2025-09-07T23:04:25,876 Created temporary directory: /tmp/pip-build-tracker-b1wz8w02 2025-09-07T23:04:25,877 Initialized build tracking at /tmp/pip-build-tracker-b1wz8w02 2025-09-07T23:04:25,877 Created build tracker: /tmp/pip-build-tracker-b1wz8w02 2025-09-07T23:04:25,877 Entered build tracker: /tmp/pip-build-tracker-b1wz8w02 2025-09-07T23:04:25,878 Created temporary directory: /tmp/pip-wheel-7e_bl3o6 2025-09-07T23:04:25,881 Created temporary directory: /tmp/pip-ephem-wheel-cache-e2j4stfa 2025-09-07T23:04:25,942 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T23:04:25,945 2 location(s) to search for versions of pyrmsd: 2025-09-07T23:04:25,945 * https://pypi.org/simple/pyrmsd/ 2025-09-07T23:04:25,945 * https://www.piwheels.org/simple/pyrmsd/ 2025-09-07T23:04:25,945 Fetching project page and analyzing links: https://pypi.org/simple/pyrmsd/ 2025-09-07T23:04:25,945 Getting page https://pypi.org/simple/pyrmsd/ 2025-09-07T23:04:25,946 Found index url https://pypi.org/simple/ 2025-09-07T23:04:26,091 Fetched page https://pypi.org/simple/pyrmsd/ as application/vnd.pypi.simple.v1+json 2025-09-07T23:04:26,092 Found link https://files.pythonhosted.org/packages/80/b5/1fd41c73d58d030d036ba78ed3a9291b1916e3975c071c521576715a41c8/pyRMSD-4.0.0.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.0.0 2025-09-07T23:04:26,093 Found link https://files.pythonhosted.org/packages/f3/30/bf5cc08908f79127fecd306e126be5984ccb30be76bcdb62a39c582975aa/pyRMSD-4.0.1.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.0.1 2025-09-07T23:04:26,093 Found link https://files.pythonhosted.org/packages/45/7e/ac00abc640a76116139741b73c6eadd1cae264bb324f62acdb43f7806847/pyRMSD-4.1.0.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.1.0 2025-09-07T23:04:26,093 Found link https://files.pythonhosted.org/packages/fb/17/cb4a46781fa84b8d974c1da54ace55674a1182c7bccd87047a8404971e41/pyRMSD-4.2.0.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.2.0 2025-09-07T23:04:26,093 Found link https://files.pythonhosted.org/packages/21/18/170ed35c7aaaae5bbb522b3c9a6bb1a7f4fd978702ea64e188975c2017aa/pyRMSD-4.2.1.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.2.1 2025-09-07T23:04:26,094 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyrmsd/ 2025-09-07T23:04:26,094 Getting page https://www.piwheels.org/simple/pyrmsd/ 2025-09-07T23:04:26,095 Found index url https://www.piwheels.org/simple/ 2025-09-07T23:04:26,197 Fetched page https://www.piwheels.org/simple/pyrmsd/ as text/html 2025-09-07T23:04:26,197 Skipping link: not a file: https://www.piwheels.org/simple/pyrmsd/ 2025-09-07T23:04:26,198 Skipping link: not a file: https://pypi.org/simple/pyrmsd/ 2025-09-07T23:04:26,221 Given no hashes to check 1 links for project 'pyrmsd': discarding no candidates 2025-09-07T23:04:26,223 Collecting pyrmsd==4.0.0 2025-09-07T23:04:26,224 Created temporary directory: /tmp/pip-unpack-qkpilyoo 2025-09-07T23:04:26,373 Downloading pyRMSD-4.0.0.tar.gz (53 kB) 2025-09-07T23:04:26,431 Added pyrmsd==4.0.0 from https://files.pythonhosted.org/packages/80/b5/1fd41c73d58d030d036ba78ed3a9291b1916e3975c071c521576715a41c8/pyRMSD-4.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-b1wz8w02' 2025-09-07T23:04:26,432 Running setup.py (path:/tmp/pip-wheel-7e_bl3o6/pyrmsd_a081c1ea18ab4c3e98a8e7376cd77103/setup.py) egg_info for package pyrmsd 2025-09-07T23:04:26,432 Created temporary directory: /tmp/pip-pip-egg-info-flvkxsn0 2025-09-07T23:04:26,432 Preparing metadata (setup.py): started 2025-09-07T23:04:26,433 Running command python setup.py egg_info 2025-09-07T23:04:28,312 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T23:04:28,318 Source in /tmp/pip-wheel-7e_bl3o6/pyrmsd_a081c1ea18ab4c3e98a8e7376cd77103 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 2025-09-07T23:04:28,318 Removed pyrmsd==4.0.0 from https://files.pythonhosted.org/packages/80/b5/1fd41c73d58d030d036ba78ed3a9291b1916e3975c071c521576715a41c8/pyRMSD-4.