2022-08-28T00:15:51,552 Created temporary directory: /tmp/pip-ephem-wheel-cache-rrvsprow 2022-08-28T00:15:51,557 Created temporary directory: /tmp/pip-build-tracker-1d558vfp 2022-08-28T00:15:51,558 Initialized build tracking at /tmp/pip-build-tracker-1d558vfp 2022-08-28T00:15:51,559 Created build tracker: /tmp/pip-build-tracker-1d558vfp 2022-08-28T00:15:51,559 Entered build tracker: /tmp/pip-build-tracker-1d558vfp 2022-08-28T00:15:51,560 Created temporary directory: /tmp/pip-wheel-sy80jazc 2022-08-28T00:15:51,631 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-08-28T00:15:51,639 2 location(s) to search for versions of chemfiles: 2022-08-28T00:15:51,639 * https://pypi.org/simple/chemfiles/ 2022-08-28T00:15:51,639 * https://www.piwheels.org/simple/chemfiles/ 2022-08-28T00:15:51,640 Fetching project page and analyzing links: https://pypi.org/simple/chemfiles/ 2022-08-28T00:15:51,641 Getting page https://pypi.org/simple/chemfiles/ 2022-08-28T00:15:51,645 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Fetching project page and analyzing links: https://www.piwheels.org/simple/chemfiles/ 2022-08-28T00:15:51,901 Getting page https://www.piwheels.org/simple/chemfiles/ 2022-08-28T00:15:51,903 Found index url https://www.piwheels.org/simple 2022-08-28T00:15:52,135 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.10.2-py2.py3-none-linux_armv7l.whl#sha256=c6425e8b59a3cad6ec1b4700d2ebb84e6d2251657ae3bc9d4402a4bf5b8e761c (from https://www.piwheels.org/simple/chemfiles/) 2022-08-28T00:15:52,136 Skipping link: No binaries permitted for chemfiles: https://www.piwheels.org/simple/chemfiles/chemfiles-0.10.2-py2.py3-none-linux_armv6l.whl#sha256=c6425e8b59a3cad6ec1b4700d2ebb84e6d2251657ae3bc9d4402a4bf5b8e761c (from https://www.piwheels.org/simple/chemfiles/) 2022-08-28T00:15:52,137 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/) 2022-08-28T00:15:52,137 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/) 2022-08-28T00:15:52,138 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/) 2022-08-28T00:15:52,138 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/) 2022-08-28T00:15:52,139 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/) 2022-08-28T00:15:52,140 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/) 2022-08-28T00:15:52,140 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/) 2022-08-28T00:15:52,141 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/) 2022-08-28T00:15:52,141 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/) 2022-08-28T00:15:52,142 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/) 2022-08-28T00:15:52,142 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/) 2022-08-28T00:15:52,143 Skipping link: not a file: https://www.piwheels.org/simple/chemfiles/ 2022-08-28T00:15:52,143 Skipping link: not a file: https://pypi.org/simple/chemfiles/ 2022-08-28T00:15:52,179 Given no hashes to check 1 links for project 'chemfiles': discarding no candidates 2022-08-28T00:15:52,210 Collecting chemfiles==0.10.3 2022-08-28T00:15:52,214 Created temporary directory: /tmp/pip-unpack-syspld9o 2022-08-28T00:15:53,386 Downloading chemfiles-0.10.3.tar.gz (3.6 MB) 2022-08-28T00:15:55,438 Added chemfiles==0.10.3 from https://files.pythonhosted.org/packages/40/ed/ad8fc9ac327b791bc20a8daf2b1ce3e83b45bed640575b6ac04ec02723ce/chemfiles-0.10.3.tar.gz#sha256=4bbb8b116492a57dbf6ddb4c84aad0133cd782e0cc0e53e4b957f2d93e6806ea to build tracker '/tmp/pip-build-tracker-1d558vfp' 2022-08-28T00:15:55,452 Created temporary directory: /tmp/pip-build-env-sdnvz598 2022-08-28T00:15:55,468 Created temporary directory: /tmp/pip-standalone-pip-b2ujsdos 2022-08-28T00:15:57,857 Installing build dependencies: started 2022-08-28T00:15:57,859 Running command pip subprocess to install build dependencies 2022-08-28T00:16:07,431 Using pip 22.1.2 from /tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip (python 3.7) 2022-08-28T00:16:09,580 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-08-28T00:16:13,763 Collecting setuptools>=44 2022-08-28T00:16:14,039 Using cached https://www.piwheels.org/simple/setuptools/setuptools-65.3.0-py3-none-any.whl (1.2 MB) 2022-08-28T00:16:14,692 Collecting wheel>=0.36 2022-08-28T00:16:14,724 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-08-28T00:16:15,325 Collecting ninja 2022-08-28T00:16:15,365 Using cached https://www.piwheels.org/simple/ninja/ninja-1.10.0.post2-cp37-cp37m-linux_armv7l.whl (91 kB) 2022-08-28T00:16:17,213 Collecting cmake 2022-08-28T00:16:20,435 Using cached https://www.piwheels.org/simple/cmake/cmake-3.24.1-cp37-cp37m-linux_armv7l.whl (15.7 MB) 2022-08-28T00:16:34,372 Installing collected packages: ninja, cmake, wheel, setuptools 2022-08-28T00:16:34,486 Creating /tmp/pip-build-env-sdnvz598/overlay/bin 2022-08-28T00:16:34,491 changing mode of /tmp/pip-build-env-sdnvz598/overlay/bin/ninja to 755 2022-08-28T00:16:47,697 changing mode of /tmp/pip-build-env-sdnvz598/overlay/bin/cmake to 755 2022-08-28T00:16:47,702 changing mode of /tmp/pip-build-env-sdnvz598/overlay/bin/cpack to 755 2022-08-28T00:16:47,706 changing mode of /tmp/pip-build-env-sdnvz598/overlay/bin/ctest to 755 2022-08-28T00:16:48,146 changing mode of /tmp/pip-build-env-sdnvz598/overlay/bin/wheel to 755 2022-08-28T00:16:53,020 Successfully installed cmake-3.24.1 ninja-1.10.0.post2 setuptools-65.3.0 wheel-0.37.1 2022-08-28T00:16:53,290 --- Logging error --- 2022-08-28T00:16:53,291 Traceback (most recent call last): 2022-08-28T00:16:53,291 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/utils/logging.py", line 177, in emit 2022-08-28T00:16:53,292 self.console.print(renderable, overflow="ignore", crop=False, style=style) 2022-08-28T00:16:53,292 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_vendor/rich/console.py", line 1752, in print 2022-08-28T00:16:53,293 extend(render(renderable, render_options)) 2022-08-28T00:16:53,293 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_vendor/rich/console.py", line 1390, in render 2022-08-28T00:16:53,293 for render_output in iter_render: 2022-08-28T00:16:53,294 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/utils/logging.py", line 134, in __rich_console__ 2022-08-28T00:16:53,294 for line in lines: 2022-08-28T00:16:53,294 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_vendor/rich/segment.py", line 245, in split_lines 2022-08-28T00:16:53,294 for segment in segments: 2022-08-28T00:16:53,295 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_vendor/rich/console.py", line 1368, in render 2022-08-28T00:16:53,295 renderable = rich_cast(renderable) 2022-08-28T00:16:53,295 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_vendor/rich/protocol.py", line 36, in rich_cast 2022-08-28T00:16:53,296 renderable = cast_method() 2022-08-28T00:16:53,296 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/self_outdated_check.py", line 130, in __rich__ 2022-08-28T00:16:53,296 pip_cmd = get_best_invocation_for_this_pip() 2022-08-28T00:16:53,297 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/utils/entrypoints.py", line 60, in get_best_invocation_for_this_pip 2022-08-28T00:16:53,297 os.path.join(binary_prefix, exe_name), 2022-08-28T00:16:53,297 File "/usr/lib/python3.7/genericpath.py", line 97, in samefile 2022-08-28T00:16:53,298 s2 = os.stat(f2) 2022-08-28T00:16:53,298 FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/pip3.7' 2022-08-28T00:16:53,298 Call stack: 2022-08-28T00:16:53,298 File "/usr/lib/python3.7/runpy.py", line 193, in _run_module_as_main 2022-08-28T00:16:53,299 "__main__", mod_spec) 2022-08-28T00:16:53,299 File "/usr/lib/python3.7/runpy.py", line 85, in _run_code 2022-08-28T00:16:53,299 exec(code, run_globals) 2022-08-28T00:16:53,300 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/__main__.py", line 31, in 2022-08-28T00:16:53,300 sys.exit(_main()) 2022-08-28T00:16:53,300 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/cli/main.py", line 70, in main 2022-08-28T00:16:53,301 return command.main(cmd_args) 2022-08-28T00:16:53,301 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/cli/base_command.py", line 101, in main 2022-08-28T00:16:53,301 return self._main(args) 2022-08-28T00:16:53,302 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/cli/base_command.py", line 223, in _main 2022-08-28T00:16:53,302 self.handle_pip_version_check(options) 2022-08-28T00:16:53,302 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/cli/req_command.py", line 148, in handle_pip_version_check 2022-08-28T00:16:53,303 pip_self_version_check(session, options) 2022-08-28T00:16:53,303 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/self_outdated_check.py", line 237, in pip_self_version_check 2022-08-28T00:16:53,303 logger.info("[present-rich] %s", upgrade_prompt) 2022-08-28T00:16:53,303 File "/usr/lib/python3.7/logging/__init__.py", line 1383, in info 2022-08-28T00:16:53,304 self._log(INFO, msg, args, **kwargs) 2022-08-28T00:16:53,304 File "/usr/lib/python3.7/logging/__init__.py", line 1519, in _log 2022-08-28T00:16:53,304 self.handle(record) 2022-08-28T00:16:53,305 File "/usr/lib/python3.7/logging/__init__.py", line 1529, in handle 2022-08-28T00:16:53,305 self.callHandlers(record) 2022-08-28T00:16:53,305 File "/usr/lib/python3.7/logging/__init__.py", line 1591, in callHandlers 2022-08-28T00:16:53,306 hdlr.handle(record) 2022-08-28T00:16:53,306 File "/usr/lib/python3.7/logging/__init__.py", line 905, in handle 2022-08-28T00:16:53,306 self.emit(record) 2022-08-28T00:16:53,306 File "/tmp/pip-standalone-pip-b2ujsdos/__env_pip__.zip/pip/_internal/utils/logging.py", line 179, in emit 2022-08-28T00:16:53,307 self.handleError(record) 2022-08-28T00:16:53,307 Message: '[present-rich] %s' 2022-08-28T00:16:53,307 Arguments: (UpgradePrompt(old='22.1.2', new='22.2.2'),) 2022-08-28T00:16:53,829 Installing build dependencies: finished with status 'done' 2022-08-28T00:16:53,856 Getting requirements to build wheel: started 2022-08-28T00:16:53,858 Running command Getting requirements to build wheel 2022-08-28T00:16:59,864 running egg_info 2022-08-28T00:17:00,487 writing src/chemfiles.egg-info/PKG-INFO 2022-08-28T00:17:01,072 writing dependency_links to src/chemfiles.egg-info/dependency_links.txt 2022-08-28T00:17:04,045 writing requirements to src/chemfiles.egg-info/requires.txt 2022-08-28T00:17:04,644 writing top-level names to src/chemfiles.egg-info/top_level.txt 2022-08-28T00:17:05,370 reading manifest file 'src/chemfiles.egg-info/SOURCES.txt' 2022-08-28T00:17:05,443 reading manifest template 'MANIFEST.in' 2022-08-28T00:17:05,445 warning: no files found matching '*' under directory 'chemfiles' 2022-08-28T00:17:05,633 no previously-included directories found matching 'lib/tests' 2022-08-28T00:17:05,635 no previously-included directories found matching 'lib/doc' 2022-08-28T00:17:05,636 adding license file 'LICENSE' 2022-08-28T00:17:05,666 writing manifest file 'src/chemfiles.egg-info/SOURCES.txt' 2022-08-28T00:17:05,899 Getting requirements to build wheel: finished with status 'done' 2022-08-28T00:17:05,922 Created temporary directory: /tmp/pip-modern-metadata-yg5qcnxe 2022-08-28T00:17:05,927 Preparing metadata (pyproject.toml): started 2022-08-28T00:17:05,930 Running command Preparing metadata (pyproject.toml) 2022-08-28T00:17:11,737 running dist_info 2022-08-28T00:17:12,396 creating /tmp/pip-modern-metadata-yg5qcnxe/chemfiles.egg-info 2022-08-28T00:17:13,027 writing /tmp/pip-modern-metadata-yg5qcnxe/chemfiles.egg-info/PKG-INFO 2022-08-28T00:17:13,624 writing dependency_links to /tmp/pip-modern-metadata-yg5qcnxe/chemfiles.egg-info/dependency_links.txt 2022-08-28T00:17:16,591 writing requirements to /tmp/pip-modern-metadata-yg5qcnxe/chemfiles.egg-info/requires.txt 2022-08-28T00:17:17,186 writing top-level names to /tmp/pip-modern-metadata-yg5qcnxe/chemfiles.egg-info/top_level.txt 2022-08-28T00:17:17,189 writing manifest file '/tmp/pip-modern-metadata-yg5qcnxe/chemfiles.egg-info/SOURCES.txt' 2022-08-28T00:17:17,921 reading manifest file '/tmp/pip-modern-metadata-yg5qcnxe/chemfiles.egg-info/SOURCES.txt' 2022-08-28T00:17:17,925 reading manifest template 'MANIFEST.in' 2022-08-28T00:17:17,927 warning: no files found matching '*' under directory 'chemfiles' 2022-08-28T00:17:18,100 no previously-included directories found matching 'lib/tests' 2022-08-28T00:17:18,102 no previously-included directories found matching 'lib/doc' 2022-08-28T00:17:18,105 adding license file 'LICENSE' 2022-08-28T00:17:18,127 writing manifest file '/tmp/pip-modern-metadata-yg5qcnxe/chemfiles.egg-info/SOURCES.txt' 2022-08-28T00:17:18,131 creating '/tmp/pip-modern-metadata-yg5qcnxe/chemfiles-0.10.3.dist-info' 2022-08-28T00:17:18,198 adding license file "LICENSE" (matched pattern "LICENSE") 2022-08-28T00:17:18,430 Preparing metadata (pyproject.toml): finished with status 'done' 2022-08-28T00:17:18,445 Source in /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc has version 0.10.3, which satisfies requirement chemfiles==0.10.3 from https://files.pythonhosted.org/packages/40/ed/ad8fc9ac327b791bc20a8daf2b1ce3e83b45bed640575b6ac04ec02723ce/chemfiles-0.10.3.tar.gz#sha256=4bbb8b116492a57dbf6ddb4c84aad0133cd782e0cc0e53e4b957f2d93e6806ea 2022-08-28T00:17:18,447 Removed chemfiles==0.10.3 from https://files.pythonhosted.org/packages/40/ed/ad8fc9ac327b791bc20a8daf2b1ce3e83b45bed640575b6ac04ec02723ce/chemfiles-0.10.3.tar.gz#sha256=4bbb8b116492a57dbf6ddb4c84aad0133cd782e0cc0e53e4b957f2d93e6806ea from build tracker '/tmp/pip-build-tracker-1d558vfp' 2022-08-28T00:17:18,456 Created temporary directory: /tmp/pip-unpack-4_9vrfx1 2022-08-28T00:17:18,458 Building wheels for collected packages: chemfiles 2022-08-28T00:17:18,468 Created temporary directory: /tmp/pip-wheel-t1wjxlx4 2022-08-28T00:17:18,468 Destination directory: /tmp/pip-wheel-t1wjxlx4 2022-08-28T00:17:18,474 Building wheel for chemfiles (pyproject.toml): started 2022-08-28T00:17:18,476 Running command Building wheel for chemfiles (pyproject.toml) 2022-08-28T00:17:23,637 running bdist_wheel 2022-08-28T00:17:23,754 running build 2022-08-28T00:17:23,754 running build_py 2022-08-28T00:17:24,394 creating build 2022-08-28T00:17:24,395 creating build/lib.linux-armv7l-cpython-37 2022-08-28T00:17:24,396 creating build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,398 copying src/chemfiles/frame.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,403 copying src/chemfiles/__init__.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,406 copying src/chemfiles/atom.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,410 copying src/chemfiles/residue.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,414 copying src/chemfiles/cell.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,419 copying src/chemfiles/utils.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,424 copying src/chemfiles/misc.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,429 copying src/chemfiles/selection.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,432 copying src/chemfiles/_c_lib.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,436 copying src/chemfiles/property.