2021-11-30T19:04:58,639 Created temporary directory: /tmp/pip-ephem-wheel-cache-68ke_1ep 2021-11-30T19:04:58,642 Created temporary directory: /tmp/pip-req-tracker-gf0sct74 2021-11-30T19:04:58,643 Initialized build tracking at /tmp/pip-req-tracker-gf0sct74 2021-11-30T19:04:58,643 Created build tracker: /tmp/pip-req-tracker-gf0sct74 2021-11-30T19:04:58,643 Entered build tracker: /tmp/pip-req-tracker-gf0sct74 2021-11-30T19:04:58,644 Created temporary directory: /tmp/pip-wheel-tagftt49 2021-11-30T19:04:58,679 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2021-11-30T19:04:58,682 2 location(s) to search for versions of chemfiles: 2021-11-30T19:04:58,682 * https://pypi.org/simple/chemfiles/ 2021-11-30T19:04:58,682 * https://www.piwheels.org/simple/chemfiles/ 2021-11-30T19:04:58,682 Fetching project page and analyzing links: https://pypi.org/simple/chemfiles/ 2021-11-30T19:04:58,683 Getting page https://pypi.org/simple/chemfiles/ 2021-11-30T19:04:58,685 Found 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https://files.pythonhosted.org/packages/66/35/f669f1d2155a8397a1553ac0ba831dd64a5968567f8f102b57cb32e5442b/chemfiles-0.8.0-py2.py3-none-manylinux1_x86_64.whl#sha256=7c963c53440c3f190376f19cde99b89ba65a9eab129c901750d92cc8e953ddf5 (from https://pypi.org/simple/chemfiles/) 2021-11-30T19:04:58,797 Skipping link: No binaries permitted for chemfiles: https://files.pythonhosted.org/packages/24/ac/b661e2ace2cef025931de46b24603be4f3a5d336275d3057e99d1f0ad044/chemfiles-0.8.0-py2.py3-none-win32.whl#sha256=7484e664716181da3faa376777c7ff10d19b87dabf7799d207870b9ff2321028 (from https://pypi.org/simple/chemfiles/) 2021-11-30T19:04:58,798 Skipping link: No binaries permitted for chemfiles: https://files.pythonhosted.org/packages/9b/f9/8b07c1ed29ee19c490c78be60711ccc097483954224729d1d7eb67aa9bf1/chemfiles-0.8.0-py2.py3-none-win_amd64.whl#sha256=1b793a3dc963b3be454a6b321ba914b9825cc61afba123d180e71cfeefcda1ed (from https://pypi.org/simple/chemfiles/) 2021-11-30T19:04:58,798 Found link 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2021-11-30T19:04:58,799 Found link https://files.pythonhosted.org/packages/6b/17/6206cf78a997a67208ed920fa296acba1cb58f5b81d20280e3b2671f57a4/chemfiles-0.9.1.tar.gz#sha256=602567a8ebfd75e7ba017a9f95e6f7d7a8e070532bd71bf1f576202c7bcad230 (from https://pypi.org/simple/chemfiles/), version: 0.9.1 2021-11-30T19:04:58,800 Skipping link: No binaries permitted for chemfiles: https://files.pythonhosted.org/packages/04/4d/171aa08aca4f0082a19fc433aea614fc7bf08cf29b5af3ac65790a56bc08/chemfiles-0.9.2-py2.py3-none-macosx_10_9_x86_64.whl#sha256=40441eed225bfa08a9f1beedf2a056ed145fdff4d59ae6d26e0053dbb16ed618 (from https://pypi.org/simple/chemfiles/) 2021-11-30T19:04:58,800 Skipping link: No binaries permitted for chemfiles: https://files.pythonhosted.org/packages/a5/93/7d9e4b8bfc572f98102f8c2b42f01d8faa777c080fd0dc04724833e8a6f3/chemfiles-0.9.2-py2.py3-none-manylinux1_i686.whl#sha256=49ea873e68e4f033b4757c8a3529f5df90a89a5949187b7cecd261501497fc70 (from https://pypi.org/simple/chemfiles/) 2021-11-30T19:04:58,800 Skipping link: No binaries permitted for chemfiles: https://files.pythonhosted.org/packages/52/4b/9e5187e2bedd6833aff6b3b722e019523977deecb360693c81d417f6c888/chemfiles-0.9.2-py2.py3-none-manylinux1_x86_64.whl#sha256=a4451dbb898af4f0d50e8f03f107887413dbc2139570eb432577a82e69ddea3e (from https://pypi.org/simple/chemfiles/) 2021-11-30T19:04:58,800 Skipping link: No binaries permitted for chemfiles: https://files.pythonhosted.org/packages/04/14/a55de824dee9d5c38748229f69001a715039c8915b24fabf9c2946581c81/chemfiles-0.9.2-py2.py3-none-win32.whl#sha256=92b5c1b504127431c67ab6539725995f788849e1bf0a0c106a9eaabcfeccaeb8 (from https://pypi.org/simple/chemfiles/) 2021-11-30T19:04:58,801 Skipping link: No binaries permitted for chemfiles: https://files.pythonhosted.org/packages/24/39/2cae9a642255077d30172fb73212ddb629b96ce1ac03372ae35e1d742fc6/chemfiles-0.9.2-py2.py3-none-win_amd64.whl#sha256=dde92d6884738b3d590efe04c4824b424b5e82f45f6a8ffc108c136548b5e22f (from 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https://www.piwheels.org/simple/chemfiles/ 2021-11-30T19:04:58,807 Getting page https://www.piwheels.org/simple/chemfiles/ 2021-11-30T19:04:58,808 Found index url https://www.piwheels.org/simple 2021-11-30T19:04:58,983 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.10.0-py2.py3-none-linux_armv6l.whl#sha256=b7f387f3badc60e5b20ff7be596a7000ff0ee1868a5f055f9a358e0ccd93b29d (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,983 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.10.0-py2.py3-none-linux_armv7l.whl#sha256=b7f387f3badc60e5b20ff7be596a7000ff0ee1868a5f055f9a358e0ccd93b29d (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,983 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.10.1-py2.py3-none-linux_armv6l.whl#sha256=37da2deccc58f6c1079b3890f091555c42f58692a2f917b049c49ca8faf274d1 (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,984 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.10.1-py2.py3-none-linux_armv7l.whl#sha256=37da2deccc58f6c1079b3890f091555c42f58692a2f917b049c49ca8faf274d1 (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,984 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.8.0-py2.py3-none-any.whl#sha256=a3f691b4690045b8ab1ef9c0f7d2c00e1bcd607e75eba7906e110bf970792a2d (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,984 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.9.1-py2.py3-none-linux_armv6l.whl#sha256=6ef1395d34e1934004558b9ee4dd123c36fd63e188d628fe54a83c5b85fcd4da (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,985 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.9.1-py2.py3-none-linux_armv7l.whl#sha256=6ef1395d34e1934004558b9ee4dd123c36fd63e188d628fe54a83c5b85fcd4da (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,985 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.9.2-py2.py3-none-linux_armv6l.whl#sha256=e67d6595a8f8c0fdbb9b6ce48f557433e4873c805454180e1209f63e9e0aa73d (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,985 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.9.2-py2.py3-none-linux_armv7l.whl#sha256=e67d6595a8f8c0fdbb9b6ce48f557433e4873c805454180e1209f63e9e0aa73d (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,985 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.9.3-py2.py3-none-linux_armv6l.whl#sha256=f9ec0c923da2543df25fac7d1eb9a79bf26b5bd4e4910d88e8c8aadc1ba98e32 (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,986 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.9.3-py2.py3-none-linux_armv7l.whl#sha256=f9ec0c923da2543df25fac7d1eb9a79bf26b5bd4e4910d88e8c8aadc1ba98e32 (from https://www.piwheels.org/simple/chemfiles/) 2021-11-30T19:04:58,986 Skipping link: not a file: https://www.piwheels.org/simple/chemfiles/ 2021-11-30T19:04:58,986 Skipping link: not a file: https://pypi.org/simple/chemfiles/ 2021-11-30T19:04:59,003 Given no hashes to check 1 links for project 'chemfiles': discarding no candidates 2021-11-30T19:04:59,019 Collecting chemfiles==0.10.2 2021-11-30T19:04:59,020 Created temporary directory: /tmp/pip-unpack-t8kh0lan 2021-11-30T19:04:59,077 Downloading chemfiles-0.10.2.tar.gz (4.1 MB) 2021-11-30T19:05:00,189 Added chemfiles==0.10.2 from