problem compiling sage-9.2.rc0 on big sur, xcode 12.01
David Joyner
wdj@jeeves sage-9.2.rc0 % which python3
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3
[yasm-1.3.0.p0] Finished installing yasm-1.3.0.p0
make[3]: Target `all-sage' not remade because of errors.
make[2]: *** [all-start] Error 2
real 940m12.196s
user 113m42.845s
sys 15m52.978s
***************************************************************
Error building Sage.
The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):
* package: python3-3.8.5
last build time: Oct 6 18:49
log file: /Users/wdj/sagefiles/sage-9.2.rc0/logs/pkgs/python3-3.8.5.log
build directory: /Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/python3-3.8.5
It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
make[1]: *** [all-start] Error 1
make: *** [all] Error 2
make: Target `default' not remade because of errors.
David Joyner
[python3-3.8.5]
[python3-3.8.5] Python build finished successfully!
[python3-3.8.5] The necessary bits to build these optional modules were not found:
[python3-3.8.5] _bz2 _curses _curses_panel
[python3-3.8.5] _gdbm ossaudiodev spwd
[python3-3.8.5] zlib
[python3-3.8.5] To find the necessary bits, look in setup.py in detect_modules() for the module's name.
[python3-3.8.5]
[python3-3.8.5]
[python3-3.8.5] The following modules found by detect_modules() in setup.py, have been
[python3-3.8.5] built by the Makefile instead, as configured by the Setup files:
[python3-3.8.5] _abc atexit pwd
[python3-3.8.5] time
[python3-3.8.5]
[python3-3.8.5] running build_scripts
[python3-3.8.5] creating build/scripts-3.8
[python3-3.8.5] copying and adjusting /Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/python3-3.8.5/src/Tools/scripts/pydoc3 -> build/scripts-3.8
[python3-3.8.5] copying and adjusting /Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/python3-3.8.5/src/Tools/scripts/idle3 -> build/scripts-3.8
[python3-3.8.5] copying and adjusting /Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/python3-3.8.5/src/Tools/scripts/2to3 -> build/scripts-3.8
[python3-3.8.5] changing mode of build/scripts-3.8/pydoc3 from 644 to 755
[python3-3.8.5] changing mode of build/scripts-3.8/idle3 from 644 to 755
[python3-3.8.5] changing mode of build/scripts-3.8/2to3 from 644 to 755
[python3-3.8.5] renaming build/scripts-3.8/pydoc3 to build/scripts-3.8/pydoc3.8
[python3-3.8.5] renaming build/scripts-3.8/idle3 to build/scripts-3.8/idle3.8
[python3-3.8.5] renaming build/scripts-3.8/2to3 to build/scripts-3.8/2to3-3.8
[python3-3.8.5] /usr/bin/install -c -m 644 ./Tools/gdb/libpython.py python.exe-gdb.py
[python3-3.8.5] clang -c -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Wstrict-prototypes -Werror=implicit-function-declaration -I./Include/internal -I. -I./Include -I/usr/local/opt/openssl/include -I/usr/local/opt/openssl/include -DPy_BUILD_CORE -o Programs/_testembed.o ./Programs/_testembed.c
[python3-3.8.5] clang -L/Users/wdj/sagefiles/sage-9.2.rc0/local/lib -Wl,-rpath,/Users/wdj/sagefiles/sage-9.2.rc0/local/lib -L/usr/local/opt/openssl/lib -L. -L/Users/wdj/sagefiles/sage-9.2.rc0/local/lib -Wl,-rpath,/Users/wdj/sagefiles/sage-9.2.rc0/local/lib -L/usr/local/opt/openssl/lib -Wl,-stack_size,1000000 -framework CoreFoundation -o Programs/_testembed Programs/_testembed.o -L. -lpython3.8 -ldl -framework CoreFoundation
[python3-3.8.5] sed -e "s,@EXENAME@,/Users/wdj/sagefiles/sage-9.2.rc0/local/bin/python3.8," < ./Misc/python-config.in >python-config.py
[python3-3.8.5] LC_ALL=C sed -e 's,\$(\([A-Za-z0-9_]*\)),\$\{\1\},g' < Misc/python-config.sh >python-config
[python3-3.8.5] Testing importing of various modules...
