50:44,270 def close(self): 2021-07-09T16:50:44,270 """Close the BINPOS file""" 2021-07-09T16:50:44,270 if self.is_open: 2021-07-09T16:50:44,271 if self.mode == b'r': 2021-07-09T16:50:44,271 close_file_read(self.fh) 2021-07-09T16:50:44,271 ^ 2021-07-09T16:50:44,271 ------------------------------------------------------------ 2021-07-09T16:50:44,271 MDTraj/binpos/binpos.pyx:275:36: Cannot convert 'void *' to Python object 2021-07-09T16:50:44,271 Error compiling Cython file: 2021-07-09T16:50:44,271 ------------------------------------------------------------ 2021-07-09T16:50:44,272 ... 2021-07-09T16:50:44,272 """Close the BINPOS file""" 2021-07-09T16:50:44,272 if self.is_open: 2021-07-09T16:50:44,272 if self.mode == b'r': 2021-07-09T16:50:44,272 close_file_read(self.fh) 2021-07-09T16:50:44,272 else: 2021-07-09T16:50:44,272 close_file_write(self.fh) 2021-07-09T16:50:44,272 ^ 2021-07-09T16:50:44,273 ------------------------------------------------------------ 2021-07-09T16:50:44,273 MDTraj/binpos/binpos.pyx:277:16: 'close_file_write' is not a constant, variable or function identifier 2021-07-09T16:50:44,273 Error compiling Cython file: 2021-07-09T16:50:44,273 ------------------------------------------------------------ 2021-07-09T16:50:44,273 ... 2021-07-09T16:50:44,273 """Close the BINPOS file""" 2021-07-09T16:50:44,273 if self.is_open: 2021-07-09T16:50:44,273 if self.mode == b'r': 2021-07-09T16:50:44,274 close_file_read(self.fh) 2021-07-09T16:50:44,274 else: 2021-07-09T16:50:44,274 close_file_write(self.fh) 2021-07-09T16:50:44,274 ^ 2021-07-09T16:50:44,274 ------------------------------------------------------------ 2021-07-09T16:50:44,274 MDTraj/binpos/binpos.pyx:277:37: Cannot convert 'void *' to Python object 2021-07-09T16:50:44,362 cythoning MDTraj/rmsd/_rmsd.pyx to MDTraj/rmsd/_rmsd.c 2021-07-09T16:50:44,372 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/MDTraj/rmsd/_rmsd.pyx 2021-07-09T16:50:44,372 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T16:50:47,248 building 'mdtraj.xtc' extension 2021-07-09T16:50:47,249 creating build/temp.linux-armv7l-3.9 2021-07-09T16:50:47,249 creating build/temp.linux-armv7l-3.9/MDTraj 2021-07-09T16:50:47,250 creating build/temp.linux-armv7l-3.9/MDTraj/xtc 2021-07-09T16:50:47,251 creating build/temp.linux-armv7l-3.9/MDTraj/xtc/src 2021-07-09T16:50:47,251 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 2021-07-09T16:50:47,431 MDTraj/xtc/src/xdrfile.c:39:10: fatal error: xdrfile.h: No such file or directory 2021-07-09T16:50:47,432 39 | #include "xdrfile.h" 2021-07-09T16:50:47,432 | ^~~~~~~~~~~ 2021-07-09T16:50:47,432 compilation terminated. 2021-07-09T16:50:47,435 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T16:50:47,689 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-09T16:50:47,689 ERROR: Failed building wheel for mdtraj 2021-07-09T16:50:47,690 Running setup.py clean for mdtraj 2021-07-09T16:50:47,690 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-qfapig3l/mdtraj_6175a7944f91466a97a8272fcc85f241/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 2021-07-09T16:50:49,015 running clean 2021-07-09T16:50:49,017 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T16:50:49,023 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T16:50:49,056 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T16:50:49,057 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T16:50:49,057 removing 'build' 2021-07-09T16:50:49,154 Failed to build mdtraj 2021-07-09T16:50:49,154 ERROR: Failed to build one or more wheels 2021-07-09T16:50:49,155 Exception information: 2021-07-09T16:50:49,155 Traceback (most recent call last): 2021-07-09T16:50:49,155 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T16:50:49,155 status = self.run(options, args) 2021-07-09T16:50:49,155 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T16:50:49,155 return func(self, options, args) 2021-07-09T16:50:49,155 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T16:50:49,155 raise CommandError( 2021-07-09T16:50:49,155 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T16:50:49,162 Removed build tracker: '/tmp/pip-req-tracker-ntms7qpn'