https://files.pythonhosted.org/packages/59/c7/d180ab9df66cbe765b94d8ba145c1723ff34c69a9a1debe5b6ab6637a6f7/chemfiles-0.10.2.tar.gz#sha256=e277725803715762f9ea787f1ed51dbc2a83a47188ca3bf5d77ddcbc527f55f9 to build tracker '/tmp/pip-req-tracker-gf0sct74' 2021-11-30T19:05:00,191 Running setup.py (path:/tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/setup.py) egg_info for package chemfiles 2021-11-30T19:05:00,191 Created temporary directory: /tmp/pip-pip-egg-info-rb91075a 2021-11-30T19:05:00,192 Running command python setup.py egg_info 2021-11-30T19:05:01,717 running egg_info 2021-11-30T19:05:01,719 creating /tmp/pip-pip-egg-info-rb91075a/chemfiles.egg-info 2021-11-30T19:05:01,720 writing /tmp/pip-pip-egg-info-rb91075a/chemfiles.egg-info/PKG-INFO 2021-11-30T19:05:01,723 writing dependency_links to /tmp/pip-pip-egg-info-rb91075a/chemfiles.egg-info/dependency_links.txt 2021-11-30T19:05:01,725 writing requirements to /tmp/pip-pip-egg-info-rb91075a/chemfiles.egg-info/requires.txt 2021-11-30T19:05:01,726 writing top-level names to /tmp/pip-pip-egg-info-rb91075a/chemfiles.egg-info/top_level.txt 2021-11-30T19:05:01,728 writing manifest file '/tmp/pip-pip-egg-info-rb91075a/chemfiles.egg-info/SOURCES.txt' 2021-11-30T19:05:01,736 reading manifest file '/tmp/pip-pip-egg-info-rb91075a/chemfiles.egg-info/SOURCES.txt' 2021-11-30T19:05:01,738 adding license file 'LICENSE' 2021-11-30T19:05:01,740 writing manifest file '/tmp/pip-pip-egg-info-rb91075a/chemfiles.egg-info/SOURCES.txt' 2021-11-30T19:05:01,827 Source in /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509 has version 0.10.2, which satisfies requirement chemfiles==0.10.2 from https://files.pythonhosted.org/packages/59/c7/d180ab9df66cbe765b94d8ba145c1723ff34c69a9a1debe5b6ab6637a6f7/chemfiles-0.10.2.tar.gz#sha256=e277725803715762f9ea787f1ed51dbc2a83a47188ca3bf5d77ddcbc527f55f9 2021-11-30T19:05:01,828 Removed chemfiles==0.10.2 from https://files.pythonhosted.org/packages/59/c7/d180ab9df66cbe765b94d8ba145c1723ff34c69a9a1debe5b6ab6637a6f7/chemfiles-0.10.2.tar.gz#sha256=e277725803715762f9ea787f1ed51dbc2a83a47188ca3bf5d77ddcbc527f55f9 from build tracker '/tmp/pip-req-tracker-gf0sct74' 2021-11-30T19:05:01,832 Created temporary directory: /tmp/pip-unpack-bmgogqs4 2021-11-30T19:05:01,833 Building wheels for collected packages: chemfiles 2021-11-30T19:05:01,837 Created temporary directory: /tmp/pip-wheel-zkynf7bm 2021-11-30T19:05:01,838 Building wheel for chemfiles (setup.py): started 2021-11-30T19:05:01,838 Destination directory: /tmp/pip-wheel-zkynf7bm 2021-11-30T19:05:01,838 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/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-zkynf7bm 2021-11-30T19:05:03,232 -------------------------------------------------------------------------------- 2021-11-30T19:05:03,232 -- Trying "Ninja" generator 2021-11-30T19:05:03,232 -------------------------------- 2021-11-30T19:05:03,232 --------------------------- 2021-11-30T19:05:03,232 ---------------------- 2021-11-30T19:05:03,232 ----------------- 2021-11-30T19:05:03,233 ------------ 2021-11-30T19:05:03,233 ------- 2021-11-30T19:05:03,233 -- 2021-11-30T19:05:03,289 Not searching for unused variables given on the command line. 2021-11-30T19:05:03,361 CMake Error: CMake was unable to find a build program corresponding to "Ninja". CMAKE_MAKE_PROGRAM is not set. You probably need to select a different build tool. 2021-11-30T19:05:03,363 -- Configuring incomplete, errors occurred! 2021-11-30T19:05:03,363 See also "/tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/_cmake_test_compile/build/CMakeFiles/CMakeOutput.log". 2021-11-30T19:05:03,375 -- 2021-11-30T19:05:03,376 ------- 2021-11-30T19:05:03,376 ------------ 2021-11-30T19:05:03,376 ----------------- 2021-11-30T19:05:03,376 ---------------------- 2021-11-30T19:05:03,376 --------------------------- 2021-11-30T19:05:03,377 -------------------------------- 2021-11-30T19:05:03,377 -- Trying "Ninja" generator - failure 2021-11-30T19:05:03,377 -------------------------------------------------------------------------------- 2021-11-30T19:05:03,378 -------------------------------------------------------------------------------- 2021-11-30T19:05:03,378 -- Trying "Unix Makefiles" generator 2021-11-30T19:05:03,378 -------------------------------- 2021-11-30T19:05:03,378 --------------------------- 2021-11-30T19:05:03,378 ---------------------- 2021-11-30T19:05:03,378 ----------------- 2021-11-30T19:05:03,379 ------------ 2021-11-30T19:05:03,379 ------- 2021-11-30T19:05:03,379 -- 2021-11-30T19:05:03,447 Not searching for unused variables given on the command line. 2021-11-30T19:05:03,782 -- The C compiler identification is GNU 8.3.0 2021-11-30T19:05:03,817 -- Check for working C compiler: /usr/bin/cc 2021-11-30T19:05:04,242 -- Check for working C compiler: /usr/bin/cc -- works 2021-11-30T19:05:04,249 -- Detecting C compiler ABI info 2021-11-30T19:05:04,680 -- Detecting C compiler ABI info - done 2021-11-30T19:05:04,748 -- Detecting C compile features 2021-11-30T19:05:04,751 -- Detecting C compile features - done 2021-11-30T19:05:05,176 -- The CXX compiler identification is GNU 8.3.0 2021-11-30T19:05:05,203 -- Check for working CXX compiler: /usr/bin/c++ 2021-11-30T19:05:05,768 -- Check for working CXX compiler: /usr/bin/c++ -- works 2021-11-30T19:05:05,774 -- Detecting CXX compiler ABI info 2021-11-30T19:05:06,339 -- Detecting CXX compiler ABI info - done 2021-11-30T19:05:06,409 -- Detecting CXX compile features 2021-11-30T19:05:06,412 -- Detecting CXX compile features - done 2021-11-30T19:05:06,421 -- Configuring done 2021-11-30T19:05:06,432 -- Generating done 2021-11-30T19:05:06,441 -- Build files have been written to: /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/_cmake_test_compile/build 2021-11-30T19:05:06,450 -- 2021-11-30T19:05:06,450 ------- 2021-11-30T19:05:06,450 ------------ 2021-11-30T19:05:06,450 ----------------- 2021-11-30T19:05:06,451 ---------------------- 2021-11-30T19:05:06,451 --------------------------- 2021-11-30T19:05:06,451 -------------------------------- 2021-11-30T19:05:06,452 -- Trying "Unix Makefiles" generator - success 2021-11-30T19:05:06,452 -------------------------------------------------------------------------------- 2021-11-30T19:05:06,468 Configuring Project 2021-11-30T19:05:06,469 Working directory: 2021-11-30T19:05:06,469 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/_skbuild/linux-armv7l-3.7/cmake-build 2021-11-30T19:05:06,469 Command: 2021-11-30T19:05:06,469 cmake /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509 -G 'Unix Makefiles' -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/_skbuild/linux-armv7l-3.7/cmake-install -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 -DPYTHON_VERSION_STRING:STRING=3.7.3 -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.7m -DPYTHON_LIBRARY:FILEPATH=/usr/lib/arm-linux-gnueabihf/libpython3.7m.so -DSKBUILD:BOOL=TRUE -DCMAKE_MODULE_PATH:PATH=/usr/local/lib/python3.7/dist-packages/skbuild/resources/cmake -DCMAKE_BUILD_TYPE:STRING=Release 2021-11-30T19:05:06,608 -- Using internal chemfiles from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib 2021-11-30T19:05:06,893 -- The C compiler identification is GNU 8.3.0 2021-11-30T19:05:07,317 -- The CXX compiler identification is GNU 8.3.0 2021-11-30T19:05:07,348 -- Check for working