Dear all,
I have implemented an algorithm related to graph homomorphism counting, and
recently I am thinking about improving its performance, so I think of
writing some of the modules/codes in Cython.
For instance, I wrote helper functions in `helper_functions.pyx`, which can
be imported sucessfully in Python 3, via `from helper_functions import *`.
However, when I run the above command in Sage notebook or Sage, the output
reads
*sage: import
helper_functions---------------------------------------------------------------------------ModuleNotFoundError
Traceback (most recent call last)Cell In [1], line
1----> 1 import helper_functionsModuleNotFoundError: No module named
'helper_functions'*
When I try to run `load("helper_functions.pyx")`, it will output a long
line of errors (see end of the post).
I searched online for relevant keywords but couldn't find good solutions to
these problems. I am on macOS 10.13.6
Thank you for your time!
Jing
sage: load("helper_functions.pyx")
Compiling ./helper_functions.pyx...
---------------------------------------------------------------------------
DistutilsExecError Traceback (most recent call last)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/unixccompiler.py:266,
in UnixCCompiler.link(self, target_desc, objects, output_filename,
output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols,
debug, extra_preargs, extra_postargs, build_temp, target_lang)
264 linker = compiler_fixup(linker, ld_args)
--> 266 self.spawn(linker + ld_args)
267 except DistutilsExecError as msg:
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/ccompiler.py:1041,
in CCompiler.spawn(self, cmd, **kwargs)
1040 def spawn(self, cmd, **kwargs):
-> 1041 spawn(cmd, dry_run=self.dry_run, **kwargs)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/spawn.py:70,
in spawn(cmd, search_path, verbose, dry_run, env)
69 cmd = cmd[0]
---> 70 raise DistutilsExecError(
71 "command {!r} failed with exit code {}".format(cmd, exitcode)
72 )
DistutilsExecError: command '/opt/local/bin/gcc' failed with exit code 1
During handling of the above exception, another exception occurred:
LinkError Traceback (most recent call last)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/sage/misc/cython.py:454,
in cython(filename, verbose, compile_message, use_cache,
create_local_c_file, annotate, sage_namespace, create_local_so_file)
453 with redirection(2, errfile, close=False):
--> 454 dist.run_command("build")
455 finally:
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/dist.py:989,
in Distribution.run_command(self, command)
986 # Postpone defaults until all explicit configuration is considered
987 # (setup() args, config files, command line and plugins)
--> 989 super().run_command(command)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/dist.py:988,
in Distribution.run_command(self, command)
987 cmd_obj.ensure_finalized()
--> 988 cmd_obj.run()
989 self.have_run[command] = 1
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/command/build.py:131,
in build.run(self)
130 for cmd_name in self.get_sub_commands():
--> 131 self.run_command(cmd_name)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:318,
in Command.run_command(self, command)
314 """Run some other command: uses the 'run_command()' method of
315 Distribution, which creates and finalizes the command object if
316 necessary and then invokes its 'run()' method.
317 """
--> 318 self.distribution.run_command(command)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/dist.py:989,
in Distribution.run_command(self, command)
986 # Postpone defaults until all explicit configuration is considered
987 # (setup() args, config files, command line and plugins)
--> 989 super().run_command(command)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/dist.py:988,
in Distribution.run_command(self, command)
987 cmd_obj.ensure_finalized()
--> 988 cmd_obj.run()
989 self.have_run[command] = 1
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/command/build_ext.py:88,
in build_ext.run(self)
87 old_inplace, self.inplace = self.inplace, 0
---> 88 _build_ext.run(self)
89 self.inplace = old_inplace
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py:345,
in build_ext.run(self)
344 # Now actually compile and link everything.
