Hello,
I would appreciate your feedback on a Sage crash that I'm facing after
several trials. Please find attached the associated report along with some
potentially relevant information below:
- Which operating system: MacOS Mojave
*$ sw_vers*
ProductName: Mac OS X
ProductVersion: 10.14.6
BuildVersion: 18G95
*$ gcc --version*
Configured with: --prefix=/Library/Developer/CommandLineTools/usr
--with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
- How Sage was installed + How to reproduce the crash:
Step 0: Downloading *sage-9.1-OSX_10.11.6-x86_64.tar.bz2* (tried also .dmg
and .app.dmg, same results) from
http://www-ftp.lip6.fr/pub/math/sagemath/osx/intel/index.html , then moving
the *Sagemath* folder into /Applications/.
Step 1: Running /Applications/SageMath/sage and adding sudo ln -s
/Applications/SageMath/sage /usr/local/bin/sage
*Results*: running sage in terminal launches sage which operates correctly.
Step 2: (Note: CPLEX is already installed and correctly configured)
Running *sage -i sage_numerical_backends_cplex* as described for Sage 9.1
in https://github.com/mkoeppe/sage-numerical-backends-cplex
*Results: *The installation is successful but now running sage yields an
error (more details in the crash report attached):
ImportError:
dlopen(/Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/
ring.cpython-37m-darwin.so, 2): Symbol not found:
__ZNSt3__16vectorIN5GiNaC2exENS_9allocatorIS2_EEE11__vallocateEm
Referenced from:
/Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/
ring.cpython-37m-darwin.so
Expected in: flat namespace
in /Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/
ring.cpython-37m-darwin.so
Thank you and best regards,
H.
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***************************************************************************
IPython post-mortem report
{'commit_hash': '033ab93c7',
'commit_source': 'installation',
'default_encoding': 'UTF-8',
'ipython_path':
'/Applications/SageMath/local/lib/python3.7/site-packages/IPython',
'ipython_version': '5.8.0',
'os_name': 'posix',
'platform': 'Darwin-18.7.0-x86_64-i386-64bit',
'sys_executable': '/Applications/SageMath/local/bin/python3',
'sys_platform': 'darwin',
'sys_version': '3.7.3 (default, May 23 2020, 09:48:14) \n'
'[Clang 7.3.0 (clang-703.0.31)]'}
***************************************************************************
***************************************************************************
Crash traceback:
---------------------------------------------------------------------------
---------------------------------------------------------------------------
ImportError Python 3.7.3: /Applications/SageMath/local/bin/python3
Wed Oct 14 18:05:59 2020
A problem occurred executing Python code. Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.
/Applications/SageMath/src/bin/sage-ipython in <module>()
1 #!/usr/bin/env sage-python
2 # -*- coding: utf-8 -*-
3 """
4 Sage IPython startup script.
5 """
6
7 # Display startup banner. Do this before anything else to give the user
8 # early feedback that Sage is starting.
9 from sage.misc.banner import banner
10 banner()
11
12 from sage.repl.interpreter import SageTerminalApp
13
14 app = SageTerminalApp.instance()
---> 15 app.initialize()
global app.initialize = <bound method TerminalIPythonApp.initialize of
<sage.repl.interpreter.SageTerminalApp object at 0x10273d278>>
16 app.start()
</Applications/SageMath/local/lib/python3.7/site-packages/decorator.py:decorator-gen-110>
in initialize(self=<sage.repl.interpreter.SageTerminalApp object>, argv=None)
/Applications/SageMath/local/lib/python3.7/site-packages/traitlets/config/application.py
in catch_config_error(method=<function TerminalIPythonApp.initialize>,
app=<sage.repl.interpreter.SageTerminalApp object>, *args=(None,), **kwargs={})
72 TRAITLETS_APPLICATION_RAISE_CONFIG_FILE_ERROR = False
73 else:
74 raise ValueError("Unsupported value for environment variable:
'TRAITLETS_APPLICATION_RAISE_CONFIG_FILE_ERROR' is set to '%s' which is none of
{'0', '1', 'false', 'true', ''}."% _envvar )
75
76
77 @decorator
78 def catch_config_error(method, app, *args, **kwargs):
79 """Method decorator for catching invalid config
(Trait/ArgumentErrors) during init.