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,440 copying src/chemfiles/trajectory.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,445 copying src/chemfiles/topology.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,449 copying src/chemfiles/_c_api.py -> build/lib.linux-armv7l-cpython-37/chemfiles 2022-08-28T00:17:24,459 running build_ext 2022-08-28T00:17:24,668 -- Using internal chemfiles from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib 2022-08-28T00:17:25,240 -- The C compiler identification is GNU 8.3.0 2022-08-28T00:17:26,100 -- The CXX compiler identification is GNU 8.3.0 2022-08-28T00:17:26,198 -- Detecting C compiler ABI info 2022-08-28T00:17:26,805 -- Detecting C compiler ABI info - done 2022-08-28T00:17:26,898 -- Check for working C compiler: /usr/bin/cc - skipped 2022-08-28T00:17:26,902 -- Detecting C compile features 2022-08-28T00:17:26,908 -- Detecting C compile features - done 2022-08-28T00:17:26,960 -- Detecting CXX compiler ABI info 2022-08-28T00:17:27,827 -- Detecting CXX compiler ABI info - done 2022-08-28T00:17:27,923 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2022-08-28T00:17:27,926 -- Detecting CXX compile features 2022-08-28T00:17:27,933 -- Detecting CXX compile features - done 2022-08-28T00:18:50,399 -- Unpacking zlib sources 2022-08-28T00:18:53,895 -- Unpacking lzma sources 2022-08-28T00:19:18,224 -- Unpacking bzip2 sources 2022-08-28T00:19:18,465 -- Unpacking fmt sources 2022-08-28T00:19:24,441 -- Unpacking toml11 sources 2022-08-28T00:19:24,691 -- Unpacking tng sources 2022-08-28T00:19:25,828 -- Unpacking molfiles sources 2022-08-28T00:19:26,382 -- Unpacking mmtf-cpp sources 2022-08-28T00:19:28,010 -- Unpacking pugixml sources 2022-08-28T00:19:28,430 -- Unpacking gemmi sources 2022-08-28T00:19:31,716 -- Configuring done 2022-08-28T00:19:32,344 -- Generating done 2022-08-28T00:19:32,475 -- Build files have been written to: /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/build/cmake-build 2022-08-28T00:19:44,866 [1/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Atom.cpp.o 2022-08-28T00:20:12,861 [2/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Connectivity.cpp.o 2022-08-28T00:20:13,582 [3/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Format.cpp.o 2022-08-28T00:20:13,583 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:20:13,583 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Format.cpp:6: 2022-08-28T00:20:13,584 /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]’: 2022-08-28T00:20:13,584 /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 2022-08-28T00:20:13,585 vector<_Tp, _Alloc>:: 2022-08-28T00:20:13,585 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:20:13,586 /usr/include/c++/8/bits/vector.tcc: In member function ‘virtual void chemfiles::TextFormat::write(const chemfiles::Frame&)’: 2022-08-28T00:20:13,586 /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 2022-08-28T00:20:13,587 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:20:13,587 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:20:17,359 [4/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/File.cpp.o 2022-08-28T00:20:21,981 [5/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/FormatMetadata.cpp.o 2022-08-28T00:20:50,800 [6/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Property.cpp.o 2022-08-28T00:20:54,902 [7/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Frame.cpp.o 2022-08-28T00:20:54,903 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:20:54,904 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Frame.cpp:8: 2022-08-28T00:20:54,904 /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]’: 2022-08-28T00:20:54,905 /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 2022-08-28T00:20:54,905 vector<_Tp, _Alloc>:: 2022-08-28T00:20:54,906 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:20:54,906 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:20:54,907 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Frame.cpp:8: 2022-08-28T00:20:54,907 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::Frame::add_atom(chemfiles::Atom, chemfiles::Vector3D, chemfiles::Vector3D)’: 2022-08-28T00:20:54,908 /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 2022-08-28T00:20:54,908 _M_realloc_insert(end(), __x); 2022-08-28T00:20:54,909 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:20:54,909 /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 2022-08-28T00:20:54,910 _M_realloc_insert(end(), __x); 2022-08-28T00:20:54,910 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:20:59,410 [8/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/FormatFactory.cpp.o 2022-08-28T00:20:59,593 [9/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Topology.cpp.o 2022-08-28T00:20:59,594 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:20:59,594 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Topology.cpp:5: 2022-08-28T00:20:59,595 /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]’: 2022-08-28T00:20:59,596 /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 2022-08-28T00:20:59,596 vector<_Tp, _Alloc>:: 2022-08-28T00:20:59,597 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:20:59,598 /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]’: 2022-08-28T00:20:59,598 /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 2022-08-28T00:20:59,599 vector<_Tp, _Alloc>:: 2022-08-28T00:20:59,599 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:20:59,600 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:20:59,600 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Topology.cpp:5: 2022-08-28T00:20:59,601 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::Topology::resize(size_t)’: 2022-08-28T00:20:59,602 /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 2022-08-28T00:20:59,602 _M_fill_insert(end(), __new_size - size(), __x); 2022-08-28T00:20:59,603 ^~~~~~~~~~~~~~ 2022-08-28T00:20:59,603 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:20:59,604 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Topology.cpp:5: 2022-08-28T00:20:59,604 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Topology::add_residue(chemfiles::Residue)’: 2022-08-28T00:20:59,605 /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 2022-08-28T00:20:59,605 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:20:59,606 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:21:04,347 [10/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Residue.cpp.o 2022-08-28T00:21:31,465 [11/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/UnitCell.cpp.o 2022-08-28T00:21:40,221 [12/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Selection.cpp.o 2022-08-28T00:21:48,829 [13/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/atom.cpp.o 2022-08-28T00:21:54,019 [14/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Trajectory.cpp.o 2022-08-28T00:21:54,020 In file included from /usr/include/c++/8/memory:65, 2022-08-28T00:21:54,020 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Trajectory.cpp:6: 2022-08-28T00:21:54,021 /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]’: 2022-08-28T00:21:54,022 /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 2022-08-28T00:21:54,022 __uninit_copy(_InputIterator __first, _InputIterator __last, 2022-08-28T00:21:54,023 ^~~~~~~~~~~~~ 2022-08-28T00:21:54,023 /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 2022-08-28T00:21:54,023 /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]’: 2022-08-28T00:21:54,024 /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 2022-08-28T00:21:54,024 return std::__uninitialized_copy<__is_trivial(_ValueType1) 2022-08-28T00:21:54,025 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:21:54,025 && __is_trivial(_ValueType2) 2022-08-28T00:21:54,026 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:21:54,026 && __assignable>:: 2022-08-28T00:21:54,027 ~~~~~~~~~~~~~~~~~~ 2022-08-28T00:21:54,027 __uninit_copy(__first, __last, __result); 2022-08-28T00:21:54,027 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:22:02,394 [15/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/cell.cpp.o 2022-08-28T00:22:25,977 [16/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/misc.cpp.o 2022-08-28T00:22:28,192 [17/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/property.cpp.o 2022-08-28T00:22:37,379 [18/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/Configuration.cpp.o 2022-08-28T00:22:37,380 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:22:37,380 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Configuration.cpp:7: 2022-08-28T00:22:37,381 /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]’: 2022-08-28T00:22:37,382 /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 2022-08-28T00:22:37,382 vector<_Tp, _Alloc>:: 2022-08-28T00:22:37,383 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:22:37,383 /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]’: 2022-08-28T00:22:37,384 /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 2022-08-28T00:22:37,385 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:22:37,385 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Configuration.cpp:7: 2022-08-28T00:22:37,386 /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]’: 2022-08-28T00:22:37,386 /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 2022-08-28T00:22:37,387 _M_realloc_insert(end(), __x); 2022-08-28T00:22:37,387 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:22:37,388 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:22:37,388 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/Configuration.cpp:7: 2022-08-28T00:22:37,389 /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]’: 2022-08-28T00:22:37,390 /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 2022-08-28T00:22:37,390 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:22:37,391 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:22:38,232 [19/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/shared_allocator.cpp.o 2022-08-28T00:22:42,873 [20/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/selection.cpp.o 2022-08-28T00:22:46,308 [21/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/frame.cpp.o 2022-08-28T00:22:49,853 [22/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/residue.cpp.o 2022-08-28T00:23:19,935 [23/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/BinaryFile.cpp.o 2022-08-28T00:23:23,097 [24/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/MemoryBuffer.cpp.o 2022-08-28T00:23:23,465 [25/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/GzFile.cpp.o 2022-08-28T00:23:24,096 [26/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/Bz2File.cpp.o 2022-08-28T00:23:26,525 [27/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/trajectory.cpp.o 2022-08-28T00:23:36,510 [28/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/capi/topology.cpp.o 2022-08-28T00:23:53,662 [29/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/MemoryFile.cpp.o 2022-08-28T00:24:02,992 [30/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/XDRFile.cpp.o 2022-08-28T00:24:03,701 [31/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/TNGFile.cpp.o 2022-08-28T00:24:07,533 [32/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/PlainFile.cpp.o 2022-08-28T00:24:13,942 [33/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/Netcdf3File.cpp.o 2022-08-28T00:24:16,171 [34/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/files/XzFile.cpp.o 2022-08-28T00:24:52,696 [35/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/DCD.cpp.o 2022-08-28T00:24:52,697 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:24:52,697 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/include/chemfiles/utils.hpp:7, 2022-08-28T00:24:52,698 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/DCD.cpp:9: 2022-08-28T00:24:52,698 /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::DCDFormat::fixed_atom_data_t&}; _Tp = chemfiles::DCDFormat::fixed_atom_data_t; _Alloc = std::allocator]’: 2022-08-28T00:24:52,699 /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 2022-08-28T00:24:52,699 vector<_Tp, _Alloc>:: 2022-08-28T00:24:52,700 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:52,700 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:24:52,701 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/include/chemfiles/utils.hpp:7, 2022-08-28T00:24:52,701 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/DCD.cpp:9: 2022-08-28T00:24:52,702 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::DCDFormat::read_header()’: 2022-08-28T00:24:52,702 /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 2022-08-28T00:24:52,703 _M_realloc_insert(end(), __x); 2022-08-28T00:24:52,703 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:24:52,703 /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 2022-08-28T00:24:52,704 _M_realloc_insert(end(), __x); 2022-08-28T00:24:52,704 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,779 [36/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/AmberNetCDF.cpp.o 2022-08-28T00:24:54,780 In file included from /usr/include/c++/8/map:61, 2022-08-28T00:24:54,780 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/include/chemfiles/Property.hpp:9, 2022-08-28T00:24:54,781 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/include/chemfiles/Atom.hpp:11, 2022-08-28T00:24:54,781 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/include/chemfiles/Topology.hpp:11, 2022-08-28T00:24:54,782 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/include/chemfiles/Frame.hpp:15, 2022-08-28T00:24:54,782 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:18: 2022-08-28T00:24:54,783 /usr/include/c++/8/bits/stl_map.h: In function ‘std::map<_Key, _Tp, _Compare, _Alloc>::map(std::initializer_list >, const _Compare&, const allocator_type&) [with _Key = std::__cxx11::basic_string; _Tp = chemfiles::netcdf3::Value; _Compare = std::less >; _Alloc = std::allocator, chemfiles::netcdf3::Value> >]’: 2022-08-28T00:24:54,783 /usr/include/c++/8/bits/stl_map.h:226:7: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,783 map(initializer_list __l, 2022-08-28T00:24:54,784 ^~~ 2022-08-28T00:24:54,784 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp: In member function ‘virtual void chemfiles::AmberTrajectory::initialize(const chemfiles::Frame&)’: 2022-08-28T00:24:54,785 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:501:25: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,785 builder.add_variable("coordinates", { 2022-08-28T00:24:54,786 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,786 /* type = */ netcdf3::constants::NC_FLOAT, 2022-08-28T00:24:54,787 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,787 /* dimensions = */ {frame_dim, atom_dim, spatial_dim}, 2022-08-28T00:24:54,788 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,788 /* attributes = */ {{"units", netcdf3::Value("angstrom")}} 