2021-07-10T02:40:38,188 Created temporary directory: /tmp/pip-ephem-wheel-cache-f7hjqw_6 2021-07-10T02:40:38,191 Created temporary directory: /tmp/pip-req-tracker-7e13k10t 2021-07-10T02:40:38,191 Initialized build tracking at /tmp/pip-req-tracker-7e13k10t 2021-07-10T02:40:38,192 Created build tracker: /tmp/pip-req-tracker-7e13k10t 2021-07-10T02:40:38,192 Entered build tracker: /tmp/pip-req-tracker-7e13k10t 2021-07-10T02:40:38,192 Created temporary directory: /tmp/pip-wheel-hdrbn62d 2021-07-10T02:40:38,226 1 location(s) to search for versions of pyrmsd: 2021-07-10T02:40:38,226 * https://pypi.org/simple/pyrmsd/ 2021-07-10T02:40:38,226 Fetching project page and analyzing links: https://pypi.org/simple/pyrmsd/ 2021-07-10T02:40:38,227 Getting page https://pypi.org/simple/pyrmsd/ 2021-07-10T02:40:38,228 Found index url https://pypi.org/simple 2021-07-10T02:40:38,318 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 2021-07-10T02:40:38,318 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 2021-07-10T02:40:38,319 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 2021-07-10T02:40:38,319 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 2021-07-10T02:40:38,319 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 2021-07-10T02:40:38,319 Skipping link: not a file: https://pypi.org/simple/pyrmsd/ 2021-07-10T02:40:38,338 Given no hashes to check 1 links for project 'pyrmsd': discarding no candidates 2021-07-10T02:40:38,356 Collecting pyrmsd==4.2.1 2021-07-10T02:40:38,358 Created temporary directory: /tmp/pip-unpack-8n0euc65 2021-07-10T02:40:38,568 Downloading pyRMSD-4.2.1.tar.gz (54 kB) 2021-07-10T02:40:38,713 Added pyrmsd==4.2.1 from https://files.pythonhosted.org/packages/21/18/170ed35c7aaaae5bbb522b3c9a6bb1a7f4fd978702ea64e188975c2017aa/pyRMSD-4.2.1.tar.gz#sha256=58c1e65c22b8fc135889c14036e5bfbb5a5b398d8e6acce8bd6854c0fa552e56 to build tracker '/tmp/pip-req-tracker-7e13k10t' 2021-07-10T02:40:38,715 Running setup.py (path:/tmp/pip-wheel-hdrbn62d/pyrmsd_1dfa105d0ad046879162210986894437/setup.py) egg_info for package pyrmsd 2021-07-10T02:40:38,715 Created temporary directory: /tmp/pip-pip-egg-info-j1drsmpn 2021-07-10T02:40:38,716 Running command python setup.py egg_info 2021-07-10T02:40:39,808 running egg_info 2021-07-10T02:40:39,810 creating /tmp/pip-pip-egg-info-j1drsmpn/pyRMSD.egg-info 2021-07-10T02:40:39,811 writing /tmp/pip-pip-egg-info-j1drsmpn/pyRMSD.egg-info/PKG-INFO 2021-07-10T02:40:39,814 writing dependency_links to /tmp/pip-pip-egg-info-j1drsmpn/pyRMSD.egg-info/dependency_links.txt 2021-07-10T02:40:39,815 writing requirements to /tmp/pip-pip-egg-info-j1drsmpn/pyRMSD.egg-info/requires.txt 2021-07-10T02:40:39,816 writing top-level names to /tmp/pip-pip-egg-info-j1drsmpn/pyRMSD.egg-info/top_level.txt 2021-07-10T02:40:39,818 writing manifest file '/tmp/pip-pip-egg-info-j1drsmpn/pyRMSD.egg-info/SOURCES.txt' 2021-07-10T02:40:40,190 reading manifest file '/tmp/pip-pip-egg-info-j1drsmpn/pyRMSD.egg-info/SOURCES.txt' 2021-07-10T02:40:40,192 adding license file 'LICENSE' 2021-07-10T02:40:40,194 writing manifest file '/tmp/pip-pip-egg-info-j1drsmpn/pyRMSD.egg-info/SOURCES.txt' 2021-07-10T02:40:40,301 Source in /tmp/pip-wheel-hdrbn62d/pyrmsd_1dfa105d0ad046879162210986894437 has version 4.2.1, which satisfies requirement pyrmsd==4.2.1 from https://files.pythonhosted.org/packages/21/18/170ed35c7aaaae5bbb522b3c9a6bb1a7f4fd978702ea64e188975c2017aa/pyRMSD-4.2.1.tar.gz#sha256=58c1e65c22b8fc135889c14036e5bfbb5a5b398d8e6acce8bd6854c0fa552e56 2021-07-10T02:40:40,302 Removed pyrmsd==4.2.1 from https://files.pythonhosted.org/packages/21/18/170ed35c7aaaae5bbb522b3c9a6bb1a7f4fd978702ea64e188975c2017aa/pyRMSD-4.2.1.tar.gz#sha256=58c1e65c22b8fc135889c14036e5bfbb5a5b398d8e6acce8bd6854c0fa552e56 from build tracker '/tmp/pip-req-tracker-7e13k10t' 2021-07-10T02:40:40,307 Created temporary directory: /tmp/pip-unpack-sr11olsj 2021-07-10T02:40:40,308 Building wheels for collected packages: pyrmsd 2021-07-10T02:40:40,311 Created temporary directory: /tmp/pip-wheel-_ubnvn6o 2021-07-10T02:40:40,312 Building wheel for pyrmsd (setup.py): started 2021-07-10T02:40:40,312 Destination directory: /tmp/pip-wheel-_ubnvn6o 2021-07-10T02:40:40,312 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-hdrbn62d/pyrmsd_1dfa105d0ad046879162210986894437/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-hdrbn62d/pyrmsd_1dfa105d0ad046879162210986894437/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-_ubnvn6o 2021-07-10T02:40:41,344 running bdist_wheel 2021-07-10T02:40:41,536 running build 2021-07-10T02:40:41,536 running build_py 2021-07-10T02:40:41,671 creating build 2021-07-10T02:40:41,671 creating build/lib.linux-armv7l-3.9 2021-07-10T02:40:41,672 creating build/lib.linux-armv7l-3.9/pyRMSD 2021-07-10T02:40:41,673 copying ./pyRMSD/__init__.py -> build/lib.linux-armv7l-3.9/pyRMSD 2021-07-10T02:40:41,674 copying ./pyRMSD/availableCalculators.py -> build/lib.linux-armv7l-3.9/pyRMSD 2021-07-10T02:40:41,676 copying ./pyRMSD/matrixHandler.py -> build/lib.linux-armv7l-3.9/pyRMSD 2021-07-10T02:40:41,678 copying ./pyRMSD/RMSDCalculator.py -> build/lib.linux-armv7l-3.9/pyRMSD 2021-07-10T02:40:41,681 creating build/lib.linux-armv7l-3.9/pyRMSD/utils 2021-07-10T02:40:41,682 copying ./pyRMSD/utils/__init__.py -> build/lib.linux-armv7l-3.9/pyRMSD/utils 2021-07-10T02:40:41,683 copying ./pyRMSD/utils/proteinReading.py -> build/lib.linux-armv7l-3.9/pyRMSD/utils 2021-07-10T02:40:41,685 copying ./pyRMSD/symmTools.py -> build/lib.linux-armv7l-3.9/pyRMSD 2021-07-10T02:40:41,690 running build_ext 2021-07-10T02:40:41,696 building 'pyRMSD.pdbReader' extension 2021-07-10T02:40:41,697 creating build/temp.linux-armv7l-3.9 2021-07-10T02:40:41,697 creating build/temp.linux-armv7l-3.9/src 2021-07-10T02:40:41,698 creating build/temp.linux-armv7l-3.9/src/pdbreaderlite 2021-07-10T02:40:41,698 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 2021-07-10T02:40:43,375 In file included from /usr/include/c++/10/vector:72, 2021-07-10T02:40:43,376 from src/pdbreaderlite/PDBReader.h:5, 2021-07-10T02:40:43,376 from src/pdbreaderlite/PDBReader.cpp:12: 2021-07-10T02:40:43,376 /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]’: 2021-07-10T02:40:43,376 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-10T02:40:43,376 426 | vector<_Tp, _Alloc>:: 2021-07-10T02:40:43,376 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T02:40:43,429 In file included from /usr/include/c++/10/vector:67, 2021-07-10T02:40:43,430 from src/pdbreaderlite/PDBReader.h:5, 2021-07-10T02:40:43,430 from src/pdbreaderlite/PDBReader.cpp:12: 2021-07-10T02:40:43,430 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void PDBReader::processATOM(std::string&, std::string&, int&)’: 2021-07-10T02:40:43,430 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-10T02:40:43,430 1198 | _M_realloc_insert(end(), __x); 2021-07-10T02:40:43,430 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-10T02:40:43,430 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-10T02:40:43,431 1198 | _M_realloc_insert(end(), __x); 2021-07-10T02:40:43,431 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-10T02:40:43,431 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-10T02:40:43,431 1198 | _M_realloc_insert(end(), __x); 2021-07-10T02:40:43,431 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-10T02:40:43,857 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 2021-07-10T02:40:44,156 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-10T02:40:44,156 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-10T02:40:44,156 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-10T02:40:44,156 from src/pdbreaderlite/PDBReaderObject.cpp:3: 2021-07-10T02:40:44,157 /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] 2021-07-10T02:40:44,157 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-10T02:40:44,157 | ^~~~~~~ 2021-07-10T02:40:45,351 src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* pdbreader_read(pdbreader*, PyObject*)’: 2021-07-10T02:40:45,352 src/pdbreaderlite/PDBReaderObject.cpp:87:55: warning: narrowing conversion of ‘self->pdbreader::reader->PDBReader::all_coordinates.