C compiler: /usr/bin/cc 2021-11-30T19:05:07,790 -- Check for working C compiler: /usr/bin/cc -- works 2021-11-30T19:05:07,796 -- Detecting C compiler ABI info 2021-11-30T19:05:08,225 -- Detecting C compiler ABI info - done 2021-11-30T19:05:08,295 -- Detecting C compile features 2021-11-30T19:05:08,298 -- Detecting C compile features - done 2021-11-30T19:05:08,321 -- Check for working CXX compiler: /usr/bin/c++ 2021-11-30T19:05:08,882 -- Check for working CXX compiler: /usr/bin/c++ -- works 2021-11-30T19:05:08,889 -- Detecting CXX compiler ABI info 2021-11-30T19:05:09,460 -- Detecting CXX compiler ABI info - done 2021-11-30T19:05:09,532 -- Detecting CXX compile features 2021-11-30T19:05:09,535 -- Detecting CXX compile features - done 2021-11-30T19:06:04,703 -- Unpacking zlib sources 2021-11-30T19:06:07,271 -- Unpacking lzma sources 2021-11-30T19:06:15,068 -- Check if the system is big endian 2021-11-30T19:06:15,068 -- Searching 16 bit integer 2021-11-30T19:06:15,540 -- Using unsigned short 2021-11-30T19:06:15,995 -- Check if the system is big endian - little endian 2021-11-30T19:06:25,600 -- Unpacking bzip2 sources 2021-11-30T19:06:25,856 -- Unpacking fmt sources 2021-11-30T19:06:29,667 -- Unpacking toml11 sources 2021-11-30T19:06:29,932 -- Unpacking netcdf sources 2021-11-30T19:07:00,464 -- Unpacking tng sources 2021-11-30T19:07:00,856 -- Check if the system is big endian 2021-11-30T19:07:00,857 -- Searching 16 bit integer 2021-11-30T19:07:00,859 -- Using unsigned short 2021-11-30T19:07:01,306 -- Check if the system is big endian - little endian 2021-11-30T19:07:01,766 -- Unpacking molfiles sources 2021-11-30T19:07:02,203 -- Unpacking mmtf-cpp sources 2021-11-30T19:07:03,319 -- Unpacking pugixml sources 2021-11-30T19:07:03,691 -- Unpacking xdrfile sources 2021-11-30T19:07:04,365 -- Unpacking gemmi sources 2021-11-30T19:07:06,675 -- Configuring done 2021-11-30T19:07:07,340 -- Generating done 2021-11-30T19:07:07,388 CMake Warning: 2021-11-30T19:07:07,388 Manually-specified variables were not used by the project: 2021-11-30T19:07:07,389 PYTHON_EXECUTABLE 2021-11-30T19:07:07,389 PYTHON_INCLUDE_DIR 2021-11-30T19:07:07,389 PYTHON_LIBRARY 2021-11-30T19:07:07,389 PYTHON_VERSION_STRING 2021-11-30T19:07:07,389 SKBUILD 2021-11-30T19:07:07,395 -- Build files have been written to: /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/_skbuild/linux-armv7l-3.7/cmake-build 2021-11-30T19:07:07,919 Scanning dependencies of target xdrfile 2021-11-30T19:07:07,988 [ 0%] Building C object lib/external/xdrfile/CMakeFiles/xdrfile.dir/src/xdrfile.c.o 2021-11-30T19:07:10,344 [ 0%] Building C object lib/external/xdrfile/CMakeFiles/xdrfile.dir/src/xdrfile_trr.c.o 2021-11-30T19:07:11,025 [ 1%] Building C object lib/external/xdrfile/CMakeFiles/xdrfile.dir/src/xdrfile_xtc.c.o 2021-11-30T19:07:11,328 [ 1%] Built target xdrfile 2021-11-30T19:07:12,839 Scanning dependencies of target chemfiles_objects 2021-11-30T19:07:12,950 [ 1%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Atom.cpp.o 2021-11-30T19:07:15,800 [ 2%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Configuration.cpp.o 2021-11-30T19:07:31,681 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:07:31,681 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Configuration.cpp:7: 2021-11-30T19:07:31,681 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const toml::value&}; _Tp = toml::value; _Alloc = std::allocator]’: 2021-11-30T19:07:31,681 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:07:31,681 vector<_Tp, _Alloc>:: 2021-11-30T19:07:31,681 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:07:34,626 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {toml::value}; _Tp = toml::value; _Alloc = std::allocator]’: 2021-11-30T19:07:34,626 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:07:55,446 In file included from /usr/include/c++/8/vector:64, 2021-11-30T19:07:55,446 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Configuration.cpp:7: 2021-11-30T19:07:55,446 /usr/include/c++/8/bits/stl_vector.h: In function ‘toml::result > toml::detail::insert_nested_key(toml::table&, const toml::value&, InputIterator, InputIterator, toml::detail::region, bool) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; Container = std::vector]’: 2021-11-30T19:07:55,446 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:07:55,446 _M_realloc_insert(end(), __x); 2021-11-30T19:07:55,446 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:07:56,900 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:07:56,900 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Configuration.cpp:7: 2021-11-30T19:07:56,900 /usr/include/c++/8/bits/vector.tcc: In function ‘toml::result, toml::detail::region >, std::__cxx11::basic_string > toml::detail::parse_array(toml::detail::location&) [with Container = std::vector]’: 2021-11-30T19:07:56,900 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:07:56,900 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:07:56,900 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:07:59,301 [ 2%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Connectivity.cpp.o 2021-11-30T19:08:09,250 [ 3%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/File.cpp.o 2021-11-30T19:08:17,979 [ 3%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Format.cpp.o 2021-11-30T19:08:21,762 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:08:21,762 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Format.cpp:6: 2021-11-30T19:08:21,762 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: 2021-11-30T19:08:21,762 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:08:21,762 vector<_Tp, _Alloc>:: 2021-11-30T19:08:21,763 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:08:26,324 /usr/include/c++/8/bits/vector.tcc: In member function ‘virtual void chemfiles::TextFormat::write(const chemfiles::Frame&)’: 2021-11-30T19:08:26,324 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:08:26,324 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:08:26,325 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:08:26,861 [ 4%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/FormatFactory.cpp.o 2021-11-30T19:08:46,917 [ 4%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/FormatMetadata.cpp.o 2021-11-30T19:08:56,358 [ 5%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Frame.cpp.o 2021-11-30T19:09:01,709 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:09:01,710 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Frame.cpp:8: 2021-11-30T19:09:01,710 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const chemfiles::Vector3D&}; _Tp = chemfiles::Vector3D; _Alloc = std::allocator]’: 2021-11-30T19:09:01,710 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:09:01,710 vector<_Tp, _Alloc>:: 2021-11-30T19:09:01,710 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:09:01,763 In file included from /usr/include/c++/8/vector:64, 2021-11-30T19:09:01,763 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Frame.cpp:8: 2021-11-30T19:09:01,763 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::Frame::add_atom(chemfiles::Atom, chemfiles::Vector3D, chemfiles::Vector3D)’: 2021-11-30T19:09:01,763 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:09:01,764 _M_realloc_insert(end(), __x); 