2021-07-09T19:39:39,963 Created temporary directory: /tmp/pip-ephem-wheel-cache-zzppgz0w
2021-07-09T19:39:39,966 Created temporary directory: /tmp/pip-req-tracker-ubt_kmcc
2021-07-09T19:39:39,966 Initialized build tracking at /tmp/pip-req-tracker-ubt_kmcc
2021-07-09T19:39:39,967 Created build tracker: /tmp/pip-req-tracker-ubt_kmcc
2021-07-09T19:39:39,967 Entered build tracker: /tmp/pip-req-tracker-ubt_kmcc
2021-07-09T19:39:39,967 Created temporary directory: /tmp/pip-wheel-olble3te
2021-07-09T19:39:40,000 1 location(s) to search for versions of pyrmsd:
2021-07-09T19:39:40,000 * https://pypi.org/simple/pyrmsd/
2021-07-09T19:39:40,001 Fetching project page and analyzing links: https://pypi.org/simple/pyrmsd/
2021-07-09T19:39:40,001 Getting page https://pypi.org/simple/pyrmsd/
2021-07-09T19:39:40,003 Found index url https://pypi.org/simple
2021-07-09T19:39:40,184   Found link https://files.pythonhosted.org/packages/80/b5/1fd41c73d58d030d036ba78ed3a9291b1916e3975c071c521576715a41c8/pyRMSD-4.0.0.tar.gz#sha256=148280a283905aa2591d0460962194d4aa2a46e3b32bcb88cb4ddf8238931efa (from https://pypi.org/simple/pyrmsd/), version: 4.0.0
2021-07-09T19:39:40,185   Found link https://files.pythonhosted.org/packages/f3/30/bf5cc08908f79127fecd306e126be5984ccb30be76bcdb62a39c582975aa/pyRMSD-4.0.1.tar.gz#sha256=f1775f6f9946e2f10e4403ad79e399bea8c772ae4ba63bc4bb0565ff233016fe (from https://pypi.org/simple/pyrmsd/), version: 4.0.1
2021-07-09T19:39:40,185   Found link https://files.pythonhosted.org/packages/45/7e/ac00abc640a76116139741b73c6eadd1cae264bb324f62acdb43f7806847/pyRMSD-4.1.0.tar.gz#sha256=f53ca30fa47b482ec2f21af0c1470f5242bb95834ed55e0e475f6c2e78b1d45a (from https://pypi.org/simple/pyrmsd/), version: 4.1.0
2021-07-09T19:39:40,185   Found link https://files.pythonhosted.org/packages/fb/17/cb4a46781fa84b8d974c1da54ace55674a1182c7bccd87047a8404971e41/pyRMSD-4.2.0.tar.gz#sha256=f0bd402dc9f365f266ebef6103ec81193039ebdc11085942ff30027f740bbc94 (from https://pypi.org/simple/pyrmsd/), version: 4.2.0
2021-07-09T19:39:40,185   Found link https://files.pythonhosted.org/packages/21/18/170ed35c7aaaae5bbb522b3c9a6bb1a7f4fd978702ea64e188975c2017aa/pyRMSD-4.2.1.tar.gz#sha256=58c1e65c22b8fc135889c14036e5bfbb5a5b398d8e6acce8bd6854c0fa552e56 (from https://pypi.org/simple/pyrmsd/), version: 4.2.1
2021-07-09T19:39:40,186 Skipping link: not a file: https://pypi.org/simple/pyrmsd/
2021-07-09T19:39:40,202 Given no hashes to check 1 links for project 'pyrmsd': discarding no candidates
2021-07-09T19:39:40,220 Collecting pyrmsd==4.0.0
2021-07-09T19:39:40,221   Created temporary directory: /tmp/pip-unpack-qyx2wmdt
2021-07-09T19:39:40,403   Downloading pyRMSD-4.0.0.tar.gz (53 kB)
2021-07-09T19:39:40,547   Added pyrmsd==4.0.0 from https://files.pythonhosted.org/packages/80/b5/1fd41c73d58d030d036ba78ed3a9291b1916e3975c071c521576715a41c8/pyRMSD-4.0.0.tar.gz#sha256=148280a283905aa2591d0460962194d4aa2a46e3b32bcb88cb4ddf8238931efa to build tracker '/tmp/pip-req-tracker-ubt_kmcc'
2021-07-09T19:39:40,548     Running setup.py (path:/tmp/pip-wheel-olble3te/pyrmsd_7d6bde95b63c45d7b9d5b7f72963bef7/setup.py) egg_info for package pyrmsd
2021-07-09T19:39:40,548     Created temporary directory: /tmp/pip-pip-egg-info-l0uh3rys
2021-07-09T19:39:40,549     Running command python setup.py egg_info
2021-07-09T19:39:41,542     running egg_info
2021-07-09T19:39:41,545     creating /tmp/pip-pip-egg-info-l0uh3rys/pyRMSD.egg-info
2021-07-09T19:39:41,546     writing /tmp/pip-pip-egg-info-l0uh3rys/pyRMSD.egg-info/PKG-INFO
2021-07-09T19:39:41,549     writing dependency_links to /tmp/pip-pip-egg-info-l0uh3rys/pyRMSD.egg-info/dependency_links.txt
