2023-10-16T09:06:45,224 Created temporary directory: /tmp/pip-build-tracker-v5lhwghk
2023-10-16T09:06:45,226 Initialized build tracking at /tmp/pip-build-tracker-v5lhwghk
2023-10-16T09:06:45,226 Created build tracker: /tmp/pip-build-tracker-v5lhwghk
2023-10-16T09:06:45,226 Entered build tracker: /tmp/pip-build-tracker-v5lhwghk
2023-10-16T09:06:45,227 Created temporary directory: /tmp/pip-wheel-9pdhgzqa
2023-10-16T09:06:45,230 Created temporary directory: /tmp/pip-ephem-wheel-cache-pc9vr29b
2023-10-16T09:06:45,253 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-10-16T09:06:45,257 2 location(s) to search for versions of adaptivepele:
2023-10-16T09:06:45,257 * https://pypi.org/simple/adaptivepele/
2023-10-16T09:06:45,257 * https://www.piwheels.org/simple/adaptivepele/
2023-10-16T09:06:45,258 Fetching project page and analyzing links: https://pypi.org/simple/adaptivepele/
2023-10-16T09:06:45,259 Getting page https://pypi.org/simple/adaptivepele/
2023-10-16T09:06:45,260 Found index url https://pypi.org/simple/
2023-10-16T09:06:45,479 Fetched page https://pypi.org/simple/adaptivepele/ as application/vnd.pypi.simple.v1+json
2023-10-16T09:06:45,481   Found link https://files.pythonhosted.org/packages/33/ee/476a691d254663e61362e5c2754180ff0b92980e6db1afc829265f001706/AdaptivePELE-1.5.1.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.5.1
2023-10-16T09:06:45,482   Found link https://files.pythonhosted.org/packages/d9/82/be65cbae39642401f6e6923e5511fd466d107920ee9673bb84581a243a4e/AdaptivePELE-1.5.2.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.5.2
2023-10-16T09:06:45,483   Found link https://files.pythonhosted.org/packages/48/3b/f12bfdcfd7f0fdcb2f58d659ff94c26666767eec4ca8454750a3241c395e/AdaptivePELE-1.6.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.6
2023-10-16T09:06:45,483   Found link https://files.pythonhosted.org/packages/d0/1b/f731952d133f4a684ae4376f67513af80d1f759b9ef4d6137767e0fc8ed9/AdaptivePELE-1.6.2.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.6.2
2023-10-16T09:06:45,484   Found link https://files.pythonhosted.org/packages/25/2c/65b787dc210294855b8f27abeb4a7761f25fce34e0b8bfd56779c679440d/AdaptivePELE-1.6.3.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.6.3
2023-10-16T09:06:45,485   Found link https://files.pythonhosted.org/packages/2b/34/d4545814438fa2992d83f5be0389f6465ab3e542ada0c02f90dbc4cc5695/AdaptivePELE-1.7.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.7
2023-10-16T09:06:45,486   Found link https://files.pythonhosted.org/packages/21/7d/8c8eb27cbe21dfcfbf80d5f16c889ee2d5bf0eec8dd8bcd03567d06bef98/AdaptivePELE-1.7.1.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.7.1
2023-10-16T09:06:45,486   Found link https://files.pythonhosted.org/packages/d2/2a/993f92a15fee18f51f48793e865e2626d51c441ba7ec4565480fad4391d6/AdaptivePELE-1.7.4.tar.gz (from https://pypi.org/simple/adaptivepele/), version: 1.7.4
2023-10-16T09:06:45,487 Fetching project page and analyzing links: https://www.piwheels.org/simple/adaptivepele/
2023-10-16T09:06:45,488 Getting page https://www.piwheels.org/simple/adaptivepele/
2023-10-16T09:06:45,489 Found index url https://www.piwheels.org/simple/
2023-10-16T09:06:45,655 Fetched page https://www.piwheels.org/simple/adaptivepele/ as text/html
2023-10-16T09:06:45,664   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp39-cp39-linux_armv7l.whl#sha256=8ba47dab67ab6fbd1e1bd022bdee1d4de408ec335fecc88108e7a3d295f378e9 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,665   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp39-cp39-linux_armv6l.whl#sha256=8ba47dab67ab6fbd1e1bd022bdee1d4de408ec335fecc88108e7a3d295f378e9 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,665   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp37-cp37m-linux_armv7l.whl#sha256=3292b60b31353aeff2e1832f504c186c202729cba0948d5ed44a194fab7eb63d (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,666   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp37-cp37m-linux_armv6l.whl#sha256=3292b60b31353aeff2e1832f504c186c202729cba0948d5ed44a194fab7eb63d (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,667   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp35-cp35m-linux_armv7l.whl#sha256=0208e16fec704fe2c144f233c3bcad9bd699844776c4d69a84cbeea650e527cf (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,667   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7.1-cp35-cp35m-linux_armv6l.whl#sha256=0208e16fec704fe2c144f233c3bcad9bd699844776c4d69a84cbeea650e527cf (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,668   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7-cp37-cp37m-linux_armv7l.whl#sha256=9ceafd1bdad9148abd951ec26b53c062af8565c6ed7df8a4833b0a5b1af150b6 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,668   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7-cp37-cp37m-linux_armv6l.whl#sha256=9ceafd1bdad9148abd951ec26b53c062af8565c6ed7df8a4833b0a5b1af150b6 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,669   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7-cp35-cp35m-linux_armv7l.whl#sha256=68bfb28f19f03bbd0d90143f2e191708ad9d2541088ece0035c08b89001d3f02 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,669   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.7-cp35-cp35m-linux_armv6l.whl#sha256=68bfb28f19f03bbd0d90143f2e191708ad9d2541088ece0035c08b89001d3f02 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,670   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.3-cp37-cp37m-linux_armv7l.whl#sha256=fc72f5016a0826fbe3b3a251f574c128cfffc1e1080f6ef21d32ae9134214087 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,670   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.3-cp37-cp37m-linux_armv6l.whl#sha256=fc72f5016a0826fbe3b3a251f574c128cfffc1e1080f6ef21d32ae9134214087 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,671   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.3-cp35-cp35m-linux_armv7l.whl#sha256=843a4ba6b03c34f08d3926f9c672ffecbe27f2d3a031f4e04cfba5ab92bf081b (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,671   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.3-cp35-cp35m-linux_armv6l.whl#sha256=843a4ba6b03c34f08d3926f9c672ffecbe27f2d3a031f4e04cfba5ab92bf081b (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,672   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp34-cp34m-linux_armv6l.whl#sha256=4f4aaf9237f2698965935feac86131663c03ebcf1f93aec451b35f8ce80d4c09 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,672   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp34-cp34m-linux_armv7l.whl#sha256=4f4aaf9237f2698965935feac86131663c03ebcf1f93aec451b35f8ce80d4c09 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,673   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp35-cp35m-linux_armv6l.whl#sha256=36de6189a08732016ffd1c173924fa40f32b8ff581b3fe9ef9593c21a09c2a1e (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,674   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp35-cp35m-linux_armv7l.whl#sha256=36de6189a08732016ffd1c173924fa40f32b8ff581b3fe9ef9593c21a09c2a1e (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,675   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp37-cp37m-linux_armv6l.whl#sha256=a444a2d3065cfad76489b3dff07638244e394ee86317ad4f9f738963ae9412e1 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,675   