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘npy_intp’ {aka ‘int’} [-Wnarrowing] 2021-07-10T02:40:45,352 87 | npy_intp dims[] = {self->reader->all_coordinates.size()}; 2021-07-10T02:40:45,352 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2021-07-10T02:40:45,353 src/pdbreaderlite/PDBReaderObject.cpp: At global scope: 2021-07-10T02:40:45,353 src/pdbreaderlite/PDBReaderObject.cpp:105:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-10T02:40:45,354 105 | "PDBReader.Reader", /*tp_name*/ 2021-07-10T02:40:45,354 | ^~~~~~~~~~~~~~~~~~ 2021-07-10T02:40:45,354 | | 2021-07-10T02:40:45,354 | const char* 2021-07-10T02:40:45,354 src/pdbreaderlite/PDBReaderObject.cpp:108:5: error: invalid conversion from ‘destructor’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-10T02:40:45,355 108 | (destructor)pdbreader_dealloc, /*tp_dealloc*/ 2021-07-10T02:40:45,355 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T02:40:45,355 | | 2021-07-10T02:40:45,355 | destructor {aka void (*)(_object*)} 2021-07-10T02:40:45,355 src/pdbreaderlite/PDBReaderObject.cpp:123:23: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-10T02:40:45,355 123 | Py_TPFLAGS_DEFAULT| Py_TPFLAGS_BASETYPE , /*tp_flags*/ 2021-07-10T02:40:45,355 src/pdbreaderlite/PDBReaderObject.cpp:124:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-10T02:40:45,355 124 | "Simple PDB reader", /* tp_doc */ 2021-07-10T02:40:45,356 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T02:40:45,356 | | 2021-07-10T02:40:45,356 | const char* 2021-07-10T02:40:45,356 src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* initpdbReader()’: 2021-07-10T02:40:45,356 src/pdbreaderlite/PDBReaderObject.cpp:153:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-10T02:40:45,356 153 | return; 2021-07-10T02:40:45,356 | ^~~~~~ 2021-07-10T02:40:45,366 src/pdbreaderlite/PDBReaderObject.cpp:155:14: error: ‘Py_InitModule3’ was not declared in this scope 2021-07-10T02:40:45,366 155 | module = Py_InitModule3("pdbReader", NULL,"Simple pdb reading"); 2021-07-10T02:40:45,366 | ^~~~~~~~~~~~~~ 2021-07-10T02:40:45,366 src/pdbreaderlite/PDBReaderObject.cpp:157:11: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-10T02:40:45,367 157 | return; 2021-07-10T02:40:45,367 | ^~~~~~ 2021-07-10T02:40:45,469 src/pdbreaderlite/PDBReaderObject.cpp:163:1: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-10T02:40:45,469 163 | } 2021-07-10T02:40:45,469 | ^ 2021-07-10T02:40:45,481 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-10T02:40:45,601 Building wheel for pyrmsd (setup.py): finished with status 'error' 2021-07-10T02:40:45,602 ERROR: Failed building wheel for pyrmsd 2021-07-10T02:40:45,603 Running setup.py clean for pyrmsd 2021-07-10T02:40:45,603 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-hdrbn62d/pyrmsd_1dfa105d0ad046879162210986894437/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-hdrbn62d/pyrmsd_1dfa105d0ad046879162210986894437/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 2021-07-10T02:40:46,608 running clean 2021-07-10T02:40:46,611 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-10T02:40:46,614 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-10T02:40:46,619 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-10T02:40:46,620 'build/scripts-3.9' does not exist -- can't clean it 2021-07-10T02:40:46,620 removing 'build' 2021-07-10T02:40:46,708 Failed to build pyrmsd 2021-07-10T02:40:46,708 ERROR: Failed to build one or more wheels 2021-07-10T02:40:46,709 Exception information: 2021-07-10T02:40:46,709 Traceback (most recent call last): 2021-07-10T02:40:46,709 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-10T02:40:46,709 status = self.run(options, args) 2021-07-10T02:40:46,709 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-10T02:40:46,709 return func(self, options, args) 2021-07-10T02:40:46,709 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-10T02:40:46,709 raise CommandError( 2021-07-10T02:40:46,709 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-10T02:40:46,712 Removed build tracker: '/tmp/pip-req-tracker-7e13k10t'