2021-07-09T19:39:41,551     writing requirements to /tmp/pip-pip-egg-info-l0uh3rys/pyRMSD.egg-info/requires.txt
2021-07-09T19:39:41,553     writing top-level names to /tmp/pip-pip-egg-info-l0uh3rys/pyRMSD.egg-info/top_level.txt
2021-07-09T19:39:41,555     writing manifest file '/tmp/pip-pip-egg-info-l0uh3rys/pyRMSD.egg-info/SOURCES.txt'
2021-07-09T19:39:41,908     reading manifest file '/tmp/pip-pip-egg-info-l0uh3rys/pyRMSD.egg-info/SOURCES.txt'
2021-07-09T19:39:41,910     adding license file 'LICENSE'
2021-07-09T19:39:41,913     writing manifest file '/tmp/pip-pip-egg-info-l0uh3rys/pyRMSD.egg-info/SOURCES.txt'
2021-07-09T19:39:42,020   Source in /tmp/pip-wheel-olble3te/pyrmsd_7d6bde95b63c45d7b9d5b7f72963bef7 has version 4.0.0, which satisfies requirement pyrmsd==4.0.0 from https://files.pythonhosted.org/packages/80/b5/1fd41c73d58d030d036ba78ed3a9291b1916e3975c071c521576715a41c8/pyRMSD-4.0.0.tar.gz#sha256=148280a283905aa2591d0460962194d4aa2a46e3b32bcb88cb4ddf8238931efa
2021-07-09T19:39:42,021   Removed pyrmsd==4.0.0 from https://files.pythonhosted.org/packages/80/b5/1fd41c73d58d030d036ba78ed3a9291b1916e3975c071c521576715a41c8/pyRMSD-4.0.0.tar.gz#sha256=148280a283905aa2591d0460962194d4aa2a46e3b32bcb88cb4ddf8238931efa from build tracker '/tmp/pip-req-tracker-ubt_kmcc'
2021-07-09T19:39:42,026 Created temporary directory: /tmp/pip-unpack-juis_wsg
2021-07-09T19:39:42,027 Building wheels for collected packages: pyrmsd
2021-07-09T19:39:42,031   Created temporary directory: /tmp/pip-wheel-dlzxrf4f
2021-07-09T19:39:42,031   Building wheel for pyrmsd (setup.py): started
2021-07-09T19:39:42,031   Destination directory: /tmp/pip-wheel-dlzxrf4f
2021-07-09T19:39:42,032   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-olble3te/pyrmsd_7d6bde95b63c45d7b9d5b7f72963bef7/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-olble3te/pyrmsd_7d6bde95b63c45d7b9d5b7f72963bef7/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-dlzxrf4f
2021-07-09T19:39:43,057   running bdist_wheel
2021-07-09T19:39:43,251   running build
2021-07-09T19:39:43,251   running build_py
2021-07-09T19:39:43,385   creating build
2021-07-09T19:39:43,386   creating build/lib.linux-armv7l-3.9
2021-07-09T19:39:43,387   creating build/lib.linux-armv7l-3.9/pyRMSD
2021-07-09T19:39:43,388   copying ./pyRMSD/__init__.py -> build/lib.linux-armv7l-3.9/pyRMSD
2021-07-09T19:39:43,389   copying ./pyRMSD/availableCalculators.py -> build/lib.linux-armv7l-3.9/pyRMSD
2021-07-09T19:39:43,391   copying ./pyRMSD/matrixHandler.py -> build/lib.linux-armv7l-3.9/pyRMSD
2021-07-09T19:39:43,393   copying ./pyRMSD/RMSDCalculator.py -> build/lib.linux-armv7l-3.9/pyRMSD
2021-07-09T19:39:43,396   creating build/lib.linux-armv7l-3.9/pyRMSD/utils
2021-07-09T19:39:43,396   copying ./pyRMSD/utils/__init__.py -> build/lib.linux-armv7l-3.9/pyRMSD/utils
2021-07-09T19:39:43,398   copying ./pyRMSD/utils/proteinReading.py -> build/lib.linux-armv7l-3.9/pyRMSD/utils
2021-07-09T19:39:43,400   copying ./pyRMSD/symmTools.py -> build/lib.linux-armv7l-3.9/pyRMSD
2021-07-09T19:39:43,406   running build_ext
2021-07-09T19:39:43,412   building 'pyRMSD.pdbReader' extension
2021-07-09T19:39:43,413   creating build/temp.linux-armv7l-3.9
2021-07-09T19:39:43,413   creating build/temp.linux-armv7l-3.9/src
2021-07-09T19:39:43,414   creating build/temp.linux-armv7l-3.9/src/pdbreaderlite
2021-07-09T19:39:43,415   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -I/usr/include/python3.9 -c src/pdbreaderlite/PDBReader.cpp -o build/temp.linux-armv7l-3.9/src/pdbreaderlite/PDBReader.o