80
81 On a TraitError (generally caused by bad config), this will print
the trait's
82 message, and exit the app.
83
84 For use on init methods, to prevent invoking excepthook on invalid
input.
85 """
86 try:
---> 87 return method(app, *args, **kwargs)
method = <function TerminalIPythonApp.initialize at 0x1035a6950>
app = <sage.repl.interpreter.SageTerminalApp object at 0x10273d278>
args = (None,)
kwargs = {}
88 except (TraitError, ArgumentError) as e:
89 app.print_help()
90 app.log.fatal("Bad config encountered during initialization:")
91 app.log.fatal(str(e))
92 app.log.debug("Config at the time: %s", app.config)
93 app.exit(1)
94
95
96 class ApplicationError(Exception):
97 pass
98
99
100 class LevelFormatter(logging.Formatter):
101 """Formatter with additional `highlevel` record
102
/Applications/SageMath/local/lib/python3.7/site-packages/IPython/terminal/ipapp.py
in initialize(self=<sage.repl.interpreter.SageTerminalApp object>, argv=None)
301
302 return super(TerminalIPythonApp, self).parse_command_line(argv)
303
304 @catch_config_error
305 def initialize(self, argv=None):
306 """Do actions after construct, but before starting the app."""
307 super(TerminalIPythonApp, self).initialize(argv)
308 if self.subapp is not None:
309 # don't bother initializing further, starting subapp
310 return
311 # print self.extra_args
312 if self.extra_args and not self.something_to_run:
313 self.file_to_run = self.extra_args[0]
314 self.init_path()
315 # create the shell
--> 316 self.init_shell()
self.init_shell = <bound method SageTerminalApp.init_shell of
<sage.repl.interpreter.SageTerminalApp object at 0x10273d278>>
317 # and draw the banner
318 self.init_banner()
319 # Now a variety of things that happen after the banner is
printed.
320 self.init_gui_pylab()
321 self.init_extensions()
322 self.init_code()
323
324 def init_shell(self):
325 """initialize the InteractiveShell instance"""
326 # Create an InteractiveShell instance.
327 # shell.display_banner should always be False for the terminal
328 # based app, because we call shell.show_banner() by hand below
329 # so the banner shows *before* all extension loading stuff.
330 self.shell = self.interactive_shell_class.instance(parent=self,
331 profile_dir=self.profile_dir,
/Applications/SageMath/local/lib/python3.7/site-packages/sage/repl/interpreter.py
in init_shell(self=<sage.repl.interpreter.SageTerminalApp object>)
772 self.shell.has_sage_extensions = SAGE_EXTENSION in
self.extensions
773
774 # Load the %lprun extension if available
775 try:
776 import line_profiler
777 except ImportError:
778 pass
779 else:
780 self.extensions.append('line_profiler')
781
782 if self.shell.has_sage_extensions:
783 self.extensions.remove(SAGE_EXTENSION)
784
785 # load sage extension here to get a crash if
786 # something is wrong with the sage library
--> 787 self.shell.extension_manager.load_extension(SAGE_EXTENSION)
self.shell.extension_manager.load_extension = <bound method
ExtensionManager.load_extension of <IPython.core.extensions.ExtensionManager
object at 0x104d3bcf8>>
global SAGE_EXTENSION = 'sage'
788
789
/Applications/SageMath/local/lib/python3.7/site-packages/IPython/core/extensions.py
in load_extension(self=<IPython.core.extensions.ExtensionManager object>,
module_str='sage')
70
71 Returns the string "already loaded" if the extension is already
loaded,
72 "no load function" if the module doesn't have a
load_ipython_extension
73 function, or None if it succeeded.
