On 27 December 2023 01:45:58 WET, Jing Guo <dev.g...@gmail.com> wrote:
>I downloaded from here https://github.com/3-manifolds/Sage_macOS/releases
>
>I was not and am not building Sage on Mac. To clarify, I’m simply “developing”
>this algorithm locally, though with the intention of submitting it to Sage
>source code.
It's most probably a bug (or a feature) of this specific app.
It could be that compilers from MacPorts interfere here.
Try temporarily moving MacPorts away or uninstall it.
>
>Jing
>2023年12月27日 +0100 02:44 Dima Pasechnik <dimp...@gmail.com>，写道：
>>
>>
>> On 27 December 2023 01:25:30 WET, Jing Guo <dev.g...@gmail.com> wrote:
>> > Sorry for the confusion. I used Sage downloaded from the website.
>>
>> it's not clear what you mean.
>> We don't distribute Sage binaries, you need to build them.
>> Please provide more details.
>>
>> >
>> > Gcc was installed with MacPorts.
>>
>> gcc (gcc.gnu.org, not Apple's "gcc")
>> cannot be used to build Sage on macOS.
>>
>>
>> >
>> > Jing
>> > 2023年12月27日 +0100 01:54 Dima Pasechnik <dimp...@gmail.com>，写道：
>> > > 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_functions
>> > > > >
>> > > > > ModuleNotFoundError: 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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>> >
>>
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