2021-11-30T19:09:01,764 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:09:01,764 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:09:01,764 _M_realloc_insert(end(), __x); 2021-11-30T19:09:01,765 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:09:07,325 [ 5%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Property.cpp.o 2021-11-30T19:09:15,758 [ 5%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Residue.cpp.o 2021-11-30T19:09:24,071 [ 6%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Selection.cpp.o 2021-11-30T19:09:35,431 [ 6%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Topology.cpp.o 2021-11-30T19:09:40,212 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:09:40,212 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Topology.cpp:5: 2021-11-30T19:09:40,212 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {chemfiles::Residue}; _Tp = chemfiles::Residue; _Alloc = std::allocator]’: 2021-11-30T19:09:40,213 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:09:40,213 vector<_Tp, _Alloc>:: 2021-11-30T19:09:40,213 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:09:40,569 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = chemfiles::Atom; _Alloc = std::allocator]’: 2021-11-30T19:09:40,569 /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:09:40,570 vector<_Tp, _Alloc>:: 2021-11-30T19:09:40,570 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:09:45,178 In file included from /usr/include/c++/8/vector:64, 2021-11-30T19:09:45,178 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Topology.cpp:5: 2021-11-30T19:09:45,178 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::Topology::resize(size_t)’: 2021-11-30T19:09:45,178 /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:09:45,178 _M_fill_insert(end(), __new_size - size(), __x); 2021-11-30T19:09:45,179 ^~~~~~~~~~~~~~ 2021-11-30T19:09:45,248 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:09:45,249 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Topology.cpp:5: 2021-11-30T19:09:45,249 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Topology::add_residue(chemfiles::Residue)’: 2021-11-30T19:09:45,249 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:09:45,249 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:09:45,249 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:09:45,694 [ 7%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Trajectory.cpp.o 2021-11-30T19:09:53,311 In file included from /usr/include/c++/8/memory:65, 2021-11-30T19:09:53,311 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/Trajectory.cpp:6: 2021-11-30T19:09:53,311 /usr/include/c++/8/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = chemfiles::Residue*; bool _TrivialValueTypes = false]’: 2021-11-30T19:09:53,312 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:09:53,312 __uninit_copy(_InputIterator __first, _InputIterator __last, 2021-11-30T19:09:53,312 ^~~~~~~~~~~~~ 2021-11-30T19:09:53,312 /usr/include/c++/8/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:09:54,033 /usr/include/c++/8/bits/stl_uninitialized.h: In member function ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = chemfiles::Residue; _Alloc = std::allocator]’: 2021-11-30T19:09:54,033 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:09:54,033 return std::__uninitialized_copy<__is_trivial(_ValueType1) 2021-11-30T19:09:54,033 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-11-30T19:09:54,033 && __is_trivial(_ValueType2) 2021-11-30T19:09:54,034 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-11-30T19:09:54,034 && __assignable>:: 2021-11-30T19:09:54,034 ~~~~~~~~~~~~~~~~~~ 2021-11-30T19:09:54,034 __uninit_copy(__first, __last, __result); 2021-11-30T19:09:54,034 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-11-30T19:09:59,672 [ 7%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/UnitCell.cpp.o 2021-11-30T19:10:08,030 [ 8%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/atom.cpp.o 2021-11-30T19:10:21,121 [ 8%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/cell.cpp.o 2021-11-30T19:10:32,562 [ 9%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/frame.cpp.o 2021-11-30T19:10:48,003 [ 9%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/misc.cpp.o 2021-11-30T19:10:58,467 [ 9%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/property.cpp.o 2021-11-30T19:11:08,718 [ 10%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/residue.cpp.o 2021-11-30T19:11:20,994 [ 10%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/selection.cpp.o 2021-11-30T19:11:31,005 [ 11%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/shared_allocator.cpp.o 2021-11-30T19:11:33,511 [ 11%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/topology.cpp.o 2021-11-30T19:11:48,428 [ 12%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/trajectory.cpp.o 2021-11-30T19:12:00,979 [ 12%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/Bz2File.cpp.o 2021-11-30T19:12:10,572 [ 13%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/GzFile.cpp.o 2021-11-30T19:12:20,021 [ 13%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/MemoryBuffer.cpp.o 2021-11-30T19:12:28,051 [ 13%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/MemoryFile.cpp.o 2021-11-30T19:12:36,055 [ 14%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/NcFile.cpp.o 2021-11-30T19:12:44,815 [ 14%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/PlainFile.cpp.o 2021-11-30T19:12:54,151 [ 15%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/TNGFile.cpp.o 2021-11-30T19:13:02,339 [ 15%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/XDRFile.cpp.o 2021-11-30T19:13:10,477 [ 16%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/XzFile.cpp.o 2021-11-30T19:13:20,025 [ 16%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/AmberNetCDF.cpp.o 2021-11-30T19:13:30,180 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp: In member function ‘void chemfiles::Amber::read_array(chemfiles::span, const string&) [with chemfiles::AmberFormat F = (chemfiles::AmberFormat)1]’: 2021-11-30T19:13:30,180 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp:207:6: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2021-11-30T19:13:30,180 void Amber::read_array(span array, const std::string& name) { 2021-11-30T19:13:30,180 ^~~~~~~~ 2021-11-30T19:13:30,241 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp: In member function ‘void chemfiles::Amber::read_array(chemfiles::span, const string&) [with chemfiles::AmberFormat F = (chemfiles::AmberFormat)0]’: 2021-11-30T19:13:30,241 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp:207:6: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2021-11-30T19:13:31,234 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp: In member function ‘void chemfiles::Amber::read_step(size_t, chemfiles::Frame&) [with chemfiles::AmberFormat F = (chemfiles::AmberFormat)1]’: 2021-11-30T19:13:31,234 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp:115:5: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2021-11-30T19:13:31,235 read_array(frame.positions(), "coordinates"); 2021-11-30T19:13:31,235 ^~~~~~~~~~ 2021-11-30T19:13:31,235 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp:118:9: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2021-11-30T19:13:31,235 