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-b1wz8w02' 2025-09-07T23:04:28,324 Created temporary directory: /tmp/pip-unpack-o5dl3sgm 2025-09-07T23:04:28,324 Created temporary directory: /tmp/pip-unpack-1kk_4eu1 2025-09-07T23:04:28,325 Building wheels for collected packages: pyrmsd 2025-09-07T23:04:28,326 Created temporary directory: /tmp/pip-wheel-o6_v0jni 2025-09-07T23:04:28,327 DEPRECATION: Building 'pyrmsd' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pyrmsd'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-07T23:04:28,328 Building wheel for pyrmsd (setup.py): started 2025-09-07T23:04:28,329 Destination directory: /tmp/pip-wheel-o6_v0jni 2025-09-07T23:04:28,329 Running command python setup.py bdist_wheel 2025-09-07T23:04:35,119 src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* pdbreader_read(pdbreader*, PyObject*)’: 2025-09-07T23:04:35,119 src/pdbreaderlite/PDBReaderObject.cpp:87:62: 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] 2025-09-07T23:04:35,119 87 | npy_intp dims[] = {self->reader->all_coordinates.size()}; 2025-09-07T23:04:35,119 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-07T23:04:35,120 src/pdbreaderlite/PDBReaderObject.cpp: At global scope: 2025-09-07T23:04:35,121 src/pdbreaderlite/PDBReaderObject.cpp:142:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:04:35,121 142 | }; 2025-09-07T23:04:35,121 | ^ 2025-09-07T23:04:35,121 src/pdbreaderlite/PDBReaderObject.cpp:105:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:04:35,121 105 | "PDBReader.Reader", /*tp_name*/ 2025-09-07T23:04:35,121 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:04:35,121 | | 2025-09-07T23:04:35,122 | const char* 2025-09-07T23:04:35,122 src/pdbreaderlite/PDBReaderObject.cpp:108:5: error: invalid conversion from ‘destructor’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:04:35,122 108 | (destructor)pdbreader_dealloc, /*tp_dealloc*/ 2025-09-07T23:04:35,122 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:04:35,122 | | 2025-09-07T23:04:35,122 | destructor {aka void (*)(_object*)} 2025-09-07T23:04:35,122 src/pdbreaderlite/PDBReaderObject.cpp:123:23: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:04:35,122 123 | Py_TPFLAGS_DEFAULT| Py_TPFLAGS_BASETYPE , /*tp_flags*/ 2025-09-07T23:04:35,123 src/pdbreaderlite/PDBReaderObject.cpp:124:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:04:35,123 124 | "Simple PDB reader", /* tp_doc */ 2025-09-07T23:04:35,123 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:04:35,123 | | 2025-09-07T23:04:35,123 | const char* 2025-09-07T23:04:35,123 src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* initpdbReader()’: 2025-09-07T23:04:35,123 src/pdbreaderlite/PDBReaderObject.cpp:153:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:04:35,123 153 | return; 2025-09-07T23:04:35,123 | ^~~~~~ 2025-09-07T23:04:35,147 src/pdbreaderlite/PDBReaderObject.cpp:155:14: error: ‘Py_InitModule3’ was not declared in this scope 2025-09-07T23:04:35,147 155 | module = Py_InitModule3("pdbReader", NULL,"Simple pdb reading"); 2025-09-07T23:04:35,147 | ^~~~~~~~~~~~~~ 2025-09-07T23:04:35,147 src/pdbreaderlite/PDBReaderObject.cpp:157:11: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:04:35,147 157 | return; 2025-09-07T23:04:35,147 | ^~~~~~ 2025-09-07T23:04:35,387 src/pdbreaderlite/PDBReaderObject.cpp:163:1: warning: control reaches end of non-void function [-Wreturn-type] 2025-09-07T23:04:35,388 163 | } 2025-09-07T23:04:35,388 | ^ 2025-09-07T23:04:35,390 src/pdbreaderlite/PDBReaderObject.cpp: At global scope: 2025-09-07T23:04:35,390 src/pdbreaderlite/PDBReaderObject.cpp:24:18: warning: ‘PyObject* pdbreader_new(PyTypeObject*, PyObject*, PyObject*)’ defined but not used [-Wunused-function] 2025-09-07T23:04:35,390 24 | static PyObject* pdbreader_new(PyTypeObject *type, PyObject *args, PyObject *kwds){ 2025-09-07T23:04:35,390 | ^~~~~~~~~~~~~ 2025-09-07T23:04:35,402 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-07T23:04:35,579 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T23:04:35,591 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T23:04:35,591 exec(compile('"'"''"'"''"'"' 2025-09-07T23:04:35,591 # This is -- a caller that pip uses to run setup.py 2025-09-07T23:04:35,591 # 2025-09-07T23:04:35,591 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T23:04:35,591 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T23:04:35,591 # - It provides a clear error message when setuptools is not installed. 2025-09-07T23:04:35,591 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T23:04:35,591 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T23:04:35,591 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T23:04:35,591 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T23:04:35,591 import os, sys, tokenize, traceback 2025-09-07T23:04:35,591 2025-09-07T23:04:35,591 try: 2025-09-07T23:04:35,591 import setuptools 2025-09-07T23:04:35,591 except ImportError: 2025-09-07T23:04:35,591 print( 2025-09-07T23:04:35,591 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T23:04:35,591 "the build environment with exception:", 2025-09-07T23:04:35,591 file=sys.stderr, 2025-09-07T23:04:35,591 ) 2025-09-07T23:04:35,591 traceback.print_exc() 2025-09-07T23:04:35,591 sys.exit(1) 2025-09-07T23:04:35,591 2025-09-07T23:04:35,591 __file__ = %r 2025-09-07T23:04:35,591 sys.argv[0] = __file__ 2025-09-07T23:04:35,591 2025-09-07T23:04:35,591 if os.path.exists(__file__): 2025-09-07T23:04:35,591 filename = __file__ 2025-09-07T23:04:35,591 with tokenize.open(__file__) as f: 2025-09-07T23:04:35,591 setup_py_code = f.read() 2025-09-07T23:04:35,591 else: 2025-09-07T23:04:35,591 filename = "" 2025-09-07T23:04:35,591 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T23:04:35,591 2025-09-07T23:04:35,591 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T23:04:35,591 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-7e_bl3o6/pyrmsd_a081c1ea18ab4c3e98a8e7376cd77103/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-o6_v0jni[/] 2025-09-07T23:04:35,591 [bold magenta]cwd[/]: /tmp/pip-wheel-7e_bl3o6/pyrmsd_a081c1ea18ab4c3e98a8e7376cd77103/ 2025-09-07T23:04:35,591 Building wheel for pyrmsd (setup.py): finished with status 'error' 2025-09-07T23:04:35,592 ERROR: Failed building wheel for pyrmsd 2025-09-07T23:04:35,593 Running setup.py clean for pyrmsd 2025-09-07T23:04:35,593 Running command python setup.py clean 2025-09-07T23:04:37,023 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T23:04:37,023 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T23:04:37,158 Failed to build pyrmsd 2025-09-07T23:04:37,159 ERROR: Failed to build one or more wheels 2025-09-07T23:04:37,160 Exception information: 2025-09-07T23:04:37,160 Traceback (most recent call last): 2025-09-07T23:04:37,160 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T23:04:37,160 status = _inner_run() 2025-09-07T23:04:37,160 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T23:04:37,160 return self.run(options, args) 2025-09-07T23:04:37,160 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T23:04:37,160 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T23:04:37,160 return func(self, options, args) 2025-09-07T23:04:37,160 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T23:04:37,160 raise CommandError("Failed to build one or more wheels") 2025-09-07T23:04:37,160 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T23:04:37,164 Removed build tracker: '/tmp/pip-build-tracker-b1wz8w02'