[python3-3.8.5] ctypes module imported OK
[python3-3.8.5] math module imported OK
[python3-3.8.5] hashlib module imported OK
[python3-3.8.5] crypt module imported OK
[python3-3.8.5] readline module imported OK
[python3-3.8.5] socket module imported OK
[python3-3.8.5] Traceback (most recent call last):
[python3-3.8.5] File "<string>", line 1, in <module>
[python3-3.8.5] ModuleNotFoundError: No module named 'zlib'
[python3-3.8.5] zlib module failed to import
[python3-3.8.5] sqlite3 module imported OK
[python3-3.8.5] _scproxy module imported OK
[python3-3.8.5] Error: One or more modules failed to import.
[python3-3.8.5]
[python3-3.8.5] real 2m55.196s
[python3-3.8.5] user 2m11.283s
[python3-3.8.5] sys 0m33.284s
[python3-3.8.5] ************************************************************************
[python3-3.8.5] Error building package python3-3.8.5
[python3-3.8.5] ************************************************************************
[python3-3.8.5] Please email sage-devel (http://groups.google.com/group/sage-devel)
[python3-3.8.5] explaining the problem and including the log file
[python3-3.8.5] /Users/wdj/sagefiles/sage-9.2.rc0/logs/pkgs/python3-3.8.5.log
[python3-3.8.5] Describe your computer, operating system, etc.
[python3-3.8.5] If you want to try to fix the problem yourself, *don't* just cd to
[python3-3.8.5] /Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/python3-3.8.5 and type 'make' or whatever is appropriate.
[python3-3.8.5] Instead, the following commands setup all environment variables
[python3-3.8.5] correctly and load a subshell for you to debug the error:
[python3-3.8.5] (cd '/Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/python3-3.8.5' && '/Users/wdj/sagefiles/sage-9.2.rc0/sage' --buildsh)
[python3-3.8.5] When you are done debugging, you can type "exit" to leave the subshell.
[python3-3.8.5] ************************************************************************
make[3]: *** [python3-no-deps] Error 1
make[2]: *** [/Users/wdj/sagefiles/sage-9.2.rc0/local/var/lib/sage/installed/python3-3.8.5] Error 2
make[1]: *** [all-build] Error 2
real 3m2.022s
user 2m14.632s
sys 0m36.375s
***************************************************************
Error building Sage.
The following package(s) may have failed to build (not necessarily
during this run of 'make all-build'):
* package: python3-3.8.5
last build time: Oct 7 10:52
log file: /Users/wdj/sagefiles/sage-9.2.rc0/logs/pkgs/python3-3.8.5.log
build directory: /Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/python3-3.8.5
It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
make: *** [all-build] Error 1
David Lowry-Duda
John H Palmieri
David Joyner
Building Sage on Big Sur is being tracked at https://trac.sagemath.org/ticket/30651; see also https://trac.sagemath.org/ticket/30494. Do you have homebrew installed, and if so, which packages? You could try forcing Sage to build its own zlib, for example, to try to get Sage's Python to find it.
[openblas-0.3.9] gfortran -O2 -m128bit-long-double -Wall -frecursive -fno-optimize-sibling-calls -m64 -fPIC -L/Users/wdj/sagefiles/sage-9.2.rc0/local/lib -Wl,-rpath,/Users/wdj/sagefiles/sage-9.2.rc0/local/lib -all_load -headerpad_max_install_names -install_name "/Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/openblas-0.3.9/src/exports/../libopenblas.0.dylib" -dynamiclib -o ../libopenblas_atomp-r0.3.9.dylib ../libopenblas_atomp-r0.3.9.a -Wl,-exported_symbols_list,osx.def -L/Users/wdj/sagefiles/sage-9.2.rc0/local/lib -L/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0 -L/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../.. -L/Users/wdj/sagefiles/sage-9.2.rc0/local/lib -L/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0 -L/usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../.. -lgfortran -lSystem -lquadmath -lm -lSystem -lgfortran -lSystem -lquadmath -lm -lSystem -lSystem
[openblas-0.3.9] ld: library not found for -lSystem
[openblas-0.3.9] collect2: error: ld returned 1 exit status
[openblas-0.3.9] make[4]: *** [libopenblas_atomp-r0.3.9.dylib] Error 1
[openblas-0.3.9] make[3]: *** [shared] Error 2
[openblas-0.3.9] ********************************************************************************
[openblas-0.3.9] Error building openblas-0.3.9
[openblas-0.3.9] ********************************************************************************
[openblas-0.3.9]
[openblas-0.3.9] real 10m21.321s
[openblas-0.3.9] user 55m3.304s
[openblas-0.3.9] sys 14m23.198s
[openblas-0.3.9] ************************************************************************
[openblas-0.3.9] Error installing package openblas-0.3.9
[openblas-0.3.9] ************************************************************************
[openblas-0.3.9] Please email sage-devel (http://groups.google.com/group/sage-devel)
[openblas-0.3.9] explaining the problem and including the log file
[openblas-0.3.9] /Users/wdj/sagefiles/sage-9.2.rc0/logs/pkgs/openblas-0.3.9.log
[openblas-0.3.9] Describe your computer, operating system, etc.