74 """
75 if module_str in self.loaded:
76 return "already loaded"
77
78 from IPython.utils.syspathcontext import prepended_to_syspath
79
80 with self.shell.builtin_trap:
81 if module_str not in sys.modules:
82 with prepended_to_syspath(self.ipython_extension_dir):
83 __import__(module_str)
84 mod = sys.modules[module_str]
---> 85 if self._call_load_ipython_extension(mod):
self._call_load_ipython_extension = <bound method
ExtensionManager._call_load_ipython_extension of
<IPython.core.extensions.ExtensionManager object at 0x104d3bcf8>>
mod = <module 'sage' from
'/Applications/SageMath/local/lib/python3.7/site-packages/sage/__init__.py'>
86 self.loaded.add(module_str)
87 else:
88 return "no load function"
89
90 def unload_extension(self, module_str):
91 """Unload an IPython extension by its module name.
92
93 This function looks up the extension's name in ``sys.modules``
and
94 simply calls ``mod.unload_ipython_extension(self)``.
95
96 Returns the string "no unload function" if the extension
doesn't define
97 a function to unload itself, "not loaded" if the extension
isn't loaded,
98 otherwise None.
99 """
100 if module_str not in self.loaded:
/Applications/SageMath/local/lib/python3.7/site-packages/IPython/core/extensions.py
in _call_load_ipython_extension(self=<IPython.core.extensions.ExtensionManager
object>, mod=<module 'sage' from
'/Applications/SageMath/local/lib/python3.7/site-packages/sage/__init__.py'>)
117 """
118 from IPython.utils.syspathcontext import prepended_to_syspath
119
120 if (module_str in self.loaded) and (module_str in sys.modules):
121 self.unload_extension(module_str)
122 mod = sys.modules[module_str]
123 with prepended_to_syspath(self.ipython_extension_dir):
124 reload(mod)
125 if self._call_load_ipython_extension(mod):
126 self.loaded.add(module_str)
127 else:
128 self.load_extension(module_str)
129
130 def _call_load_ipython_extension(self, mod):
131 if hasattr(mod, 'load_ipython_extension'):
--> 132 mod.load_ipython_extension(self.shell)
mod.load_ipython_extension = <function load_ipython_extension at
0x1027cb8c8>
self.shell = <sage.repl.interpreter.SageTerminalInteractiveShell object
at 0x10269bbe0>
133 return True
134
135 def _call_unload_ipython_extension(self, mod):
136 if hasattr(mod, 'unload_ipython_extension'):
137 mod.unload_ipython_extension(self.shell)
138 return True
139
140 def install_extension(self, url, filename=None):
141 """Download and install an IPython extension.
142
143 If filename is given, the file will be so named (inside the
extension
144 directory). Otherwise, the name from the URL will be used. The
file must
145 have a .py or .zip extension; otherwise, a ValueError will be
raised.
146
147 Returns the full path to the installed file.
/Applications/SageMath/local/lib/python3.7/site-packages/sage/__init__.py in
load_ipython_extension(*args=(<sage.repl.interpreter.SageTerminalInteractiveShell
object>,))
1 __all__ = ['all']
2
3 # Set sage.__version__ to the current version number. This is analogous
4 # to many other Python packages.
5 from sage.version import version as __version__
6
7 # Make sure that the correct zlib library is loaded. This is needed
8 # to prevent the system zlib to be loaded instead of the Sage one.
9 # See https://trac.sagemath.org/ticket/23122
10 import zlib
11
12 # IPython calls this when starting up
13 def load_ipython_extension(*args):
14 import sage.repl.ipython_extension
---> 15 sage.repl.ipython_extension.load_ipython_extension(*args)
sage.repl.ipython_extension.load_ipython_extension = <function
load_ipython_extension at 0x104f76840>
args = (<sage.repl.interpreter.SageTerminalInteractiveShell object at
0x10269bbe0>,)
16
17
18 # Monkey-patch inspect.isfunction() to support Cython functions.
19 def isfunction(obj):
20 """
21 Check whether something is a function.
22
23 We assume that anything which has a genuine ``__code__``
24 attribute (not using ``__getattr__`` overrides) is a function.
25 This is meant to support Cython functions.
26
27 EXAMPLES::
28
29 sage: from inspect import isfunction
30 sage: def f(): pass
31 sage: isfunction(f)
/Applications/SageMath/local/lib/python3.7/site-packages/sage/repl/ipython_extension.py
in wrapper(*args=(<sage.repl.interpreter.SageTerminalInteractiveShell
object>,), **kwargs={})
549 ....: if work:
550 ....: return 'foo worked'
551 ....: raise RuntimeError("foo didn't work")
552 sage: foo(False)
553 Traceback (most recent call last):
554 ...