read_array(*frame.velocities(), "velocities"); 2021-11-30T19:13:31,235 ^~~~~~~~~~ 2021-11-30T19:13:31,427 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp: In member function ‘void chemfiles::Amber::read_step(size_t, chemfiles::Frame&) [with chemfiles::AmberFormat F = (chemfiles::AmberFormat)0]’: 2021-11-30T19:13:31,428 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp:115:5: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2021-11-30T19:13:31,428 read_array(frame.positions(), "coordinates"); 2021-11-30T19:13:31,428 ^~~~~~~~~~ 2021-11-30T19:13:31,428 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/AmberNetCDF.cpp:118:9: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2021-11-30T19:13:31,428 read_array(*frame.velocities(), "velocities"); 2021-11-30T19:13:31,428 ^~~~~~~~~~ 2021-11-30T19:13:31,902 [ 17%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/CIF.cpp.o 2021-11-30T19:13:44,927 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:13:44,928 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/CIF.cpp:11: 2021-11-30T19:13:44,928 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::SmallStructure::Site&}; _Tp = gemmi::SmallStructure::Site; _Alloc = std::allocator]’: 2021-11-30T19:13:44,928 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:13:44,928 vector<_Tp, _Alloc>:: 2021-11-30T19:13:44,928 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:13:45,114 In file included from /usr/include/c++/8/vector:64, 2021-11-30T19:13:45,114 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/CIF.cpp:11: 2021-11-30T19:13:45,114 /usr/include/c++/8/bits/stl_vector.h: In member function ‘std::vector gemmi::SmallStructure::get_all_unit_cell_sites() const’: 2021-11-30T19:13:45,115 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:13:45,115 _M_realloc_insert(end(), __x); 2021-11-30T19:13:45,115 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:13:45,116 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:13:45,116 _M_realloc_insert(end(), __x); 2021-11-30T19:13:45,116 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:13:46,227 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:13:46,228 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/CIF.cpp:11: 2021-11-30T19:13:46,228 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::SmallStructure::AtomType&}; _Tp = gemmi::SmallStructure::AtomType; _Alloc = std::allocator]’: 2021-11-30T19:13:46,228 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:13:46,228 vector<_Tp, _Alloc>:: 2021-11-30T19:13:46,228 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:13:46,719 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33&, gemmi::Vec3&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: 2021-11-30T19:13:46,720 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:13:46,788 /usr/include/c++/8/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const SG*) [with SG = gemmi::SpaceGroup]’: 2021-11-30T19:13:46,788 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:13:46,789 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:13:46,789 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:13:47,208 In file included from /usr/include/c++/8/vector:64, 2021-11-30T19:13:47,209 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/CIF.cpp:11: 2021-11-30T19:13:47,209 /usr/include/c++/8/bits/stl_vector.h: In function ‘gemmi::SmallStructure gemmi::make_small_structure_from_block(const gemmi::cif::Block&)’: 2021-11-30T19:13:47,209 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:13:47,209 _M_realloc_insert(end(), __x); 2021-11-30T19:13:47,209 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:13:47,213 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:13:47,213 _M_realloc_insert(end(), __x); 2021-11-30T19:13:47,213 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:13:48,077 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:13:48,077 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/CIF.cpp:11: 2021-11-30T19:13:48,077 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::SmallStructure&}; _Tp = gemmi::SmallStructure; _Alloc = std::allocator]’: 2021-11-30T19:13:48,078 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:13:48,078 vector<_Tp, _Alloc>:: 2021-11-30T19:13:48,078 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:13:54,478 In file included from /usr/include/c++/8/vector:64, 2021-11-30T19:13:54,479 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/CIF.cpp:11: 2021-11-30T19:13:54,479 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::CIFFormat::init_()’: 2021-11-30T19:13:54,479 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:13:54,479 _M_realloc_insert(end(), __x); 2021-11-30T19:13:54,479 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:13:54,876 [ 17%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/CML.cpp.o 2021-11-30T19:14:07,980 [ 17%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/CSSR.cpp.o 2021-11-30T19:14:19,876 [ 18%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/GRO.cpp.o 2021-11-30T19:14:32,053 [ 18%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/LAMMPSData.cpp.o 2021-11-30T19:14:41,229 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:14:41,230 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/LAMMPSData.cpp:11: 2021-11-30T19:14:41,230 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]’: 2021-11-30T19:14:41,230 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector, double>, std::allocator, double> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator, double>*, std::vector, double>, std::allocator, double> > > >’} changed in GCC 7.1 2021-11-30T19:14:41,230 vector<_Tp, _Alloc>:: 2021-11-30T19:14:41,230 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:14:47,804 /usr/include/c++/8/bits/vector.tcc: In constructor ‘chemfiles::DataTypes::DataTypes(const chemfiles::Topology&)’: 2021-11-30T19:14:47,804 /usr/include/c++/8/bits/vector.tcc:343:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, double>*, std::vector, double>, std::allocator, double> > > >’ changed in GCC 7.1 2021-11-30T19:14:47,804 _M_realloc_insert(begin() + __n, std::move(__v)); 2021-11-30T19:14:47,804 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:14:49,020 [ 19%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/LAMMPSTrajectory.cpp.o 2021-11-30T19:15:02,534 [ 19%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/MMTF.cpp.o 2021-11-30T19:15:22,425 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:15:22,425 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/MMTF.cpp:8: 2021-11-30T19:15:22,426 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {chemfiles::Residue&}; _Tp = chemfiles::Residue; _Alloc = std::allocator]’: 2021-11-30T19:15:22,426 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:15:22,426 vector<_Tp, _Alloc>:: 2021-11-30T19:15:22,426 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:15:22,866 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::MMTFFormat::apply_symmetry(chemfiles::Frame&)’: 2021-11-30T19:15:22,866 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:15:22,866 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:15:22,866 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:15:31,019 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/MMTF.cpp: In member function ‘void chemfiles::MMTFFormat::read_group(chemfiles::Frame&, size_t, chemfiles::Residue&, chemfiles::span)’: 2021-11-30T19:15:31,019 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/MMTF.cpp:294:6: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2021-11-30T19:15:31,020 void MMTFFormat::read_group(Frame& frame, size_t group_type, Residue& residue, span positions) { 2021-11-30T19:15:31,020 ^~~~~~~~~~ 2021-11-30T19:15:31,227 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/MMTF.cpp: In member function ‘void chemfiles::MMTFFormat::read_model(chemfiles::Frame&)’: 2021-11-30T19:15:31,227 /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/MMTF.cpp:235:23: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2021-11-30T19:15:31,227 read_group(frame, group_type, residue, positions); 2021-11-30T19:15:31,227 ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-11-30T19:15:32,476 [ 20%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/MOL2.cpp.o 2021-11-30T19:15:45,539 [ 20%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/Molfile.cpp.o 2021-11-30T19:15:52,384 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:15:52,384 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/Molfile.cpp:14: 2021-11-30T19:15:52,384 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {chemfiles::Frame}; _Tp = chemfiles::Frame; _Alloc = std::allocator]’: 2021-11-30T19:15:52,385 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:15:52,385 vector<_Tp, _Alloc>:: 2021-11-30T19:15:52,385 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:15:58,477 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Molfile::read(chemfiles::Frame&) [with chemfiles::MolfileFormat F = (chemfiles::MolfileFormat)0]’: 2021-11-30T19:15:58,478 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:15:58,478 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:15:58,478 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:15:58,579 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Molfile::read(chemfiles::Frame&) [with chemfiles::MolfileFormat F = (chemfiles::MolfileFormat)1]’: 2021-11-30T19:15:58,580 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:15:58,580 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:15:58,580 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:15:58,682 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Molfile::read(chemfiles::Frame&) [with chemfiles::MolfileFormat F = (chemfiles::MolfileFormat)2]’: 2021-11-30T19:15:58,682 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:15:58,682 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:15:58,682 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:15:58,783 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Molfile::read(chemfiles::Frame&) [with chemfiles::MolfileFormat F = (chemfiles::MolfileFormat)3]’: 2021-11-30T19:15:58,784 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:15:58,784 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:15:58,784 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:15:59,082 [ 21%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/PDB.cpp.o 2021-11-30T19:16:07,173 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:16:07,173 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/PDB.cpp:12: 2021-11-30T19:16:07,173 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]’: 2021-11-30T19:16:07,174 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:16:07,174 vector<_Tp, _Alloc>:: 2021-11-30T19:16:07,174 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:16:13,869 /usr/include/c++/8/bits/vector.tcc: In member function ‘virtual void chemfiles::PDBFormat::write_next(const chemfiles::Frame&)’: 2021-11-30T19:16:13,869 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:16:13,869 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:16:13,869 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:16:13,870 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:16:13,870 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:16:13,870 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:16:15,241 [ 21%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/SDF.cpp.o 2021-11-30T19:16:26,904 [ 21%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/SMI.cpp.o 2021-11-30T19:16:35,109 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:16:35,109 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/SMI.cpp:14: 2021-11-30T19:16:35,109 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {chemfiles::Residue}; _Tp = chemfiles::Residue; _Alloc = std::allocator]’: 2021-11-30T19:16:35,109 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:16:35,109 vector<_Tp, _Alloc>:: 2021-11-30T19:16:35,110 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:16:35,203 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {chemfiles::Residue}; _Tp = chemfiles::Residue; _Alloc = std::allocator]’: 2021-11-30T19:16:35,203 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:16:35,203 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:16:35,204 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:16:42,401 /usr/include/c++/8/bits/vector.tcc: In member function ‘virtual void chemfiles::SMIFormat::read_next(chemfiles::Frame&)’: 2021-11-30T19:16:42,402 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:16:42,402 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:16:42,402 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:16:43,105 [ 22%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/TNG.cpp.o 2021-11-30T19:16:47,911 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:16:47,911 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/TNG.cpp:9: 2021-11-30T19:16:47,911 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: 2021-11-30T19:16:47,912 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:16:47,912 vector<_Tp, _Alloc>:: 2021-11-30T19:16:47,912 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:16:53,318 In file included from /usr/include/c++/8/vector:64, 2021-11-30T19:16:53,318 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/TNG.cpp:9: 2021-11-30T19:16:53,318 /usr/include/c++/8/bits/stl_vector.h: In constructor ‘chemfiles::TNGFormat::TNGFormat(std::__cxx11::string, chemfiles::File::Mode, chemfiles::File::Compression)’: 2021-11-30T19:16:53,318 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:16:53,318 _M_realloc_insert(end(), __x); 2021-11-30T19:16:53,319 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:16:53,569 [ 22%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/TRR.cpp.o 2021-11-30T19:17:03,058 [ 23%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/Tinker.cpp.o 2021-11-30T19:17:14,914 [ 23%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/XTC.cpp.o 2021-11-30T19:17:24,135 [ 24%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/XYZ.cpp.o 2021-11-30T19:17:39,110 [ 24%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/mmCIF.cpp.o 2021-11-30T19:17:46,142 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:17:46,143 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/mmCIF.cpp:8: 2021-11-30T19:17:46,143 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: 2021-11-30T19:17:46,143 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:17:46,143 vector<_Tp, _Alloc>:: 2021-11-30T19:17:46,143 