[openblas-0.3.9] If you want to try to fix the problem yourself, *don't* just cd to
[openblas-0.3.9] /Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/openblas-0.3.9 and type 'make' or whatever is appropriate.
[openblas-0.3.9] Instead, the following commands setup all environment variables
[openblas-0.3.9] correctly and load a subshell for you to debug the error:
[openblas-0.3.9] (cd '/Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/openblas-0.3.9' && '/Users/wdj/sagefiles/sage-9.2.rc0/sage' --buildsh)
[openblas-0.3.9] When you are done debugging, you can type "exit" to leave the subshell.
[openblas-0.3.9] ************************************************************************
make[2]: *** [openblas-no-deps] Error 1
make[1]: *** [/Users/wdj/sagefiles/sage-9.2.rc0/local/var/lib/sage/installed/openblas-0.3.9] Error 2
real 10m32.344s
user 55m7.812s
sys 14m30.548s
***************************************************************
Error building Sage.
The following package(s) may have failed to build (not necessarily
during this run of 'make openblas'):
* package: openblas-0.3.9
last build time: Oct 7 14:38
log file: /Users/wdj/sagefiles/sage-9.2.rc0/logs/pkgs/openblas-0.3.9.log
build directory: /Users/wdj/sagefiles/sage-9.2.rc0/local/var/tmp/sage/build/openblas-0.3.9
It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
make: *** [openblas] Error 1
Hope this helps.
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David Joyner
sage -f [opts] [packages] is a shortcut for force-building specified packages. If you examine the output of `sage -advanced` on a commandline, this is noted there. The command `sage -advanced` is a more complete version of the typical help command `sage -h`.
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John H Palmieri
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Dima Pasechnik
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slelievre
David Joyner
I think you should report this at #30651, including details of which homebrew packages you've installed. It was suggested at https://trac.sagemath.org/ticket/30494#comment:92 that homebrew's gfortran may not work with Big Sur, so you might want to install Sage's version of that, too.
./configure --enable-universalsdk=$(xcodebuild -version -sdk macosx Path) --with-universal-archs=intel-64
source /Users/wdj/sagefiles/sage-9.2.rc0/.homebrew-build-env
./config.status --recheck && ./config.status
./sage -f gfortran
and probably other stuff)
wdj@jeeves sage-9.2.rc0 % ./sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.2.rc0, Release Date: 2020-10-05 │
│ Using Python 3.8.5. Type "help()" for help. │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable. ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
---------------------------------------------------------------------------
---------------------------------------------------------------------------
ModuleNotFoundErrorPython 3.8.5: /Users/wdj/sagefiles/sage-9.2.rc0/local/bin/python3
Thu Oct 8 13:27:16 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.
~/sagefiles/sage-9.2.rc0/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 0x104527880>>
16 app.start()
</Users/wdj/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/decorator.py:decorator-gen-113> in initialize(self=<sage.repl.interpreter.SageTerminalApp object>, argv=None)
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/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 0x105f83af0>
app = <sage.repl.interpreter.SageTerminalApp object at 0x104527880>
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
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/IPython/terminal/ipapp.py in initialize(self=<sage.repl.interpreter.SageTerminalApp object>, argv=None)
302
303 return super(TerminalIPythonApp, self).parse_command_line(argv)
304
305 @catch_config_error
306 def initialize(self, argv=None):
307 """Do actions after construct, but before starting the app."""