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6.2-cp37-cp37m-linux_armv7l.whl#sha256=a444a2d3065cfad76489b3dff07638244e394ee86317ad4f9f738963ae9412e1 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,675   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6-cp34-cp34m-linux_armv6l.whl#sha256=bb8b9f8f462d1c73c4a799c01c4e9913f7f3047d5b536180b305caaaa283e0d8 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,676   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6-cp34-cp34m-linux_armv7l.whl#sha256=bb8b9f8f462d1c73c4a799c01c4e9913f7f3047d5b536180b305caaaa283e0d8 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,676   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6-cp35-cp35m-linux_armv6l.whl#sha256=be4d1c98b4b7053819231567db9e10f930245d5dbcd03c764cfedc72479568ae (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,677   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.6-cp35-cp35m-linux_armv7l.whl#sha256=be4d1c98b4b7053819231567db9e10f930245d5dbcd03c764cfedc72479568ae (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,678   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp34-cp34m-linux_armv6l.whl#sha256=803d5b49a0992dd6aab76657a4fd7da709ba29ae19ef407b3c263abcfa9cef71 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,678   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp34-cp34m-linux_armv7l.whl#sha256=803d5b49a0992dd6aab76657a4fd7da709ba29ae19ef407b3c263abcfa9cef71 (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,679   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp35-cp35m-linux_armv7l.whl#sha256=7bee2048d0a5a4bf74907584a5db700ec2fe7aa35a7682a87c05ad5e92d00c5f (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,679   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.2-cp35-cp35m-linux_armv6l.whl#sha256=7bee2048d0a5a4bf74907584a5db700ec2fe7aa35a7682a87c05ad5e92d00c5f (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,680   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.1-cp35-cp35m-linux_armv6l.whl#sha256=11454cd28dbb1fac72eedb48155487d4e6a36fe5bf4ba70d1df2f81984690f5f (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,680   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.1-cp35-cp35m-linux_armv7l.whl#sha256=11454cd28dbb1fac72eedb48155487d4e6a36fe5bf4ba70d1df2f81984690f5f (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,681   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.1-cp34-cp34m-linux_armv7l.whl#sha256=ae482fbe798dddf382cbba7468496c022b12752804d218c198b78c1183e5342a (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,682   Skipping link: No binaries permitted for adaptivepele: https://www.piwheels.org/simple/adaptivepele/AdaptivePELE-1.5.1-cp34-cp34m-linux_armv6l.whl#sha256=ae482fbe798dddf382cbba7468496c022b12752804d218c198b78c1183e5342a (from https://www.piwheels.org/simple/adaptivepele/)
2023-10-16T09:06:45,682 Skipping link: not a file: https://www.piwheels.org/simple/adaptivepele/
2023-10-16T09:06:45,683 Skipping link: not a file: https://pypi.org/simple/adaptivepele/
2023-10-16T09:06:45,702 Given no hashes to check 1 links for project 'adaptivepele': discarding no candidates
2023-10-16T09:06:45,720 Collecting adaptivepele==1.7.4
2023-10-16T09:06:45,722   Created temporary directory: /tmp/pip-unpack-vsv93ouq
2023-10-16T09:06:45,938   Downloading AdaptivePELE-1.7.4.tar.gz (219 kB)
2023-10-16T09:06:46,286   Added adaptivepele==1.7.4 from https://files.pythonhosted.org/packages/d2/2a/993f92a15fee18f51f48793e865e2626d51c441ba7ec4565480fad4391d6/AdaptivePELE-1.7.4.tar.gz to build tracker '/tmp/pip-build-tracker-v5lhwghk'
2023-10-16T09:06:46,288   Running setup.py (path:/tmp/pip-wheel-9pdhgzqa/adaptivepele_1b2729e943984970bad4b01533c692a0/setup.py) egg_info for package adaptivepele
2023-10-16T09:06:46,289   Created temporary directory: /tmp/pip-pip-egg-info-65vf_we_
2023-10-16T09:06:46,289   Preparing metadata (setup.py): started
2023-10-16T09:06:46,290   Running command python setup.py egg_info
2023-10-16T09:06:47,263   Warning: 'classifiers' should be a list, got type 'tuple'
2023-10-16T09:06:47,638   running egg_info
2023-10-16T09:06:47,640   creating /tmp/pip-pip-egg-info-65vf_we_/AdaptivePELE.egg-info
2023-10-16T09:06:47,666   writing /tmp/pip-pip-egg-info-65vf_we_/AdaptivePELE.egg-info/PKG-INFO
2023-10-16T09:06:47,670   writing dependency_links to /tmp/pip-pip-egg-info-65vf_we_/AdaptivePELE.egg-info/dependency_links.txt
2023-10-16T09:06:47,672   writing requirements to /tmp/pip-pip-egg-info-65vf_we_/AdaptivePELE.egg-info/requires.txt
2023-10-16T09:06:47,673   writing top-level names to /tmp/pip-pip-egg-info-65vf_we_/AdaptivePELE.egg-info/top_level.txt
2023-10-16T09:06:47,674   writing manifest file '/tmp/pip-pip-egg-info-65vf_we_/AdaptivePELE.egg-info/SOURCES.txt'
2023-10-16T09:06:47,763   reading manifest file '/tmp/pip-pip-egg-info-65vf_we_/AdaptivePELE.egg-info/SOURCES.txt'
2023-10-16T09:06:47,764   reading manifest template 'MANIFEST.in'
2023-10-16T09:06:47,776   warning: no files found matching 'utils.c' under directory 'AdaptivePELE/freeEnergies'
2023-10-16T09:06:47,783   warning: no files found matching 'utils*.so' under directory 'AdaptivePELE/freeEnergies'
2023-10-16T09:06:47,784   adding license file 'LICENSE'
2023-10-16T09:06:47,789   writing manifest file '/tmp/pip-pip-egg-info-65vf_we_/AdaptivePELE.egg-info/SOURCES.txt'
2023-10-16T09:06:47,932   Preparing metadata (setup.py): finished with status 'done'
2023-10-16T09:06:47,936   Source in /tmp/pip-wheel-9pdhgzqa/adaptivepele_1b2729e943984970bad4b01533c692a0 has version 1.7.4, which satisfies requirement adaptivepele==1.7.4 from https://files.pythonhosted.org/packages/d2/2a/993f92a15fee18f51f48793e865e2626d51c441ba7ec4565480fad4391d6/AdaptivePELE-1.7.4.tar.gz
2023-10-16T09:06:47,937   Removed adaptivepele==1.7.4 from https://files.pythonhosted.org/packages/d2/2a/993f92a15fee18f51f48793e865e2626d51c441ba7ec4565480fad4391d6/AdaptivePELE-1.7.4.tar.gz from build tracker '/tmp/pip-build-tracker-v5lhwghk'
2023-10-16T09:06:47,942 Created temporary directory: /tmp/pip-unpack-wne7qpjh
2023-10-16T09:06:47,943 Created temporary directory: /tmp/pip-unpack-c70q7p9o
2023-10-16T09:06:47,950 Building wheels for collected packages: adaptivepele
2023-10-16T09:06:47,955   Created temporary directory: /tmp/pip-wheel-6mi225i2
2023-10-16T09:06:47,955   Building wheel for adaptivepele (setup.py): started
2023-10-16T09:06:47,957   Destination directory: /tmp/pip-wheel-6mi225i2
2023-10-16T09:06:47,958   Running command python setup.py bdist_wheel
2023-10-16T09:06:48,815   Warning: 'classifiers' should be a list, got type 'tuple'
2023-10-16T09:06:49,185   running bdist_wheel
2023-10-16T09:06:49,258   running build
2023-10-16T09:06:49,259   running build_py
2023-10-16T09:06:49,286   creating build
2023-10-16T09:06:49,287   creating build/lib.linux-armv7l-cpython-311
2023-10-16T09:06:49,288   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE
2023-10-16T09:06:49,289   copying AdaptivePELE/adaptiveSampling.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE
2023-10-16T09:06:49,292   copying AdaptivePELE/makeRelease.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE
2023-10-16T09:06:49,294   copying AdaptivePELE/runAllTests.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE
2023-10-16T09:06:49,296   copying AdaptivePELE/automateRoundsAdaptive.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE
2023-10-16T09:06:49,298   copying AdaptivePELE/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE
2023-10-16T09:06:49,300   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,301   copying AdaptivePELE/tests/testReporter.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,303   copying AdaptivePELE/tests/testClustering.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,306   copying AdaptivePELE/tests/testMD.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,308   copying AdaptivePELE/tests/testSpawning.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,310   copying AdaptivePELE/tests/testDensityCalculator.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,312   copying AdaptivePELE/tests/testMD_CUDA.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,314   copying AdaptivePELE/tests/testAdaptiveSampling.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,316   copying AdaptivePELE/tests/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,318   copying AdaptivePELE/tests/testAtomset.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,320   copying AdaptivePELE/tests/testSimulationRunner.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,322   copying AdaptivePELE/tests/testThresholdcalculator.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests
2023-10-16T09:06:49,325   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,326   copying AdaptivePELE/analysis/networkCM.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,328   copying AdaptivePELE/analysis/pathwayRMSD.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,330   copying AdaptivePELE/analysis/addRejectedSteps.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,332   copying AdaptivePELE/analysis/writeClusteringStructures.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,334   copying AdaptivePELE/analysis/dehidratate_and_align.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,335   copying AdaptivePELE/analysis/clusterAdaptiveRun.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,338   copying AdaptivePELE/analysis/unbinding.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,339   copying AdaptivePELE/analysis/convertTrajectory.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,341   copying AdaptivePELE/analysis/interactivePlot.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,344   copying AdaptivePELE/analysis/cluster.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,346   copying AdaptivePELE/analysis/filter_by_radius.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,348   copying AdaptivePELE/analysis/analysis_utils.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,350   copying AdaptivePELE/analysis/makeRMSDClustering.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,352   copying AdaptivePELE/analysis/selectOnPlot.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,354   copying AdaptivePELE/analysis/plotSpawningClusters.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,356   copying AdaptivePELE/analysis/standarize_MD_energies.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,358   copying AdaptivePELE/analysis/autoCorrelation.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,360   copying AdaptivePELE/analysis/makePNGs.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,362   copying AdaptivePELE/analysis/generateBox.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,364   copying AdaptivePELE/analysis/findfirstbindingevent.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,366   copying AdaptivePELE/analysis/plotRMSF.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,368   copying AdaptivePELE/analysis/identifyClusterSnapshot.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,370   copying AdaptivePELE/analysis/analyse.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,372   copying AdaptivePELE/analysis/clusters_lagtime_grid.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,374   copying AdaptivePELE/analysis/writeNetworkFiles.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,376   copying AdaptivePELE/analysis/plotAdaptive.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,378   copying AdaptivePELE/analysis/simple_postprocessing.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,380   copying AdaptivePELE/analysis/histCM.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,382   copying AdaptivePELE/analysis/plot3DNetwork.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,384   copying AdaptivePELE/analysis/numberOfClusters.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,386   copying AdaptivePELE/analysis/extract_ligand_traj.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,388   copying AdaptivePELE/analysis/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,389   copying AdaptivePELE/analysis/bestStructs.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,392   copying AdaptivePELE/analysis/splitTrajectory.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,394   copying AdaptivePELE/analysis/writeTrajToSnapshot.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,395   copying AdaptivePELE/analysis/crossValidationClustering.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,397   copying AdaptivePELE/analysis/count_clusters.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,399   copying AdaptivePELE/analysis/correctRMSD.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,402   copying AdaptivePELE/analysis/compareClustering.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,404   copying AdaptivePELE/analysis/calculateSASAvalues.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,406   copying AdaptivePELE/analysis/reportSimulation.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,408   copying AdaptivePELE/analysis/simulationToCsv.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,410   copying AdaptivePELE/analysis/analyseClustering.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,412   copying AdaptivePELE/analysis/foldersFirstBindingEvent.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,413   copying AdaptivePELE/analysis/trajectory_processing.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,415   copying AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,418   copying AdaptivePELE/analysis/calculateDistances.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis
2023-10-16T09:06:49,420   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering
2023-10-16T09:06:49,421   copying AdaptivePELE/clustering/thresholdcalculatortypes.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering
2023-10-16T09:06:49,423   copying AdaptivePELE/clustering/thresholdcalculator.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering
2023-10-16T09:06:49,425   copying AdaptivePELE/clustering/clustering.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering
2023-10-16T09:06:49,428   copying AdaptivePELE/clustering/clusteringTypes.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering
2023-10-16T09:06:49,430   copying AdaptivePELE/clustering/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering
2023-10-16T09:06:49,432   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning
2023-10-16T09:06:49,433   copying AdaptivePELE/spawning/densitycalculator.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning
2023-10-16T09:06:49,435   copying AdaptivePELE/spawning/spawning.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning
2023-10-16T09:06:49,439   copying AdaptivePELE/spawning/spawningTypes.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning
2023-10-16T09:06:49,441   copying AdaptivePELE/spawning/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning
2023-10-16T09:06:49,442   copying AdaptivePELE/spawning/densitycalculatortypes.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning
2023-10-16T09:06:49,444   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/validator
2023-10-16T09:06:49,445   copying AdaptivePELE/validator/controlFileValidator.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/validator
2023-10-16T09:06:49,447   copying AdaptivePELE/validator/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/validator
2023-10-16T09:06:49,449   copying AdaptivePELE/validator/validatorBlockNames.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/validator
2023-10-16T09:06:49,452   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities
2023-10-16T09:06:49,453   copying AdaptivePELE/utilities/generate_topology_object.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities
2023-10-16T09:06:49,454   copying AdaptivePELE/utilities/utilities.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities
2023-10-16T09:06:49,457   copying AdaptivePELE/utilities/clusteringUtilities.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities
2023-10-16T09:06:49,459   copying AdaptivePELE/utilities/PDBLoader.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities
2023-10-16T09:06:49,462   copying AdaptivePELE/utilities/conda_deployment.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities
2023-10-16T09:06:49,463   copying AdaptivePELE/utilities/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities
2023-10-16T09:06:49,465   copying AdaptivePELE/utilities/synchronization.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities
2023-10-16T09:06:49,468   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset
2023-10-16T09:06:49,469   copying AdaptivePELE/atomset/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset
2023-10-16T09:06:49,470   copying AdaptivePELE/atomset/setup.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset
2023-10-16T09:06:49,472   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation
2023-10-16T09:06:49,473   copying AdaptivePELE/simulation/openmm_simulations.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation
2023-10-16T09:06:49,476   copying AdaptivePELE/simulation/simulationrunner.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation
2023-10-16T09:06:49,479   copying AdaptivePELE/simulation/simulationTypes.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation
2023-10-16T09:06:49,481   copying AdaptivePELE/simulation/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation
2023-10-16T09:06:49,483   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants
2023-10-16T09:06:49,484   copying AdaptivePELE/constants/blockNames.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants
2023-10-16T09:06:49,486   copying AdaptivePELE/constants/constants.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants
2023-10-16T09:06:49,488   copying AdaptivePELE/constants/buildEnvironments.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants
2023-10-16T09:06:49,490   copying AdaptivePELE/constants/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants
2023-10-16T09:06:49,491   copying AdaptivePELE/constants/symmetries.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants
2023-10-16T09:06:49,494   creating build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,495   copying AdaptivePELE/freeEnergies/extractCoords.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,497   copying AdaptivePELE/freeEnergies/estimate.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,499   copying AdaptivePELE/freeEnergies/runMarkovChainModel.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,502   copying AdaptivePELE/freeEnergies/calculateDGiterations.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,503   copying AdaptivePELE/freeEnergies/cluster.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,506   copying AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,507   copying AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,509   copying AdaptivePELE/freeEnergies/checkDetailedBalance.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,511   copying AdaptivePELE/freeEnergies/estimateDGAdaptive.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,513   copying AdaptivePELE/freeEnergies/__init__.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,515   copying AdaptivePELE/freeEnergies/prepareMSMFolders.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,517   copying AdaptivePELE/freeEnergies/extendTrajectories.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,519   copying AdaptivePELE/freeEnergies/estimateDG.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,521   copying AdaptivePELE/freeEnergies/getRepresentativeStructures.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,523   copying AdaptivePELE/freeEnergies/computeDeltaG.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,525   copying AdaptivePELE/freeEnergies/utilitiesFreeEnergies.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,527   copying AdaptivePELE/freeEnergies/computeDGGrid.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,529   copying AdaptivePELE/freeEnergies/ownBuildMSM.py -> build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:06:49,538   running build_ext
2023-10-16T09:06:50,263   Compiling AdaptivePELE/atomset/atomset.pyx because it changed.
2023-10-16T09:06:50,264   [1/1] Cythonizing AdaptivePELE/atomset/atomset.pyx
2023-10-16T09:06:51,339   /usr/local/lib/python3.11/dist-packages/Cython/Compiler/Main.py:384: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-wheel-9pdhgzqa/adaptivepele_1b2729e943984970bad4b01533c692a0/AdaptivePELE/atomset/atomset.pxd
2023-10-16T09:06:51,339     tree = Parsing.p_module(s, pxd, full_module_name)
2023-10-16T09:06:55,048   building 'AdaptivePELE.atomset.atomset' extension
2023-10-16T09:06:55,049   creating build/temp.linux-armv7l-cpython-311
2023-10-16T09:06:55,049   creating build/temp.linux-armv7l-cpython-311/AdaptivePELE
2023-10-16T09:06:55,050   creating build/temp.linux-armv7l-cpython-311/AdaptivePELE/atomset
2023-10-16T09:06:55,051   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -IAdaptivePELE -IAdaptivePELE/atomset -I/usr/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c AdaptivePELE/atomset/atomset.c -o build/temp.linux-armv7l-cpython-311/AdaptivePELE/atomset/atomset.o
2023-10-16T09:06:55,497   In file included from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-10-16T09:06:55,497                    from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-10-16T09:06:55,498                    from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-10-16T09:06:55,498                    from AdaptivePELE/atomset/atomset.c:1171:
2023-10-16T09:06:55,499   /usr/local/lib/python3.11/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]
2023-10-16T09:06:55,499      17 | #warning "Using deprecated NumPy API, disable it with " \
2023-10-16T09:06:55,500         |  ^~~~~~~
2023-10-16T09:11:23,783   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/AdaptivePELE/atomset/atomset.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset/atomset.cpython-311-arm-linux-gnueabihf.so
2023-10-16T09:11:23,965   Compiling AdaptivePELE/atomset/SymmetryContactMapEvaluator.pyx because it changed.