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:17:46,285 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {chemfiles::Residue}; _Tp = chemfiles::Residue; _Alloc = std::allocator]’: 2021-11-30T19:17:46,285 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:17:46,285 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:17:51,538 In file included from /usr/include/c++/8/vector:64, 2021-11-30T19:17:51,538 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/mmCIF.cpp:8: 2021-11-30T19:17:51,538 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::mmCIFFormat::init_()’: 2021-11-30T19:17:51,538 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:17:51,539 _M_realloc_insert(end(), __x); 2021-11-30T19:17:51,539 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:17:51,540 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:17:51,540 _M_realloc_insert(end(), __x); 2021-11-30T19:17:51,540 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:17:52,185 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:17:52,185 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/formats/mmCIF.cpp:8: 2021-11-30T19:17:52,185 /usr/include/c++/8/bits/vector.tcc: In member function ‘virtual void chemfiles::mmCIFFormat::read(chemfiles::Frame&)’: 2021-11-30T19:17:52,185 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:17:52,186 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:17:52,186 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:17:52,989 [ 24%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/guess_format.cpp.o 2021-11-30T19:18:01,547 [ 25%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/parse.cpp.o 2021-11-30T19:18:11,392 [ 25%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/pdb_connectivity.cpp.o 2021-11-30T19:18:21,570 [ 26%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/periodic_table.cpp.o 2021-11-30T19:18:27,708 [ 26%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/selections/NumericValues.cpp.o 2021-11-30T19:18:35,467 [ 27%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/selections/expr.cpp.o 2021-11-30T19:18:48,088 [ 27%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/selections/lexer.cpp.o 2021-11-30T19:18:51,842 In file included from /usr/include/c++/8/vector:69, 2021-11-30T19:18:51,843 from /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/lib/src/selections/lexer.cpp:8: 2021-11-30T19:18:51,843 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {chemfiles::selections::Token}; _Tp = chemfiles::selections::Token; _Alloc = std::allocator]’: 2021-11-30T19:18:51,843 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2021-11-30T19:18:51,843 vector<_Tp, _Alloc>:: 2021-11-30T19:18:51,843 ^~~~~~~~~~~~~~~~~~~ 2021-11-30T19:18:51,892 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {chemfiles::selections::Token}; _Tp = chemfiles::selections::Token; _Alloc = std::allocator]’: 2021-11-30T19:18:51,892 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-11-30T19:18:51,892 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-11-30T19:18:51,892 ^~~~~~~~~~~~~~~~~ 2021-11-30T19:18:57,275 [ 28%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/selections/parser.cpp.o 2021-11-30T19:19:14,467 [ 28%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/utils.cpp.o 2021-11-30T19:19:16,425 [ 28%] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/warnings.cpp.o 2021-11-30T19:19:18,396 [ 28%] Built target chemfiles_objects 2021-11-30T19:19:18,506 Scanning dependencies of target zlib 2021-11-30T19:19:18,576 [ 28%] Building C object lib/external/zlib/CMakeFiles/zlib.dir/adler32.c.o 2021-11-30T19:19:18,936 [ 29%] Building C object 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lib/external/molfiles/CMakeFiles/molfiles.dir/src/dcdplugin.c.o 2021-11-30T19:21:43,727 [ 99%] Building CXX object lib/external/molfiles/CMakeFiles/molfiles.dir/src/gromacsplugin.cxx.o 2021-11-30T19:21:46,115 [ 99%] Building C object lib/external/molfiles/CMakeFiles/molfiles.dir/src/moldenplugin.c.o 2021-11-30T19:21:47,927 [100%] Building C object lib/external/molfiles/CMakeFiles/molfiles.dir/src/psfplugin.c.o 2021-11-30T19:21:49,287 [100%] Built target molfiles 2021-11-30T19:21:49,359 Scanning dependencies of target chemfiles 2021-11-30T19:21:49,464 [100%] Linking CXX shared library libchemfiles.so 2021-11-30T19:21:52,318 [100%] Built target chemfiles 2021-11-30T19:21:52,386 Scanning dependencies of target build_chemfiles 2021-11-30T19:21:52,452 [100%] Built target build_chemfiles 2021-11-30T19:21:52,602 Install the project... 2021-11-30T19:21:52,652 -- Install configuration: "Release" 2021-11-30T19:21:52,656 -- Installing: /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/_skbuild/linux-armv7l-3.7/cmake-install/chemfiles/libchemfiles.so.0.10.2 2021-11-30T19:21:52,735 -- Installing: /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/_skbuild/linux-armv7l-3.7/cmake-install/chemfiles/libchemfiles.so.0.10 2021-11-30T19:21:52,737 -- Installing: /tmp/pip-wheel-tagftt49/chemfiles_1460ed86e4c74d4ea52120f75bb33509/_skbuild/linux-armv7l-3.7/cmake-install/chemfiles/libchemfiles.so 2021-11-30T19:21:52,755 copying chemfiles/clib.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/clib.py 2021-11-30T19:21:52,757 copying chemfiles/misc.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/misc.py 2021-11-30T19:21:52,759 copying chemfiles/topology.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/topology.py 2021-11-30T19:21:52,762 copying chemfiles/property.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/property.py 2021-11-30T19:21:52,764 copying chemfiles/cell.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/cell.py 2021-11-30T19:21:52,767 copying chemfiles/ffi.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/ffi.py 2021-11-30T19:21:52,770 copying chemfiles/atom.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/atom.py 2021-11-30T19:21:52,772 copying chemfiles/trajectory.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/trajectory.py 2021-11-30T19:21:52,777 copying chemfiles/frame.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/frame.py 2021-11-30T19:21:52,779 copying chemfiles/selection.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/selection.py 2021-11-30T19:21:52,781 copying chemfiles/__init__.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/__init__.py 2021-11-30T19:21:52,783 copying chemfiles/utils.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/utils.py 2021-11-30T19:21:52,785 copying chemfiles/residue.py -> _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/residue.py 2021-11-30T19:21:52,832 running bdist_wheel 2021-11-30T19:21:52,836 running build 2021-11-30T19:21:52,836 running build_py 2021-11-30T19:21:52,838 creating _skbuild/linux-armv7l-3.7/setuptools/lib 2021-11-30T19:21:52,839 creating _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,840 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/clib.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,842 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/misc.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,844 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/topology.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,846 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/property.