2022-08-28T00:24:54,789 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,789 }); 2022-08-28T00:24:54,800 ~~ 2022-08-28T00:24:54,801 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:507:25: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,801 builder.add_variable("cell_lengths", { 2022-08-28T00:24:54,802 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,802 /* type = */ netcdf3::constants::NC_FLOAT, 2022-08-28T00:24:54,803 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,803 /* dimensions = */ {frame_dim, cell_spatial_dim}, 2022-08-28T00:24:54,804 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,804 /* attributes = */ {{"units", netcdf3::Value("angstrom")}} 2022-08-28T00:24:54,805 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,805 }); 2022-08-28T00:24:54,806 ~~ 2022-08-28T00:24:54,806 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:513:25: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,807 builder.add_variable("cell_angles", { 2022-08-28T00:24:54,807 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,808 /* type = */ netcdf3::constants::NC_FLOAT, 2022-08-28T00:24:54,808 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,809 /* dimensions = */ {frame_dim, cell_angular_dim}, 2022-08-28T00:24:54,809 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,840 /* attributes = */ {{"units", netcdf3::Value("degree")}} 2022-08-28T00:24:54,840 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,841 }); 2022-08-28T00:24:54,841 ~~ 2022-08-28T00:24:54,842 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:520:29: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,842 builder.add_variable("velocities", { 2022-08-28T00:24:54,843 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,843 /* type = */ netcdf3::constants::NC_FLOAT, 2022-08-28T00:24:54,844 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,844 /* dimensions = */ {frame_dim, atom_dim, spatial_dim}, 2022-08-28T00:24:54,845 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,845 /* attributes = */ {{"units", netcdf3::Value("angstrom/picosecond")}}, 2022-08-28T00:24:54,846 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,846 }); 2022-08-28T00:24:54,846 ~~ 2022-08-28T00:24:54,847 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp: In member function ‘virtual void chemfiles::AmberRestart::initialize(const chemfiles::Frame&)’: 2022-08-28T00:24:54,847 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:622:25: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,848 builder.add_variable("coordinates", { 2022-08-28T00:24:54,848 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,849 /* type = */ netcdf3::constants::NC_DOUBLE, 2022-08-28T00:24:54,861 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,861 /* dimensions = */ {atom_dim, spatial_dim}, 2022-08-28T00:24:54,862 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,862 /* attributes = */ {{"units", netcdf3::Value("angstrom")}} 2022-08-28T00:24:54,863 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,863 }); 2022-08-28T00:24:54,863 ~~ 2022-08-28T00:24:54,864 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:628:25: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,864 builder.add_variable("cell_lengths", { 2022-08-28T00:24:54,864 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,865 /* type = */ netcdf3::constants::NC_DOUBLE, 2022-08-28T00:24:54,865 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,865 /* dimensions = */ {cell_spatial_dim}, 2022-08-28T00:24:54,866 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,866 /* attributes = */ {{"units", netcdf3::Value("angstrom")}} 2022-08-28T00:24:54,866 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,867 }); 2022-08-28T00:24:54,867 ~~ 2022-08-28T00:24:54,867 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:634:25: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,868 builder.add_variable("cell_angles", { 2022-08-28T00:24:54,868 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,868 /* type = */ netcdf3::constants::NC_DOUBLE, 2022-08-28T00:24:54,869 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,869 /* dimensions = */ {cell_angular_dim}, 2022-08-28T00:24:54,874 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,874 /* attributes = */ {{"units", netcdf3::Value("degree")}} 2022-08-28T00:24:54,874 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,875 }); 2022-08-28T00:24:54,875 ~~ 2022-08-28T00:24:54,876 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:641:29: note: parameter passing for argument of type ‘std::initializer_list, chemfiles::netcdf3::Value> >’ changed in GCC 7.1 2022-08-28T00:24:54,876 builder.add_variable("velocities", { 2022-08-28T00:24:54,876 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,877 /* type = */ netcdf3::constants::NC_DOUBLE, 2022-08-28T00:24:54,877 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,878 /* dimensions = */ {atom_dim, spatial_dim}, 2022-08-28T00:24:54,878 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,879 /* attributes = */ {{"units", netcdf3::Value("angstrom/femptosecond")}} 2022-08-28T00:24:54,879 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:24:54,880 }); 2022-08-28T00:24:54,880 ~~ 2022-08-28T00:24:54,880 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp: In member function ‘void chemfiles::AmberNetCDFBase::read_array(chemfiles::AmberNetCDFBase::variable_scale_t&, chemfiles::span)’: 2022-08-28T00:24:54,881 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:320:6: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2022-08-28T00:24:54,881 void AmberNetCDFBase::read_array(variable_scale_t& variable, span array) { 2022-08-28T00:24:54,882 ^~~~~~~~~~~~~~~ 2022-08-28T00:24:54,882 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp: In member function ‘void chemfiles::AmberNetCDFBase::write_array(chemfiles::AmberNetCDFBase::variable_scale_t&, chemfiles::span)’: 2022-08-28T00:24:54,883 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/AmberNetCDF.cpp:382:6: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2022-08-28T00:24:54,883 void AmberNetCDFBase::write_array(variable_scale_t& variable, span array) { 2022-08-28T00:24:54,884 ^~~~~~~~~~~~~~~ 2022-08-28T00:24:57,775 [37/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/CML.cpp.o 2022-08-28T00:25:06,930 [38/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/GRO.cpp.o 2022-08-28T00:25:09,144 [39/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/CSSR.cpp.o 2022-08-28T00:25:41,710 [40/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/Tinker.cpp.o 2022-08-28T00:25:50,842 [41/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/CIF.cpp.o 2022-08-28T00:25:50,843 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:25:50,843 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/CIF.cpp:11: 2022-08-28T00:25:50,844 /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]’: 2022-08-28T00:25:50,844 /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 2022-08-28T00:25:50,844 vector<_Tp, _Alloc>:: 2022-08-28T00:25:50,845 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:25:50,845 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:25:50,846 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/CIF.cpp:11: 2022-08-28T00:25:50,846 /usr/include/c++/8/bits/stl_vector.h: In member function ‘std::vector gemmi::SmallStructure::get_all_unit_cell_sites() const’: 2022-08-28T00:25:50,847 /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 2022-08-28T00:25:50,847 _M_realloc_insert(end(), __x); 2022-08-28T00:25:50,847 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:25:50,848 /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 2022-08-28T00:25:50,848 _M_realloc_insert(end(), __x); 2022-08-28T00:25:50,848 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:25:50,849 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:25:50,850 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/CIF.cpp:11: 2022-08-28T00:25:50,851 /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]’: 2022-08-28T00:25:50,851 /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 2022-08-28T00:25:50,852 vector<_Tp, _Alloc>:: 2022-08-28T00:25:50,852 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:25:50,853 /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]’: 2022-08-28T00:25:50,853 /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 2022-08-28T00:25:50,854 /usr/include/c++/8/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const SG*) [with SG = gemmi::SpaceGroup]’: 2022-08-28T00:25:50,854 /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 2022-08-28T00:25:50,855 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:25:50,855 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:25:50,856 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:25:50,856 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/CIF.cpp:11: 2022-08-28T00:25:50,857 /usr/include/c++/8/bits/stl_vector.h: In function ‘gemmi::SmallStructure gemmi::make_small_structure_from_block(const gemmi::cif::Block&)’: 2022-08-28T00:25:50,857 /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 2022-08-28T00:25:50,858 _M_realloc_insert(end(), __x); 2022-08-28T00:25:50,858 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:25:50,859 /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 2022-08-28T00:25:50,859 _M_realloc_insert(end(), __x); 2022-08-28T00:25:50,880 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:25:50,881 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:25:50,881 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/CIF.cpp:11: 2022-08-28T00:25:50,882 /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]’: 2022-08-28T00:25:50,882 /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 2022-08-28T00:25:50,883 vector<_Tp, _Alloc>:: 2022-08-28T00:25:50,883 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:25:50,884 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:25:50,885 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/CIF.cpp:11: 2022-08-28T00:25:50,885 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::CIFFormat::init_()’: 2022-08-28T00:25:50,886 /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 2022-08-28T00:25:50,886 _M_realloc_insert(end(), __x); 2022-08-28T00:25:50,887 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:26:02,153 [42/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/LAMMPSData.cpp.o 2022-08-28T00:26:02,154 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:26:02,154 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/LAMMPSData.cpp:11: 2022-08-28T00:26:02,155 /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> >]’: 2022-08-28T00:26:02,155 /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 2022-08-28T00:26:02,156 vector<_Tp, _Alloc>:: 2022-08-28T00:26:02,157 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:26:02,157 /usr/include/c++/8/bits/vector.tcc: In constructor ‘chemfiles::DataTypes::DataTypes(const chemfiles::Topology&)’: 2022-08-28T00:26:02,158 /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 2022-08-28T00:26:02,159 _M_realloc_insert(begin() + __n, std::move(__v)); 2022-08-28T00:26:02,160 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:26:03,308 [43/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/LAMMPSTrajectory.cpp.o 2022-08-28T00:26:04,455 [44/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/MOL2.cpp.o 2022-08-28T00:26:37,031 [45/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/Molfile.cpp.o 2022-08-28T00:26:37,032 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:26:37,033 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/Molfile.cpp:14: 2022-08-28T00:26:37,033 /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]’: 2022-08-28T00:26:37,034 /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 2022-08-28T00:26:37,034 vector<_Tp, _Alloc>:: 2022-08-28T00:26:37,035 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:26:37,035 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Molfile::read(chemfiles::Frame&) [with chemfiles::MolfileFormat F = (chemfiles::MolfileFormat)1]’: 2022-08-28T00:26:37,036 /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 2022-08-28T00:26:37,036 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:26:37,037 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:26:37,037 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Molfile::read(chemfiles::Frame&) [with chemfiles::MolfileFormat F = (chemfiles::MolfileFormat)2]’: 2022-08-28T00:26:37,038 /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 2022-08-28T00:26:37,038 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:26:37,039 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:26:37,039 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::Molfile::read(chemfiles::Frame&) [with chemfiles::MolfileFormat F = (chemfiles::MolfileFormat)3]’: 2022-08-28T00:26:37,040 /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 2022-08-28T00:26:37,041 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:26:37,041 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:26:51,128 [46/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/SDF.cpp.o 2022-08-28T00:26:51,513 [47/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/TNG.cpp.o 2022-08-28T00:26:51,514 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:26:51,514 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/TNG.cpp:9: 2022-08-28T00:26:51,515 /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]’: 2022-08-28T00:26:51,515 /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 2022-08-28T00:26:51,516 vector<_Tp, _Alloc>:: 2022-08-28T00:26:51,517 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:26:51,517 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:26:51,517 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/TNG.cpp:9: 2022-08-28T00:26:51,518 /usr/include/c++/8/bits/stl_vector.h: In constructor ‘chemfiles::TNGFormat::TNGFormat(std::__cxx11::string, chemfiles::File::Mode, chemfiles::File::Compression)’: 2022-08-28T00:26:51,518 /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 2022-08-28T00:26:51,519 _M_realloc_insert(end(), __x); 2022-08-28T00:26:51,519 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:26:59,873 [48/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/PDB.cpp.o 2022-08-28T00:26:59,873 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:26:59,874 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/PDB.cpp:12: 2022-08-28T00:26:59,874 /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]’: 2022-08-28T00:26:59,875 /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 2022-08-28T00:26:59,875 vector<_Tp, _Alloc>:: 2022-08-28T00:26:59,876 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:26:59,876 /usr/include/c++/8/bits/vector.tcc: In member function ‘virtual void chemfiles::PDBFormat::write_next(const chemfiles::Frame&)’: 2022-08-28T00:26:59,877 /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 2022-08-28T00:26:59,877 