2023-10-16T09:11:23,966   [1/1] Cythonizing AdaptivePELE/atomset/SymmetryContactMapEvaluator.pyx
2023-10-16T09:11:23,978   /usr/local/lib/python3.11/dist-packages/Cython/Compiler/Main.py:384: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-wheel-9pdhgzqa/adaptivepele_1b2729e943984970bad4b01533c692a0/AdaptivePELE/atomset/SymmetryContactMapEvaluator.pxd
2023-10-16T09:11:23,978     tree = Parsing.p_module(s, pxd, full_module_name)
2023-10-16T09:11:25,730   building 'AdaptivePELE.atomset.SymmetryContactMapEvaluator' extension
2023-10-16T09:11:25,731   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -IAdaptivePELE -IAdaptivePELE/atomset -I/usr/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c AdaptivePELE/atomset/SymmetryContactMapEvaluator.c -o build/temp.linux-armv7l-cpython-311/AdaptivePELE/atomset/SymmetryContactMapEvaluator.o
2023-10-16T09:11:26,123   In file included from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-10-16T09:11:26,124                    from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-10-16T09:11:26,125                    from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-10-16T09:11:26,125                    from AdaptivePELE/atomset/SymmetryContactMapEvaluator.c:1171:
2023-10-16T09:11:26,126   /usr/local/lib/python3.11/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]
2023-10-16T09:11:26,126      17 | #warning "Using deprecated NumPy API, disable it with " \
2023-10-16T09:11:26,127         |  ^~~~~~~
2023-10-16T09:11:48,784   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/AdaptivePELE/atomset/SymmetryContactMapEvaluator.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset/SymmetryContactMapEvaluator.cpython-311-arm-linux-gnueabihf.so
2023-10-16T09:11:48,922   Compiling AdaptivePELE/atomset/RMSDCalculator.pyx because it changed.
2023-10-16T09:11:48,922   [1/1] Cythonizing AdaptivePELE/atomset/RMSDCalculator.pyx
2023-10-16T09:11:48,934   /usr/local/lib/python3.11/dist-packages/Cython/Compiler/Main.py:384: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-wheel-9pdhgzqa/adaptivepele_1b2729e943984970bad4b01533c692a0/AdaptivePELE/atomset/RMSDCalculator.pxd
2023-10-16T09:11:48,935     tree = Parsing.p_module(s, pxd, full_module_name)
2023-10-16T09:11:50,263   building 'AdaptivePELE.atomset.RMSDCalculator' extension
2023-10-16T09:11:50,264   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -IAdaptivePELE -IAdaptivePELE/atomset -I/usr/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c AdaptivePELE/atomset/RMSDCalculator.c -o build/temp.linux-armv7l-cpython-311/AdaptivePELE/atomset/RMSDCalculator.o
2023-10-16T09:11:50,650   In file included from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-10-16T09:11:50,651                    from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-10-16T09:11:50,651                    from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-10-16T09:11:50,652                    from AdaptivePELE/atomset/RMSDCalculator.c:1171:
2023-10-16T09:11:50,653   /usr/local/lib/python3.11/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]
2023-10-16T09:11:50,653      17 | #warning "Using deprecated NumPy API, disable it with " \
2023-10-16T09:11:50,654         |  ^~~~~~~
2023-10-16T09:12:02,618   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/AdaptivePELE/atomset/RMSDCalculator.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset/RMSDCalculator.cpython-311-arm-linux-gnueabihf.so
2023-10-16T09:12:02,776   Compiling AdaptivePELE/freeEnergies/utils.pyx because it changed.
2023-10-16T09:12:02,776   [1/1] Cythonizing AdaptivePELE/freeEnergies/utils.pyx
2023-10-16T09:12:07,247   building 'AdaptivePELE.freeEnergies.utils' extension
2023-10-16T09:12:07,248   creating build/temp.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies
2023-10-16T09:12:07,248   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -IAdaptivePELE -IAdaptivePELE/freeEnergies -I/usr/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c AdaptivePELE/freeEnergies/utils.c -o build/temp.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/utils.o
2023-10-16T09:12:07,649   In file included from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-10-16T09:12:07,650                    from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-10-16T09:12:07,651                    from /usr/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-10-16T09:12:07,651                    from AdaptivePELE/freeEnergies/utils.c:1171:
2023-10-16T09:12:07,652   /usr/local/lib/python3.11/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]
2023-10-16T09:12:07,652      17 | #warning "Using deprecated NumPy API, disable it with " \
2023-10-16T09:12:07,652         |  ^~~~~~~
2023-10-16T09:12:38,943   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/utils.cpython-311-arm-linux-gnueabihf.so
2023-10-16T09:12:39,124   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-10-16T09:12:39,125   !!

2023-10-16T09:12:39,126           ********************************************************************************
2023-10-16T09:12:39,126           Please avoid running ``setup.py`` directly.
2023-10-16T09:12:39,127           Instead, use pypa/build, pypa/installer or other
2023-10-16T09:12:39,127           standards-based tools.

2023-10-16T09:12:39,128           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-10-16T09:12:39,129           ********************************************************************************

2023-10-16T09:12:39,130   !!
2023-10-16T09:12:39,130     self.initialize_options()
2023-10-16T09:12:39,150   installing to build/bdist.linux-armv7l/wheel
2023-10-16T09:12:39,150   running install
2023-10-16T09:12:39,175   running install_lib
2023-10-16T09:12:39,200   creating build/bdist.linux-armv7l
2023-10-16T09:12:39,201   creating build/bdist.linux-armv7l/wheel
2023-10-16T09:12:39,202   creating build/bdist.linux-armv7l/wheel/AdaptivePELE
2023-10-16T09:12:39,204   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,205   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testReporter.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,207   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testClustering.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,209   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testMD.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,212   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testSpawning.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,214   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testDensityCalculator.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,217   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testMD_CUDA.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,219   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testAdaptiveSampling.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,221   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,223   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testAtomset.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,226   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testSimulationRunner.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,227   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/tests/testThresholdcalculator.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/tests
2023-10-16T09:12:39,230   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/adaptiveSampling.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE
2023-10-16T09:12:39,233   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,234   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/networkCM.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,236   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/pathwayRMSD.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,238   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/addRejectedSteps.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,240   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/writeClusteringStructures.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,242   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/dehidratate_and_align.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,243   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/clusterAdaptiveRun.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,246   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/unbinding.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,247   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/convertTrajectory.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,249   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/interactivePlot.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,252   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/cluster.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,255   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/filter_by_radius.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,257   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/analysis_utils.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,259   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/makeRMSDClustering.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,261   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/selectOnPlot.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,263   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/plotSpawningClusters.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,265   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/standarize_MD_energies.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,267   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/autoCorrelation.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,270   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/makePNGs.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,271   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/generateBox.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,274   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/findfirstbindingevent.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,275   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/plotRMSF.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,277   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/identifyClusterSnapshot.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,279   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/analyse.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,281   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/clusters_lagtime_grid.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,283   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/writeNetworkFiles.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,285   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/plotAdaptive.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,287   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/simple_postprocessing.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,289   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/histCM.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,291   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/plot3DNetwork.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,293   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/numberOfClusters.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,295   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/extract_ligand_traj.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,297   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,298   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/bestStructs.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,300   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/splitTrajectory.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,302   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/writeTrajToSnapshot.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,304   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/crossValidationClustering.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,306   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/count_clusters.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,308   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/correctRMSD.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,310   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/compareClustering.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,313   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/calculateSASAvalues.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,315   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/reportSimulation.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,317   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/simulationToCsv.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,319   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/analyseClustering.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,321   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/foldersFirstBindingEvent.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,323   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/trajectory_processing.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,325   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,327   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/analysis/calculateDistances.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/analysis
2023-10-16T09:12:39,330   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/clustering
2023-10-16T09:12:39,331   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering/thresholdcalculatortypes.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/clustering
2023-10-16T09:12:39,333   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering/thresholdcalculator.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/clustering
2023-10-16T09:12:39,335   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering/clustering.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/clustering
2023-10-16T09:12:39,340   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering/clusteringTypes.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/clustering
2023-10-16T09:12:39,342   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/clustering
2023-10-16T09:12:39,344   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/spawning
2023-10-16T09:12:39,345   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning/densitycalculator.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/spawning
2023-10-16T09:12:39,347   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning/spawning.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/spawning
2023-10-16T09:12:39,351   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning/spawningTypes.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/spawning
2023-10-16T09:12:39,353   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/spawning
2023-10-16T09:12:39,355   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/spawning/densitycalculatortypes.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/spawning
2023-10-16T09:12:39,356   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/makeRelease.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE
2023-10-16T09:12:39,359   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/validator
2023-10-16T09:12:39,360   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/validator/controlFileValidator.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/validator
2023-10-16T09:12:39,362   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/validator/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/validator
2023-10-16T09:12:39,364   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/validator/validatorBlockNames.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/validator
2023-10-16T09:12:39,366   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/runAllTests.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE
2023-10-16T09:12:39,368   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2023-10-16T09:12:39,369   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities/generate_topology_object.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2023-10-16T09:12:39,371   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities/utilities.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2023-10-16T09:12:39,374   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities/clusteringUtilities.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2023-10-16T09:12:39,376   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities/PDBLoader.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2023-10-16T09:12:39,379   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities/conda_deployment.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2023-10-16T09:12:39,380   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2023-10-16T09:12:39,382   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/utilities/synchronization.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/utilities
2023-10-16T09:12:39,384   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/automateRoundsAdaptive.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE
2023-10-16T09:12:39,387   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/atomset
2023-10-16T09:12:39,388   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset/atomset.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/AdaptivePELE/atomset
2023-10-16T09:12:39,419   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/atomset
2023-10-16T09:12:39,421   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset/setup.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/atomset
2023-10-16T09:12:39,423   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset/RMSDCalculator.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/AdaptivePELE/atomset
2023-10-16T09:12:39,432   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/atomset/SymmetryContactMapEvaluator.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/AdaptivePELE/atomset
2023-10-16T09:12:39,459   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/simulation
2023-10-16T09:12:39,460   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation/openmm_simulations.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/simulation
2023-10-16T09:12:39,463   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation/simulationrunner.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/simulation
2023-10-16T09:12:39,466   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation/simulationTypes.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/simulation
2023-10-16T09:12:39,468   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/simulation
2023-10-16T09:12:39,470   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/constants
2023-10-16T09:12:39,471   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants/blockNames.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/constants
2023-10-16T09:12:39,473   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants/constants.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/constants
2023-10-16T09:12:39,475   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants/buildEnvironments.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/constants
2023-10-16T09:12:39,477   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/constants
2023-10-16T09:12:39,479   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/constants/symmetries.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/constants
2023-10-16T09:12:39,480   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE
2023-10-16T09:12:39,483   creating build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,484   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/extractCoords.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,486   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,513   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/estimate.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,516   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/runMarkovChainModel.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,518   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/calculateDGiterations.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,521   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/cluster.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,523   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,526   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,528   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/checkDetailedBalance.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,530   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/estimateDGAdaptive.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,532   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/__init__.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,534   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/prepareMSMFolders.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,536   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/extendTrajectories.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,539   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/estimateDG.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,542   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/getRepresentativeStructures.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,544   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/computeDeltaG.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,546   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/utilitiesFreeEnergies.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,549   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/computeDGGrid.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,552   copying build/lib.linux-armv7l-cpython-311/AdaptivePELE/freeEnergies/ownBuildMSM.py -> build/bdist.linux-armv7l/wheel/AdaptivePELE/freeEnergies
2023-10-16T09:12:39,554   running install_egg_info
2023-10-16T09:12:39,628   running egg_info
2023-10-16T09:12:39,652   writing AdaptivePELE.egg-info/PKG-INFO
2023-10-16T09:12:39,655   writing dependency_links to AdaptivePELE.egg-info/dependency_links.txt
2023-10-16T09:12:39,657   writing requirements to AdaptivePELE.egg-info/requires.txt
2023-10-16T09:12:39,658   writing top-level names to AdaptivePELE.egg-info/top_level.txt
2023-10-16T09:12:39,706   reading manifest file 'AdaptivePELE.egg-info/SOURCES.txt'
2023-10-16T09:12:39,711   reading manifest template 'MANIFEST.in'
2023-10-16T09:12:39,730   warning: no files found matching 'utils*.so' under directory 'AdaptivePELE/freeEnergies'
2023-10-16T09:12:39,731   adding license file 'LICENSE'
2023-10-16T09:12:39,737   writing manifest file 'AdaptivePELE.egg-info/SOURCES.txt'
2023-10-16T09:12:39,739   Copying AdaptivePELE.egg-info to build/bdist.linux-armv7l/wheel/AdaptivePELE-1.7.4-py3.11.egg-info
2023-10-16T09:12:39,750   running install_scripts
2023-10-16T09:12:39,804   creating build/bdist.linux-armv7l/wheel/AdaptivePELE-1.7.4.dist-info/WHEEL
2023-10-16T09:12:39,807   creating '/tmp/pip-wheel-6mi225i2/AdaptivePELE-1.7.4-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-10-16T09:12:39,809   adding 'AdaptivePELE/__init__.py'
2023-10-16T09:12:39,814   adding 'AdaptivePELE/adaptiveSampling.py'
2023-10-16T09:12:39,816   adding 'AdaptivePELE/automateRoundsAdaptive.py'
2023-10-16T09:12:39,817   adding 'AdaptivePELE/makeRelease.py'
2023-10-16T09:12:39,819   adding 'AdaptivePELE/runAllTests.py'
2023-10-16T09:12:39,822   adding 'AdaptivePELE/analysis/__init__.py'
2023-10-16T09:12:39,824   adding 'AdaptivePELE/analysis/addRejectedSteps.py'
2023-10-16T09:12:39,825   adding 'AdaptivePELE/analysis/analyse.py'
2023-10-16T09:12:39,827   adding 'AdaptivePELE/analysis/analyseClustering.py'
2023-10-16T09:12:39,828   adding 'AdaptivePELE/analysis/analysis_utils.py'
2023-10-16T09:12:39,830   adding 'AdaptivePELE/analysis/autoCorrelation.py'
2023-10-16T09:12:39,832   adding 'AdaptivePELE/analysis/backtrackAdaptiveTrajectory.py'
2023-10-16T09:12:39,833   adding 'AdaptivePELE/analysis/bestStructs.py'
2023-10-16T09:12:39,835   adding 'AdaptivePELE/analysis/calculateDistances.py'
2023-10-16T09:12:39,837   adding 'AdaptivePELE/analysis/calculateSASAvalues.py'
2023-10-16T09:12:39,839   adding 'AdaptivePELE/analysis/cluster.py'
2023-10-16T09:12:39,841   adding 'AdaptivePELE/analysis/clusterAdaptiveRun.py'
2023-10-16T09:12:39,843   adding 'AdaptivePELE/analysis/clusters_lagtime_grid.py'
2023-10-16T09:12:39,844   adding 'AdaptivePELE/analysis/compareClustering.py'
2023-10-16T09:12:39,846   adding 'AdaptivePELE/analysis/convertTrajectory.py'
2023-10-16T09:12:39,847   adding 'AdaptivePELE/analysis/correctRMSD.py'
2023-10-16T09:12:39,849   adding 'AdaptivePELE/analysis/count_clusters.py'