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,848 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/cell.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,851 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/ffi.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,854 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/atom.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,856 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/trajectory.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,858 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/frame.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,861 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/selection.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,863 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/__init__.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,865 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/utils.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,867 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/residue.py -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,875 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/libchemfiles.so -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:52,963 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/libchemfiles.so.0.10.2 -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:53,053 copying _skbuild/linux-armv7l-3.7/cmake-install/chemfiles/libchemfiles.so.0.10 -> _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles 2021-11-30T19:21:53,150 copied 13 files 2021-11-30T19:21:53,151 running build_ext 2021-11-30T19:21:53,152 installing to _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel 2021-11-30T19:21:53,152 running install 2021-11-30T19:21:53,154 running install_lib 2021-11-30T19:21:53,156 creating _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l 2021-11-30T19:21:53,156 creating _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel 2021-11-30T19:21:53,159 creating _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,160 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/libchemfiles.so.0.10 -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,248 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/clib.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,250 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/misc.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,253 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/libchemfiles.so -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,337 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/topology.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,339 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/property.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,341 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/cell.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,343 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/ffi.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,346 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/atom.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,349 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/trajectory.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,351 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/frame.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,353 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/selection.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,356 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/libchemfiles.so.0.10.2 -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,447 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/__init__.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,449 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/utils.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,451 copying _skbuild/linux-armv7l-3.7/setuptools/lib/chemfiles/residue.py -> _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles 2021-11-30T19:21:53,453 copied 16 files 2021-11-30T19:21:53,453 running install_egg_info 2021-11-30T19:21:53,465 running egg_info 2021-11-30T19:21:53,466 creating chemfiles.egg-info 2021-11-30T19:21:53,467 writing chemfiles.egg-info/PKG-INFO 2021-11-30T19:21:53,470 writing dependency_links to chemfiles.egg-info/dependency_links.txt 2021-11-30T19:21:53,472 writing requirements to chemfiles.egg-info/requires.txt 2021-11-30T19:21:53,473 writing top-level names to chemfiles.egg-info/top_level.txt 2021-11-30T19:21:53,475 writing manifest file 'chemfiles.egg-info/SOURCES.txt' 2021-11-30T19:21:53,480 reading manifest file 'chemfiles.egg-info/SOURCES.txt' 2021-11-30T19:21:53,481 adding license file 'LICENSE' 2021-11-30T19:21:53,485 writing manifest file 'chemfiles.egg-info/SOURCES.txt' 2021-11-30T19:21:53,486 Copying chemfiles.egg-info to _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles-0.10.2-py3.7.egg-info 2021-11-30T19:21:53,500 running install_scripts 2021-11-30T19:21:53,583 copied 0 files 2021-11-30T19:21:53,600 adding license file "LICENSE" (matched pattern "LICENSE") 2021-11-30T19:21:53,604 creating _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel/chemfiles-0.10.2.dist-info/WHEEL 2021-11-30T19:21:53,607 creating '/tmp/pip-wheel-zkynf7bm/chemfiles-0.10.2-py2.py3-none-linux_armv7l.whl' and adding '_skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel' to it 2021-11-30T19:21:53,610 adding 'chemfiles/__init__.py' 2021-11-30T19:21:53,611 adding 'chemfiles/atom.py' 2021-11-30T19:21:53,613 adding 'chemfiles/cell.py' 2021-11-30T19:21:53,615 adding 'chemfiles/clib.py' 2021-11-30T19:21:53,619 adding 'chemfiles/ffi.py' 2021-11-30T19:21:53,621 adding 'chemfiles/frame.py' 2021-11-30T19:21:54,413 adding 'chemfiles/libchemfiles.so' 2021-11-30T19:21:55,234 adding 'chemfiles/libchemfiles.so.0.10' 2021-11-30T19:21:56,055 adding 'chemfiles/libchemfiles.so.0.10.2' 2021-11-30T19:21:56,091 adding 'chemfiles/misc.py' 2021-11-30T19:21:56,093 adding 'chemfiles/property.py' 2021-11-30T19:21:56,094 adding 'chemfiles/residue.py' 2021-11-30T19:21:56,095 adding 'chemfiles/selection.py' 2021-11-30T19:21:56,097 adding 'chemfiles/topology.py' 2021-11-30T19:21:56,099 adding 'chemfiles/trajectory.py' 2021-11-30T19:21:56,100 adding 'chemfiles/utils.py' 2021-11-30T19:21:56,103 adding 'chemfiles-0.10.2.dist-info/LICENSE' 2021-11-30T19:21:56,104 adding 'chemfiles-0.10.2.dist-info/METADATA' 2021-11-30T19:21:56,105 adding 'chemfiles-0.10.2.dist-info/WHEEL' 2021-11-30T19:21:56,106 adding 'chemfiles-0.10.2.dist-info/top_level.txt' 2021-11-30T19:21:56,106 adding 'chemfiles-0.10.2.dist-info/RECORD' 2021-11-30T19:21:56,192 removing _skbuild/linux-armv7l-3.7/setuptools/bdist.linux-armv7l/wheel 2021-11-30T19:21:56,303 Building wheel for chemfiles (setup.py): finished with status 'done' 2021-11-30T19:21:56,365 Created wheel for chemfiles: filename=chemfiles-0.10.2-py2.py3-none-linux_armv7l.whl size=4755992 sha256=c6425e8b59a3cad6ec1b4700d2ebb84e6d2251657ae3bc9d4402a4bf5b8e761c 2021-11-30T19:21:56,365 Stored in directory: /tmp/pip-ephem-wheel-cache-68ke_1ep/wheels/f2/15/e0/7201afd41365f41e8118b4b8968029f0ee6c0703d0aacfbe5c 2021-11-30T19:21:56,377 Successfully built chemfiles 2021-11-30T19:21:56,549 Removed build tracker: '/tmp/pip-req-tracker-gf0sct74'