it seems you have gcc in /opt/local - what is it?
Not very usual. Normally speaking gcc on macOS is Apple's clang. How have you
built (?) Sage?
On 26 December 2023 14:52:23 WET, Jing Guo <dev.g...@gmail.com> wrote:
>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
>
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