2023-10-16T09:12:39,850   adding 'AdaptivePELE/analysis/crossValidationClustering.py'
2023-10-16T09:12:39,852   adding 'AdaptivePELE/analysis/dehidratate_and_align.py'
2023-10-16T09:12:39,853   adding 'AdaptivePELE/analysis/extract_ligand_traj.py'
2023-10-16T09:12:39,855   adding 'AdaptivePELE/analysis/filter_by_radius.py'
2023-10-16T09:12:39,856   adding 'AdaptivePELE/analysis/findfirstbindingevent.py'
2023-10-16T09:12:39,857   adding 'AdaptivePELE/analysis/foldersFirstBindingEvent.py'
2023-10-16T09:12:39,859   adding 'AdaptivePELE/analysis/generateBox.py'
2023-10-16T09:12:39,860   adding 'AdaptivePELE/analysis/histCM.py'
2023-10-16T09:12:39,862   adding 'AdaptivePELE/analysis/identifyClusterSnapshot.py'
2023-10-16T09:12:39,864   adding 'AdaptivePELE/analysis/interactivePlot.py'
2023-10-16T09:12:39,866   adding 'AdaptivePELE/analysis/makePNGs.py'
2023-10-16T09:12:39,868   adding 'AdaptivePELE/analysis/makeRMSDClustering.py'
2023-10-16T09:12:39,869   adding 'AdaptivePELE/analysis/networkCM.py'
2023-10-16T09:12:39,871   adding 'AdaptivePELE/analysis/numberOfClusters.py'
2023-10-16T09:12:39,872   adding 'AdaptivePELE/analysis/pathwayRMSD.py'
2023-10-16T09:12:39,874   adding 'AdaptivePELE/analysis/plot3DNetwork.py'
2023-10-16T09:12:39,876   adding 'AdaptivePELE/analysis/plotAdaptive.py'
2023-10-16T09:12:39,878   adding 'AdaptivePELE/analysis/plotRMSF.py'
2023-10-16T09:12:39,879   adding 'AdaptivePELE/analysis/plotSpawningClusters.py'
2023-10-16T09:12:39,881   adding 'AdaptivePELE/analysis/reportSimulation.py'
2023-10-16T09:12:39,883   adding 'AdaptivePELE/analysis/selectOnPlot.py'
2023-10-16T09:12:39,884   adding 'AdaptivePELE/analysis/simple_postprocessing.py'
2023-10-16T09:12:39,886   adding 'AdaptivePELE/analysis/simulationToCsv.py'
2023-10-16T09:12:39,887   adding 'AdaptivePELE/analysis/splitTrajectory.py'
2023-10-16T09:12:39,889   adding 'AdaptivePELE/analysis/standarize_MD_energies.py'
2023-10-16T09:12:39,890   adding 'AdaptivePELE/analysis/trajectory_processing.py'
2023-10-16T09:12:39,892   adding 'AdaptivePELE/analysis/unbinding.py'
2023-10-16T09:12:39,893   adding 'AdaptivePELE/analysis/writeClusteringStructures.py'
2023-10-16T09:12:39,894   adding 'AdaptivePELE/analysis/writeNetworkFiles.py'
2023-10-16T09:12:39,895   adding 'AdaptivePELE/analysis/writeTrajToSnapshot.py'
2023-10-16T09:12:40,003   adding 'AdaptivePELE/atomset/RMSDCalculator.cpython-311-arm-linux-gnueabihf.so'
2023-10-16T09:12:40,191   adding 'AdaptivePELE/atomset/SymmetryContactMapEvaluator.cpython-311-arm-linux-gnueabihf.so'
2023-10-16T09:12:40,199   adding 'AdaptivePELE/atomset/__init__.py'
2023-10-16T09:12:40,582   adding 'AdaptivePELE/atomset/atomset.cpython-311-arm-linux-gnueabihf.so'
2023-10-16T09:12:40,599   adding 'AdaptivePELE/atomset/setup.py'
2023-10-16T09:12:40,601   adding 'AdaptivePELE/clustering/__init__.py'
2023-10-16T09:12:40,610   adding 'AdaptivePELE/clustering/clustering.py'
2023-10-16T09:12:40,612   adding 'AdaptivePELE/clustering/clusteringTypes.py'
2023-10-16T09:12:40,614   adding 'AdaptivePELE/clustering/thresholdcalculator.py'
2023-10-16T09:12:40,615   adding 'AdaptivePELE/clustering/thresholdcalculatortypes.py'
2023-10-16T09:12:40,617   adding 'AdaptivePELE/constants/__init__.py'
2023-10-16T09:12:40,618   adding 'AdaptivePELE/constants/blockNames.py'
2023-10-16T09:12:40,620   adding 'AdaptivePELE/constants/buildEnvironments.py'
2023-10-16T09:12:40,621   adding 'AdaptivePELE/constants/constants.py'
2023-10-16T09:12:40,622   adding 'AdaptivePELE/constants/symmetries.py'
2023-10-16T09:12:40,624   adding 'AdaptivePELE/freeEnergies/__init__.py'
2023-10-16T09:12:40,625   adding 'AdaptivePELE/freeEnergies/calculateAdaptiveDGiterations.py'
2023-10-16T09:12:40,626   adding 'AdaptivePELE/freeEnergies/calculateDGiterations.py'
2023-10-16T09:12:40,628   adding 'AdaptivePELE/freeEnergies/checkDetailedBalance.py'
2023-10-16T09:12:40,630   adding 'AdaptivePELE/freeEnergies/cluster.py'
2023-10-16T09:12:40,631   adding 'AdaptivePELE/freeEnergies/computeDGGrid.py'
2023-10-16T09:12:40,633   adding 'AdaptivePELE/freeEnergies/computeDeltaG.py'
2023-10-16T09:12:40,635   adding 'AdaptivePELE/freeEnergies/estimate.py'
2023-10-16T09:12:40,637   adding 'AdaptivePELE/freeEnergies/estimateDG.py'
2023-10-16T09:12:40,639   adding 'AdaptivePELE/freeEnergies/estimateDGAdaptive.py'
2023-10-16T09:12:40,640   adding 'AdaptivePELE/freeEnergies/extendTrajectories.py'
2023-10-16T09:12:40,644   adding 'AdaptivePELE/freeEnergies/extractCoords.py'
2023-10-16T09:12:40,646   adding 'AdaptivePELE/freeEnergies/getRepresentativeStructures.py'
2023-10-16T09:12:40,647   adding 'AdaptivePELE/freeEnergies/ownBuildMSM.py'
2023-10-16T09:12:40,648   adding 'AdaptivePELE/freeEnergies/prepareMSMFolders.py'
2023-10-16T09:12:40,650   adding 'AdaptivePELE/freeEnergies/runMarkovChainModel.py'
2023-10-16T09:12:40,651   adding 'AdaptivePELE/freeEnergies/utilitiesFreeEnergies.py'
2023-10-16T09:12:40,885   adding 'AdaptivePELE/freeEnergies/utils.cpython-311-arm-linux-gnueabihf.so'
2023-10-16T09:12:40,895   adding 'AdaptivePELE/freeEnergies/writeExtractedCoordsAsPDB.py'
2023-10-16T09:12:40,897   adding 'AdaptivePELE/simulation/__init__.py'
2023-10-16T09:12:40,901   adding 'AdaptivePELE/simulation/openmm_simulations.py'
2023-10-16T09:12:40,902   adding 'AdaptivePELE/simulation/simulationTypes.py'
2023-10-16T09:12:40,911   adding 'AdaptivePELE/simulation/simulationrunner.py'
2023-10-16T09:12:40,914   adding 'AdaptivePELE/spawning/__init__.py'
2023-10-16T09:12:40,915   adding 'AdaptivePELE/spawning/densitycalculator.py'
2023-10-16T09:12:40,916   adding 'AdaptivePELE/spawning/densitycalculatortypes.py'
2023-10-16T09:12:40,922   adding 'AdaptivePELE/spawning/spawning.py'
2023-10-16T09:12:40,924   adding 'AdaptivePELE/spawning/spawningTypes.py'
2023-10-16T09:12:40,926   adding 'AdaptivePELE/tests/__init__.py'
2023-10-16T09:12:40,928   adding 'AdaptivePELE/tests/testAdaptiveSampling.py'
2023-10-16T09:12:40,930   adding 'AdaptivePELE/tests/testAtomset.py'
2023-10-16T09:12:40,932   adding 'AdaptivePELE/tests/testClustering.py'
2023-10-16T09:12:40,933   adding 'AdaptivePELE/tests/testDensityCalculator.py'
2023-10-16T09:12:40,934   adding 'AdaptivePELE/tests/testMD.py'
2023-10-16T09:12:40,936   adding 'AdaptivePELE/tests/testMD_CUDA.py'
2023-10-16T09:12:40,937   adding 'AdaptivePELE/tests/testReporter.py'
2023-10-16T09:12:40,938   adding 'AdaptivePELE/tests/testSimulationRunner.py'
2023-10-16T09:12:40,940   adding 'AdaptivePELE/tests/testSpawning.py'
2023-10-16T09:12:40,942   adding 'AdaptivePELE/tests/testThresholdcalculator.py'
2023-10-16T09:12:40,946   adding 'AdaptivePELE/utilities/PDBLoader.py'
2023-10-16T09:12:40,947   adding 'AdaptivePELE/utilities/__init__.py'
2023-10-16T09:12:40,948   adding 'AdaptivePELE/utilities/clusteringUtilities.py'
2023-10-16T09:12:40,950   adding 'AdaptivePELE/utilities/conda_deployment.py'
2023-10-16T09:12:40,951   adding 'AdaptivePELE/utilities/generate_topology_object.py'
2023-10-16T09:12:40,953   adding 'AdaptivePELE/utilities/synchronization.py'
2023-10-16T09:12:40,958   adding 'AdaptivePELE/utilities/utilities.py'
2023-10-16T09:12:40,959   adding 'AdaptivePELE/validator/__init__.py'
2023-10-16T09:12:40,961   adding 'AdaptivePELE/validator/controlFileValidator.py'
2023-10-16T09:12:40,963   adding 'AdaptivePELE/validator/validatorBlockNames.py'
2023-10-16T09:12:40,965   adding 'AdaptivePELE-1.7.4.dist-info/LICENSE'
2023-10-16T09:12:40,966   adding 'AdaptivePELE-1.7.4.dist-info/METADATA'
2023-10-16T09:12:40,967   adding 'AdaptivePELE-1.7.4.dist-info/WHEEL'
2023-10-16T09:12:40,968   adding 'AdaptivePELE-1.7.4.dist-info/top_level.txt'
2023-10-16T09:12:40,970   adding 'AdaptivePELE-1.7.4.dist-info/RECORD'
2023-10-16T09:12:40,994   removing build/bdist.linux-armv7l/wheel
2023-10-16T09:12:41,555   Building wheel for adaptivepele (setup.py): finished with status 'done'
2023-10-16T09:12:41,584   Created wheel for adaptivepele: filename=AdaptivePELE-1.7.4-cp311-cp311-linux_armv7l.whl size=2096568 sha256=8322937309a7efabf90fbc15d3d59ca9db71870cd9bb872bc4fefc2548447801
2023-10-16T09:12:41,585   Stored in directory: /tmp/pip-ephem-wheel-cache-pc9vr29b/wheels/03/88/52/d4c8aee53385e1c2880f20b149d80df67cb38e3849d4acea93
2023-10-16T09:12:41,599 Successfully built adaptivepele
2023-10-16T09:12:41,669 Removed build tracker: '/tmp/pip-build-tracker-v5lhwghk'