--> 345 self.build_extensions()
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py:467,
in build_ext.build_extensions(self)
466 else:
--> 467 self._build_extensions_serial()
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py:493,
in build_ext._build_extensions_serial(self)
492 with self._filter_build_errors(ext):
--> 493 self.build_extension(ext)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/command/build_ext.py:249,
in build_ext.build_extension(self, ext)
248 self.compiler = self.shlib_compiler
--> 249 _build_ext.build_extension(self, ext)
250 if ext._needs_stub:
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/Cython/Distutils/build_ext.py:135,
in build_ext.build_extension(self, ext)
134 ext.sources = new_ext.sources
--> 135 super(build_ext, self).build_extension(ext)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py:572,
in build_ext.build_extension(self, ext)
570 language = ext.language or self.compiler.detect_language(sources)
--> 572 self.compiler.link_shared_object(
573 objects,
574 ext_path,
575 libraries=self.get_libraries(ext),
576 library_dirs=ext.library_dirs,
577 runtime_library_dirs=ext.runtime_library_dirs,
578 extra_postargs=extra_args,
579 export_symbols=self.get_export_symbols(ext),
580 debug=self.debug,
581 build_temp=self.build_temp,
582 target_lang=language,
583 )
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/ccompiler.py:752,
in CCompiler.link_shared_object(self, objects, output_filename, output_dir,
libraries, library_dirs, runtime_library_dirs, export_symbols, debug,
extra_preargs, extra_postargs, build_temp, target_lang)
737 def link_shared_object(
738 self,
739 objects,
(...)
750 target_lang=None,
751 ):
--> 752 self.link(
753 CCompiler.SHARED_OBJECT,
754 objects,
755 output_filename,
756 output_dir,
757 libraries,
758 library_dirs,
759 runtime_library_dirs,
760 export_symbols,
761 debug,
762 extra_preargs,
763 extra_postargs,
764 build_temp,
765 target_lang,
766 )
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/setuptools/_distutils/unixccompiler.py:268,
in UnixCCompiler.link(self, target_desc, objects, output_filename,
output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols,
debug, extra_preargs, extra_postargs, build_temp, target_lang)
267 except DistutilsExecError as msg:
--> 268 raise LinkError(msg)
269 else:
LinkError: command '/opt/local/bin/gcc' failed with exit code 1
During handling of the above exception, another exception occurred:
RuntimeError Traceback (most recent call last)
Cell In [2], line 1
----> 1 load("helper_functions.pyx")
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/sage/misc/persist.pyx:175,
in sage.misc.persist.load (build/cythonized/sage/misc/persist.c:4520)()
173
174 if sage.repl.load.is_loadable_filename(filename):
--> 175 sage.repl.load.load(filename, globals())
176 return
177
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/sage/repl/load.py:277,
in load(filename, globals, attach)
275 if attach:
276 add_attached_file(fpath)
--> 277 exec(load_cython(fpath), globals)
278 elif ext == '.f' or ext == '.f90':
279 from sage.misc.inline_fortran import fortran
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/sage/repl/load.py:68,
in load_cython(name)
55 """
56 Helper function to load a Cython file.
57
(...)
65 module.
66 """
67 from sage.misc.cython import cython
---> 68 mod, dir = cython(name, compile_message=True, use_cache=True)
69 import sys
70 sys.path.append(dir)
File
/private/var/tmp/sage-10.2-current/local/var/lib/sage/venv-python3.11.1/lib/python3.11/site-packages/sage/misc/cython.py:460,
in cython(filename, verbose, compile_message, use_cache,
create_local_c_file, annotate, sage_namespace, create_local_so_file)
458 except Exception as msg:
459 msg = str(msg) + "\n" + distutils_messages
--> 460 raise RuntimeError(msg.strip())
462 if verbose >= 0:
463 sys.stderr.write(distutils_messages)
RuntimeError: command '/opt/local/bin/gcc' failed with exit code 1
ld: unknown option: -platform_version
collect2: error: ld returned 1 exit status
--
You received this message because you are subscribed to the Google Groups
"sage-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to sage-devel+unsubscr...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/sage-devel/de6d51f4-17de-45d8-a5b7-d4a5d5f4b570n%40googlegroups.com.