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:26:59,878 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:26:59,878 /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 2022-08-28T00:26:59,879 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:26:59,879 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:27:18,390 [49/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/MMTF.cpp.o 2022-08-28T00:27:18,391 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:27:18,392 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/MMTF.cpp:8: 2022-08-28T00:27:18,393 /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]’: 2022-08-28T00:27:18,393 /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 2022-08-28T00:27:18,394 vector<_Tp, _Alloc>:: 2022-08-28T00:27:18,394 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:27:18,395 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::MMTFFormat::apply_symmetry(chemfiles::Frame&)’: 2022-08-28T00:27:18,396 /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 2022-08-28T00:27:18,396 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:27:18,397 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:27:18,397 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/MMTF.cpp: In member function ‘void chemfiles::MMTFFormat::read_group(chemfiles::Frame&, size_t, chemfiles::Residue&, chemfiles::span)’: 2022-08-28T00:27:18,398 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/MMTF.cpp:294:6: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2022-08-28T00:27:18,398 void MMTFFormat::read_group(Frame& frame, size_t group_type, Residue& residue, span positions) { 2022-08-28T00:27:18,399 ^~~~~~~~~~ 2022-08-28T00:27:18,410 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/MMTF.cpp: In member function ‘void chemfiles::MMTFFormat::read_model(chemfiles::Frame&)’: 2022-08-28T00:27:18,411 /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/MMTF.cpp:235:23: note: parameter passing for argument of type ‘chemfiles::span’ changed in GCC 7.1 2022-08-28T00:27:18,413 read_group(frame, group_type, residue, positions); 2022-08-28T00:27:18,414 ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-28T00:27:18,510 [50/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/SMI.cpp.o 2022-08-28T00:27:18,512 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:27:18,513 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/SMI.cpp:14: 2022-08-28T00:27:18,514 /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]’: 2022-08-28T00:27:18,514 /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 2022-08-28T00:27:18,515 vector<_Tp, _Alloc>:: 2022-08-28T00:27:18,515 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:27:18,515 /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]’: 2022-08-28T00:27:18,516 /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 2022-08-28T00:27:18,516 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:27:18,517 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:27:18,517 /usr/include/c++/8/bits/vector.tcc: In member function ‘virtual void chemfiles::SMIFormat::read_next(chemfiles::Frame&)’: 2022-08-28T00:27:18,517 /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 2022-08-28T00:27:18,518 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:27:18,518 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:27:26,022 [51/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/warnings.cpp.o 2022-08-28T00:27:27,981 [52/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/TRR.cpp.o 2022-08-28T00:27:27,981 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:27:27,982 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/TRR.cpp:9: 2022-08-28T00:27:27,982 /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 = {int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: 2022-08-28T00:27:27,983 /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 2022-08-28T00:27:27,983 vector<_Tp, _Alloc>:: 2022-08-28T00:27:27,984 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:27:27,984 /usr/include/c++/8/bits/vector.tcc: In member function ‘void chemfiles::TRRFormat::determine_frame_offsets()’: 2022-08-28T00:27:27,985 /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 2022-08-28T00:27:27,985 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:27:27,986 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:27:29,035 [53/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/XTC.cpp.o 2022-08-28T00:27:51,778 [54/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/periodic_table.cpp.o 2022-08-28T00:27:52,963 [55/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/guess_format.cpp.o 2022-08-28T00:27:57,387 [56/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/mmCIF.cpp.o 2022-08-28T00:27:57,388 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:27:57,389 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/mmCIF.cpp:8: 2022-08-28T00:27:57,390 /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]’: 2022-08-28T00:27:57,390 /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 2022-08-28T00:27:57,391 vector<_Tp, _Alloc>:: 2022-08-28T00:27:57,392 ^~~~~~~~~~~~~~~~~~~ 2022-08-28T00:27:57,392 /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]’: 2022-08-28T00:27:57,393 /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 2022-08-28T00:27:57,394 /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 2022-08-28T00:27:57,394 In file included from /usr/include/c++/8/vector:64, 2022-08-28T00:27:57,395 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/mmCIF.cpp:8: 2022-08-28T00:27:57,396 /usr/include/c++/8/bits/stl_vector.h: In member function ‘void chemfiles::mmCIFFormat::init_()’: 2022-08-28T00:27:57,396 /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 2022-08-28T00:27:57,396 _M_realloc_insert(end(), __x); 2022-08-28T00:27:57,397 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:27:57,397 /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 2022-08-28T00:27:57,398 _M_realloc_insert(end(), __x); 2022-08-28T00:27:57,398 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:27:57,399 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:27:57,410 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/formats/mmCIF.cpp:8: 2022-08-28T00:27:57,411 /usr/include/c++/8/bits/vector.tcc: In member function ‘virtual void chemfiles::mmCIFFormat::read(chemfiles::Frame&)’: 2022-08-28T00:27:57,412 /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 2022-08-28T00:27:57,412 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-28T00:27:57,413 ^~~~~~~~~~~~~~~~~ 2022-08-28T00:28:05,324 [57/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/formats/XYZ.cpp.o 2022-08-28T00:28:08,143 [58/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/parse.cpp.o 2022-08-28T00:28:14,630 [59/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/pdb_connectivity.cpp.o 2022-08-28T00:28:16,480 [60/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/utils.cpp.o 2022-08-28T00:28:17,168 [61/181] Building C object lib/external/lzma/CMakeFiles/lzma.dir/liblzma/check/crc64_table.c.o 2022-08-28T00:28:18,168 [62/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/adler32.c.o 2022-08-28T00:28:18,925 [63/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/compress.c.o 2022-08-28T00:28:19,970 [64/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/selections/NumericValues.cpp.o 2022-08-28T00:28:21,013 [65/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/crc32.c.o 2022-08-28T00:28:21,446 [66/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/gzclose.c.o 2022-08-28T00:28:23,435 [67/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/gzlib.c.o 2022-08-28T00:28:26,460 [68/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/gzread.c.o 2022-08-28T00:28:28,349 [69/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/gzwrite.c.o 2022-08-28T00:28:28,953 [70/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/deflate.c.o 2022-08-28T00:28:31,771 [71/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/infback.c.o 2022-08-28T00:28:33,598 [72/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/inftrees.c.o 2022-08-28T00:28:35,307 [73/181] Building C object lib/external/zlib/CMakeFiles/zlib.dir/inffast.c.o 2022-08-28T00:28:36,249 [74/181] Building CXX object lib/CMakeFiles/chemfiles_objects.dir/src/selections/lexer.cpp.o 2022-08-28T00:28:36,250 In file included from /usr/include/c++/8/vector:69, 2022-08-28T00:28:36,250 from /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/lib/src/selections/lexer.cpp:8: 2022-08-28T00:28:36,251 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) 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2022-08-28T00:30:21,807 [179/181] Linking CXX shared library lib/libchemfiles.so.0.10.3 2022-08-28T00:30:21,847 [180/181] Creating library symlink lib/libchemfiles.so.0.10 lib/libchemfiles.so 2022-08-28T00:30:21,848 [180/181] Install the project... 2022-08-28T00:30:21,883 -- Install configuration: "Release" 2022-08-28T00:30:21,887 -- Installing: /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/build/lib.linux-armv7l-cpython-37/chemfiles/libchemfiles.so.0.10.3 2022-08-28T00:30:22,083 -- Installing: /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/build/lib.linux-armv7l-cpython-37/chemfiles/libchemfiles.so.0.10 2022-08-28T00:30:22,086 -- Installing: /tmp/pip-wheel-sy80jazc/chemfiles_149db8633c4e4d9481fa69b53bf30bfc/build/lib.linux-armv7l-cpython-37/chemfiles/libchemfiles.so 2022-08-28T00:30:22,766 installing to build/bdist.linux-armv7l/wheel 2022-08-28T00:30:22,767 running install 2022-08-28T00:30:22,830 running install_lib 2022-08-28T00:30:23,461 creating build/bdist.linux-armv7l 2022-08-28T00:30:23,462 creating build/bdist.linux-armv7l/wheel 2022-08-28T00:30:23,466 creating build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,469 copying build/lib.linux-armv7l-cpython-37/chemfiles/libchemfiles.so.0.10 -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,652 copying build/lib.linux-armv7l-cpython-37/chemfiles/frame.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,657 copying build/lib.linux-armv7l-cpython-37/chemfiles/libchemfiles.so.0.10.3 -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,810 copying build/lib.linux-armv7l-cpython-37/chemfiles/__init__.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,814 copying build/lib.linux-armv7l-cpython-37/chemfiles/atom.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,819 copying build/lib.linux-armv7l-cpython-37/chemfiles/residue.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,823 copying build/lib.linux-armv7l-cpython-37/chemfiles/cell.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,828 copying build/lib.linux-armv7l-cpython-37/chemfiles/utils.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,832 copying build/lib.linux-armv7l-cpython-37/chemfiles/misc.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,837 copying build/lib.linux-armv7l-cpython-37/chemfiles/selection.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,841 copying build/lib.linux-armv7l-cpython-37/chemfiles/libchemfiles.so -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,991 copying build/lib.linux-armv7l-cpython-37/chemfiles/_c_lib.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,995 copying build/lib.linux-armv7l-cpython-37/chemfiles/property.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:23,999 copying build/lib.linux-armv7l-cpython-37/chemfiles/trajectory.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:24,003 copying build/lib.linux-armv7l-cpython-37/chemfiles/topology.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:24,008 copying build/lib.linux-armv7l-cpython-37/chemfiles/_c_api.py -> build/bdist.linux-armv7l/wheel/chemfiles 2022-08-28T00:30:24,013 running install_egg_info 2022-08-28T00:30:25,304 running egg_info 2022-08-28T00:30:25,929 writing src/chemfiles.egg-info/PKG-INFO 2022-08-28T00:30:26,521 writing dependency_links to src/chemfiles.egg-info/dependency_links.txt 2022-08-28T00:30:29,471 writing requirements to src/chemfiles.egg-info/requires.txt 2022-08-28T00:30:30,067 writing top-level names to src/chemfiles.egg-info/top_level.txt 2022-08-28T00:30:30,116 reading manifest file 'src/chemfiles.egg-info/SOURCES.txt' 2022-08-28T00:30:30,186 reading manifest template 'MANIFEST.in' 2022-08-28T00:30:30,188 warning: no files found matching '*' under directory 'chemfiles' 2022-08-28T00:30:30,361 no previously-included directories found matching 'lib/tests' 2022-08-28T00:30:30,364 no previously-included directories found matching 'lib/doc' 2022-08-28T00:30:30,365 adding license file 'LICENSE' 2022-08-28T00:30:30,396 writing manifest file 'src/chemfiles.egg-info/SOURCES.txt' 2022-08-28T00:30:30,400 Copying src/chemfiles.egg-info to build/bdist.linux-armv7l/wheel/chemfiles-0.10.3-py3.7.egg-info 2022-08-28T00:30:30,490 adding license file "LICENSE" (matched pattern "LICENSE") 2022-08-28T00:30:30,528 creating build/bdist.linux-armv7l/wheel/chemfiles-0.10.3.dist-info/WHEEL 2022-08-28T00:30:30,534 creating '/tmp/pip-wheel-t1wjxlx4/tmpbghugdks/chemfiles-0.10.3-py2.py3-none-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-08-28T00:30:30,539 adding 'chemfiles/__init__.py' 2022-08-28T00:30:30,548 adding 'chemfiles/_c_api.py' 2022-08-28T00:30:30,552 adding 'chemfiles/_c_lib.py' 2022-08-28T00:30:30,556 adding 'chemfiles/atom.py' 2022-08-28T00:30:30,560 adding 'chemfiles/cell.py' 2022-08-28T00:30:30,565 adding 'chemfiles/frame.py' 2022-08-28T00:30:32,306 adding 'chemfiles/libchemfiles.so' 2022-08-28T00:30:34,120 adding 'chemfiles/libchemfiles.so.0.10' 2022-08-28T00:30:35,933 adding 'chemfiles/libchemfiles.so.0.10.3' 2022-08-28T00:30:36,010 adding 'chemfiles/misc.py' 2022-08-28T00:30:36,013 adding 'chemfiles/property.py' 2022-08-28T00:30:36,016 adding 'chemfiles/residue.py' 2022-08-28T00:30:36,020 adding 'chemfiles/selection.py' 2022-08-28T00:30:36,024 adding 'chemfiles/topology.py' 2022-08-28T00:30:36,028 adding 'chemfiles/trajectory.py' 2022-08-28T00:30:36,032 adding 'chemfiles/utils.py' 2022-08-28T00:30:36,037 adding 'chemfiles-0.10.3.dist-info/LICENSE' 2022-08-28T00:30:36,040 adding 'chemfiles-0.10.3.dist-info/METADATA' 2022-08-28T00:30:36,042 adding 'chemfiles-0.10.3.dist-info/WHEEL' 2022-08-28T00:30:36,045 adding 'chemfiles-0.10.3.dist-info/top_level.txt' 2022-08-28T00:30:36,048 adding 'chemfiles-0.10.3.dist-info/RECORD' 2022-08-28T00:30:36,192 removing build/bdist.linux-armv7l/wheel 2022-08-28T00:30:36,458 Building wheel for chemfiles (pyproject.toml): finished with status 'done' 2022-08-28T00:30:36,709 Created wheel for chemfiles: filename=chemfiles-0.10.3-py2.py3-none-linux_armv7l.whl size=4235692 sha256=4bdfa15db2d8d36b60c64662902d473998c0d358f33c460ba32b6c7e318f38ff 2022-08-28T00:30:36,711 Stored in directory: /tmp/pip-ephem-wheel-cache-rrvsprow/wheels/3b/36/a5/a8702d07dbba3ebd3783a426c153ecc2741f1698250c6ca07d 2022-08-28T00:30:36,739 Successfully built chemfiles 2022-08-28T00:30:37,073 Removed build tracker: '/tmp/pip-build-tracker-1d558vfp'