555 RuntimeError: foo didn't work
556 sage: foo(True)
557 'foo worked'
558 sage: foo(False)
559 sage: foo(True)
560 """
561 @wraps(func)
562 def wrapper(*args, **kwargs):
563 if not wrapper.has_run:
--> 564 result = func(*args, **kwargs)
result = undefined
global func = undefined
args = (<sage.repl.interpreter.SageTerminalInteractiveShell object at
0x10269bbe0>,)
kwargs = {}
565 wrapper.has_run = True
566 return result
567 wrapper.has_run = False
568 return wrapper
569
570
571 @run_once
572 def load_ipython_extension(ip):
573 """
574 Load the extension in IPython.
575 """
576 # this modifies ip
577 SageCustomizations(shell=ip)
/Applications/SageMath/local/lib/python3.7/site-packages/sage/repl/ipython_extension.py
in
load_ipython_extension(ip=<sage.repl.interpreter.SageTerminalInteractiveShell
object>)
562 def wrapper(*args, **kwargs):
563 if not wrapper.has_run:
564 result = func(*args, **kwargs)
565 wrapper.has_run = True
566 return result
567 wrapper.has_run = False
568 return wrapper
569
570
571 @run_once
572 def load_ipython_extension(ip):
573 """
574 Load the extension in IPython.
575 """
576 # this modifies ip
--> 577 SageCustomizations(shell=ip)
global SageCustomizations = <class
'sage.repl.ipython_extension.SageCustomizations'>
global shell = undefined
ip = <sage.repl.interpreter.SageTerminalInteractiveShell object at
0x10269bbe0>
/Applications/SageMath/local/lib/python3.7/site-packages/sage/repl/ipython_extension.py
in __init__(self=<sage.repl.ipython_extension.SageCustomizations object>,
shell=<sage.repl.interpreter.SageTerminalInteractiveShell object>)
420 def __init__(self, shell=None):
421 """
422 Initialize the Sage plugin.
423 """
424 self.shell = shell
425
426 self.auto_magics = SageMagics(shell)
427 self.shell.register_magics(self.auto_magics)
428
429 import sage.misc.edit_module as edit_module
430 self.shell.set_hook('editor', edit_module.edit_devel)
431
432 self.init_inspector()
433 self.init_line_transforms()
434
--> 435 import sage.all # until sage's import hell is fixed
sage.all = undefined
436
437 self.shell.verbose_quit = True
438 self.set_quit_hook()
439
440 self.register_interface_magics()
441
442 if SAGE_IMPORTALL == 'yes':
443 self.init_environment()
444
445 def register_interface_magics(self):
446 """
447 Register magics for each of the Sage interfaces
448 """
449 from sage.repl.interface_magic import InterfaceMagic
450 InterfaceMagic.register_all(self.shell)
/Applications/SageMath/local/lib/python3.7/site-packages/sage/all.py in
<module>()
119 from sage.misc.all import * # takes a while
120 from sage.typeset.all import *
121 from sage.repl.all import *
122
123 from sage.misc.sh import sh
124
125 from sage.libs.all import *
126 from sage.data_structures.all import *
127 from sage.doctest.all import *
128
129 from sage.structure.all import *
130 from sage.rings.all import *
131 from sage.arith.all import *
132 from sage.matrix.all import *
133
--> 134 from sage.symbolic.all import *
global sage.symbolic.all = undefined
135 from sage.modules.all import *
136 from sage.monoids.all import *
137 from sage.algebras.all import *
138 from sage.modular.all import *
139 from sage.sat.all import *
140 from sage.schemes.all import *
141 from sage.graphs.all import *
142 from sage.groups.all import *
143 from sage.arith.power import generic_power as power
144 from sage.databases.all import *
145 from sage.categories.all import *
146 from sage.sets.all import *
147 from sage.probability.all import *
148 from sage.interfaces.all import *
149
/Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/all.py
in <module>()
1 from __future__ import absolute_import
2
----> 3 from sage.libs.pynac.pynac import I
global sage.libs.pynac.pynac = undefined
global I = undefined
4 i = I
5
6 from .ring import SR