308 super(TerminalIPythonApp, self).initialize(argv)
309 if self.subapp is not None:
310 # don't bother initializing further, starting subapp
311 return
312 # print self.extra_args
313 if self.extra_args and not self.something_to_run:
314 self.file_to_run = self.extra_args[0]
315 self.init_path()
316 # create the shell
--> 317 self.init_shell()
self.init_shell = <bound method SageTerminalApp.init_shell of <sage.repl.interpreter.SageTerminalApp object at 0x104527880>>
318 # and draw the banner
319 self.init_banner()
320 # Now a variety of things that happen after the banner is printed.
321 self.init_gui_pylab()
322 self.init_extensions()
323 self.init_code()
324
325 def init_shell(self):
326 """initialize the InteractiveShell instance"""
327 # Create an InteractiveShell instance.
328 # shell.display_banner should always be False for the terminal
329 # based app, because we call shell.show_banner() by hand below
330 # so the banner shows *before* all extension loading stuff.
331 self.shell = self.interactive_shell_class.instance(parent=self,
332 profile_dir=self.profile_dir,
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/sage/repl/interpreter.py in init_shell(self=<sage.repl.interpreter.SageTerminalApp object>)
755 Initialize the :class:`SageInteractiveShell` instance.
756
757 .. note::
758
759 This code is based on
760 :meth:`TerminalIPythonApp.init_shell`.
761
762 EXAMPLES::
763
764 sage: from sage.repl.interpreter import SageTerminalApp
765 sage: app = SageTerminalApp.instance()
766 sage: app.shell
767 <sage.repl.interpreter.SageTestShell object at 0x...>
768 """
769 # Shell initialization
--> 770 self.shell = self.shell_class.instance(
self.shell = None
self.shell_class.instance = <bound method SingletonConfigurable.instance of <class 'sage.repl.interpreter.SageTerminalInteractiveShell'>>
global parent = undefined
self = <sage.repl.interpreter.SageTerminalApp object at 0x104527880>
global config = undefined
self.config = {'TerminalIPythonApp': {'display_banner': False, 'verbose_crash': True, 'test_shell': False, 'shell_class': <class 'sage.repl.interpreter.SageTerminalInteractiveShell'>}, 'InteractiveShell': {'prompts_class': <class 'sage.repl.prompts.SagePrompts'>, 'ast_node_interactivity': 'all', 'colors': 'LightBG', 'simple_prompt': False, 'term_title': True, 'confirm_exit': False, 'separate_in': ''}, 'TerminalInteractiveShell': {'prompts_class': <class 'sage.repl.prompts.SagePrompts'>, 'ast_node_interactivity': 'all', 'colors': 'LightBG', 'simple_prompt': False, 'term_title': True, 'confirm_exit': False, 'separate_in': ''}, 'InteractiveShellApp': {'extensions': ['sage']}, 'SageTerminalApp': {'force_interact': True}}
global profile_dir = undefined
self.profile_dir = <IPython.core.profiledir.ProfileDir object at 0x105fa5be0>
global ipython_dir = undefined
self.ipython_dir = '/Users/wdj/.sage/ipython-5.0.0'
771 parent=self,
772 config=self.config,
773 profile_dir=self.profile_dir,
774 ipython_dir=self.ipython_dir)
775 self.shell.configurables.append(self)
776 self.shell.has_sage_extensions = SAGE_EXTENSION in self.extensions
777
778 # Load the %lprun extension if available
779 try:
780 import line_profiler
781 except ImportError:
782 pass
783 else:
784 self.extensions.append('line_profiler')
785
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/traitlets/config/configurable.py in instance(cls=<class 'sage.repl.interpreter.SageTerminalInteractiveShell'>, *args=(), **kwargs={'config': {'TerminalIPythonApp': {'display_banner': False,...']}, 'SageTerminalApp': {'force_interact': True}}, 'ipython_dir': '/Users/wdj/.sage/ipython-5.0.0', 'parent': <sage.repl.interpreter.SageTerminalApp object>, 'profile_dir': <IPython.core.profiledir.ProfileDir object>})
397 >>> class Foo(SingletonConfigurable): pass
398 >>> foo = Foo.instance()
399 >>> foo == Foo.instance()
400 True
401
402 Create a subclass that is retrived using the base class instance::