2021-07-09T19:39:45,125   In file included from /usr/include/c++/10/vector:72,
2021-07-09T19:39:45,126                    from src/pdbreaderlite/PDBReader.h:5,
2021-07-09T19:39:45,126                    from src/pdbreaderlite/PDBReader.cpp:12:
2021-07-09T19:39:45,126   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
2021-07-09T19:39:45,127   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
2021-07-09T19:39:45,127     426 |       vector<_Tp, _Alloc>::
2021-07-09T19:39:45,127         |       ^~~~~~~~~~~~~~~~~~~
2021-07-09T19:39:45,180   In file included from /usr/include/c++/10/vector:67,
2021-07-09T19:39:45,180                    from src/pdbreaderlite/PDBReader.h:5,
2021-07-09T19:39:45,180                    from src/pdbreaderlite/PDBReader.cpp:12:
2021-07-09T19:39:45,180   /usr/include/c++/10/bits/stl_vector.h: In member function ‘void PDBReader::processATOM(std::string&, std::string&, int&)’:
2021-07-09T19:39:45,181   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2021-07-09T19:39:45,181    1198 |    _M_realloc_insert(end(), __x);
2021-07-09T19:39:45,181         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-09T19:39:45,181   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2021-07-09T19:39:45,181    1198 |    _M_realloc_insert(end(), __x);
2021-07-09T19:39:45,181         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-09T19:39:45,181   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2021-07-09T19:39:45,182    1198 |    _M_realloc_insert(end(), __x);
2021-07-09T19:39:45,182         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-09T19:39:45,602   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -I/usr/include/python3.9 -c src/pdbreaderlite/PDBReaderObject.cpp -o build/temp.linux-armv7l-3.9/src/pdbreaderlite/PDBReaderObject.o
2021-07-09T19:39:45,882   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-09T19:39:45,882                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-09T19:39:45,882                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-09T19:39:45,882                    from src/pdbreaderlite/PDBReaderObject.cpp:3:
2021-07-09T19:39:45,883   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-09T19:39:45,883      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-09T19:39:45,883         |  ^~~~~~~
2021-07-09T19:39:47,082   src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* pdbreader_read(pdbreader*, PyObject*)’:
2021-07-09T19:39:47,082   src/pdbreaderlite/PDBReaderObject.cpp:87:55: warning: narrowing conversion of ‘self->pdbreader::reader->PDBReader::all_coordinates.std::vector<double>::size()’ from ‘std::vector<double>::size_type’ {aka ‘unsigned int’} to ‘npy_intp’ {aka ‘int’} [-Wnarrowing]
2021-07-09T19:39:47,083      87 |  npy_intp dims[] = {self->reader->all_coordinates.size()};
2021-07-09T19:39:47,083         |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
2021-07-09T19:39:47,084   src/pdbreaderlite/PDBReaderObject.cpp: At global scope:
2021-07-09T19:39:47,084   src/pdbreaderlite/PDBReaderObject.cpp:105:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive]
2021-07-09T19:39:47,084     105 |     "PDBReader.Reader",       /*tp_name*/
2021-07-09T19:39:47,085         |     ^~~~~~~~~~~~~~~~~~
2021-07-09T19:39:47,085         |     |
2021-07-09T19:39:47,085         |     const char*
2021-07-09T19:39:47,085   src/pdbreaderlite/PDBReaderObject.cpp:108:5: error: invalid conversion from ‘destructor’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive]
2021-07-09T19:39:47,086     108 |     (destructor)pdbreader_dealloc, /*tp_dealloc*/