7 from .constants import (pi, e, NaN, golden_ratio, log2, euler_gamma,
catalan,
8 khinchin, twinprime, mertens, glaisher)
9 from .expression import Expression, solve_diophantine, hold
10 from .callable import CallableSymbolicExpressionRing
11
12 from sage.symbolic.relation import solve, solve_mod, solve_ineq
13 from sage.symbolic.assumptions import assume, forget, assumptions,
assuming
14
15 from .units import units
/Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/expression.pxd
in init sage.libs.pynac.pynac
(build/cythonized/sage/libs/pynac/pynac.cpp:30410)()
1 from sage.libs.pynac.pynac cimport GEx
2 from sage.structure.element cimport CommutativeRingElement
3
----> 4 cdef class Expression(CommutativeRingElement):
global cdef = undefined
global Expression = undefined
global CommutativeRingElement = undefined
5 cdef GEx _gobj
6 cpdef _add_(self, other)
7 cpdef _mul_(self, other)
8 cpdef _pow_(self, other)
9 cdef Expression coerce_in(self, z)
10 cpdef object _eval_self(self, R)
11 cpdef object _convert(self, R)
12 cpdef bint is_polynomial(self, var)
13 cpdef bint is_relational(self)
14 cpdef bint is_infinity(self)
15 cpdef bint is_positive_infinity(self)
16 cpdef bint is_negative_infinity(self)
17 cpdef object pyobject(self)
18 cpdef Expression _subs_expr(self, expr)
19 cpdef int _cmp_add(Expression left, Expression right) except -2
20 cpdef int _cmp_mul(Expression left, Expression right) except -2
21 cdef bint _rel_equal1(Expression self, Expression other) except -1
22 cdef bint _rel_equal2(Expression self, Expression other) except -1
23
24 cpdef bint is_Expression(x)
25 cdef Expression new_Expression_from_GEx(parent, GEx juice)
26 cdef Expression new_Expression_from_pyobject(parent, x)
/Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/expression.pyx
in init sage.symbolic.expression
(build/cythonized/sage/symbolic/expression.cpp:75237)()
145 # Copyright (C) 2008 William Stein <wst...@gmail.com>
146 # Copyright (C) 2008 Burcin Erocal <bur...@erocal.org>
147 #
148 # This program is free software: you can redistribute it and/or modify
149 # it under the terms of the GNU General Public License as published by
150 # the Free Software Foundation, either version 2 of the License, or
151 # (at your option) any later version.
152 # https://www.gnu.org/licenses/
153 #
****************************************************************************
154
155 from cysignals.signals cimport sig_on, sig_off
156 from sage.ext.cplusplus cimport ccrepr, ccreadstr
157
158 from inspect import isfunction
159 import operator
--> 160 from . import ring
global ring = undefined
161 import sage.rings.integer
162 import sage.rings.rational
163
164 from cpython.object cimport Py_EQ, Py_NE, Py_LE, Py_GE, Py_LT, Py_GT
165
166 from sage.cpython.string cimport str_to_bytes
167 from sage.symbolic.comparison import mixed_order
168 from sage.symbolic.getitem cimport OperandsWrapper
169 from sage.symbolic.series cimport SymbolicSeries
170 from sage.symbolic.complexity_measures import string_length
171 from sage.symbolic.function import get_sfunction_from_serial,
SymbolicFunction
172 cimport sage.symbolic.comparison
173 from sage.rings.rational import Rational
174 from sage.misc.derivative import multi_derivative
175 from sage.misc.decorators import sage_wraps
ImportError:
dlopen(/Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so,
2): Symbol not found:
__ZNSt3__16vectorIN5GiNaC2exENS_9allocatorIS2_EEE11__vallocateEm
Referenced from:
/Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so
Expected in: flat namespace
in
/Applications/SageMath/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so
***************************************************************************
History of session input:
*** Last line of input (may not be in above history):