2021-07-09T19:39:47,086         |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T19:39:47,086         |     |
2021-07-09T19:39:47,086         |     destructor {aka void (*)(_object*)}
2021-07-09T19:39:47,086   src/pdbreaderlite/PDBReaderObject.cpp:123:23: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive]
2021-07-09T19:39:47,086     123 |     Py_TPFLAGS_DEFAULT| Py_TPFLAGS_BASETYPE , /*tp_flags*/
2021-07-09T19:39:47,086   src/pdbreaderlite/PDBReaderObject.cpp:124:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization
2021-07-09T19:39:47,086     124 |     "Simple PDB reader",           /* tp_doc */
2021-07-09T19:39:47,086         |     ^~~~~~~~~~~~~~~~~~~
2021-07-09T19:39:47,087         |     |
2021-07-09T19:39:47,087         |     const char*
2021-07-09T19:39:47,087   src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* initpdbReader()’:
2021-07-09T19:39:47,087   src/pdbreaderlite/PDBReaderObject.cpp:153:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive]
2021-07-09T19:39:47,087     153 |         return;
2021-07-09T19:39:47,087         |         ^~~~~~
2021-07-09T19:39:47,097   src/pdbreaderlite/PDBReaderObject.cpp:155:14: error: ‘Py_InitModule3’ was not declared in this scope
2021-07-09T19:39:47,097     155 |     module = Py_InitModule3("pdbReader", NULL,"Simple pdb reading");
2021-07-09T19:39:47,097         |              ^~~~~~~~~~~~~~
2021-07-09T19:39:47,097   src/pdbreaderlite/PDBReaderObject.cpp:157:11: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive]
2021-07-09T19:39:47,097     157 |           return;
2021-07-09T19:39:47,098         |           ^~~~~~
2021-07-09T19:39:47,201   src/pdbreaderlite/PDBReaderObject.cpp:163:1: warning: control reaches end of non-void function [-Wreturn-type]
2021-07-09T19:39:47,201     163 | }
2021-07-09T19:39:47,201         | ^
2021-07-09T19:39:47,213   error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1
2021-07-09T19:39:47,333   Building wheel for pyrmsd (setup.py): finished with status 'error'
2021-07-09T19:39:47,334   ERROR: Failed building wheel for pyrmsd
2021-07-09T19:39:47,334   Running setup.py clean for pyrmsd
2021-07-09T19:39:47,335   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-olble3te/pyrmsd_7d6bde95b63c45d7b9d5b7f72963bef7/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-olble3te/pyrmsd_7d6bde95b63c45d7b9d5b7f72963bef7/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
2021-07-09T19:39:48,372   running clean
2021-07-09T19:39:48,374   removing 'build/temp.linux-armv7l-3.9' (and everything under it)
2021-07-09T19:39:48,377   removing 'build/lib.linux-armv7l-3.9' (and everything under it)
2021-07-09T19:39:48,381   'build/bdist.linux-armv7l' does not exist -- can't clean it
2021-07-09T19:39:48,382   'build/scripts-3.9' does not exist -- can't clean it
2021-07-09T19:39:48,382   removing 'build'
2021-07-09T19:39:48,469 Failed to build pyrmsd
2021-07-09T19:39:48,469 ERROR: Failed to build one or more wheels
2021-07-09T19:39:48,470 Exception information:
2021-07-09T19:39:48,470 Traceback (most recent call last):
2021-07-09T19:39:48,470   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main
2021-07-09T19:39:48,470     status = self.run(options, args)
2021-07-09T19:39:48,470   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
2021-07-09T19:39:48,470     return func(self, options, args)
2021-07-09T19:39:48,470   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run
2021-07-09T19:39:48,470     raise CommandError(
2021-07-09T19:39:48,470 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2021-07-09T19:39:48,473 Removed build tracker: '/tmp/pip-req-tracker-ubt_kmcc'