403
404 >>> class Bar(SingletonConfigurable): pass
405 >>> class Bam(Bar): pass
406 >>> bam = Bam.instance()
407 >>> bam == Bar.instance()
408 True
409 """
410 # Create and save the instance
411 if cls._instance is None:
--> 412 inst = cls(*args, **kwargs)
inst = undefined
cls = <class 'sage.repl.interpreter.SageTerminalInteractiveShell'>
args = ()
kwargs = {'parent': <sage.repl.interpreter.SageTerminalApp object at 0x104527880>, 'config': {'TerminalIPythonApp': {'display_banner': False, 'verbose_crash': True, 'test_shell': False, 'shell_class': <class 'sage.repl.interpreter.SageTerminalInteractiveShell'>}, 'InteractiveShell': {'prompts_class': <class 'sage.repl.prompts.SagePrompts'>, 'ast_node_interactivity': 'all', 'colors': 'LightBG', 'simple_prompt': False, 'term_title': True, 'confirm_exit': False, 'separate_in': ''}, 'TerminalInteractiveShell': {'prompts_class': <class 'sage.repl.prompts.SagePrompts'>, 'ast_node_interactivity': 'all', 'colors': 'LightBG', 'simple_prompt': False, 'term_title': True, 'confirm_exit': False, 'separate_in': ''}, 'InteractiveShellApp': {'extensions': ['sage']}, 'SageTerminalApp': {'force_interact': True}}, 'profile_dir': <IPython.core.profiledir.ProfileDir object at 0x105fa5be0>, 'ipython_dir': '/Users/wdj/.sage/ipython-5.0.0'}
413 # Now make sure that the instance will also be returned by
414 # parent classes' _instance attribute.
415 for subclass in cls._walk_mro():
416 subclass._instance = inst
417
418 if isinstance(cls._instance, cls):
419 return cls._instance
420 else:
421 raise MultipleInstanceError(
422 'Multiple incompatible subclass instances of '
423 '%s are being created.' % cls.__name__
424 )
425
426 @classmethod
427 def initialized(cls):
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/IPython/terminal/interactiveshell.py in __init__(self=<sage.repl.interpreter.SageTerminalInteractiveShell object>, *args=(), **kwargs={'config': {'TerminalIPythonApp': {'display_banner': False,...']}, 'SageTerminalApp': {'force_interact': True}}, 'ipython_dir': '/Users/wdj/.sage/ipython-5.0.0', 'parent': <sage.repl.interpreter.SageTerminalApp object>, 'profile_dir': <IPython.core.profiledir.ProfileDir object>})
504
505 def init_alias(self):
506 # The parent class defines aliases that can be safely used with any
507 # frontend.
508 super(TerminalInteractiveShell, self).init_alias()
509
510 # Now define aliases that only make sense on the terminal, because they
511 # need direct access to the console in a way that we can't emulate in
512 # GUI or web frontend
513 if os.name == 'posix':
514 for cmd in ('clear', 'more', 'less', 'man'):
515 self.alias_manager.soft_define_alias(cmd, cmd)
516
517
518 def __init__(self, *args, **kwargs):
--> 519 super(TerminalInteractiveShell, self).__init__(*args, **kwargs)
global super = undefined
global TerminalInteractiveShell = <class 'IPython.terminal.interactiveshell.TerminalInteractiveShell'>
self.__init__ = <bound method TerminalInteractiveShell.__init__ of <sage.repl.interpreter.SageTerminalInteractiveShell object at 0x105fa5dc0>>
args = ()
kwargs = {'parent': <sage.repl.interpreter.SageTerminalApp object at 0x104527880>, 'config': {'TerminalIPythonApp': {'display_banner': False, 'verbose_crash': True, 'test_shell': False, 'shell_class': <class 'sage.repl.interpreter.SageTerminalInteractiveShell'>}, 'InteractiveShell': {'prompts_class': <class 'sage.repl.prompts.SagePrompts'>, 'ast_node_interactivity': 'all', 'colors': 'LightBG', 'simple_prompt': False, 'term_title': True, 'confirm_exit': False, 'separate_in': ''}, 'TerminalInteractiveShell': {'prompts_class': <class 'sage.repl.prompts.SagePrompts'>, 'ast_node_interactivity': 'all', 'colors': 'LightBG', 'simple_prompt': False, 'term_title': True, 'confirm_exit': False, 'separate_in': ''}, 'InteractiveShellApp': {'extensions': ['sage']}, 'SageTerminalApp': {'force_interact': True}}, 'profile_dir': <IPython.core.profiledir.ProfileDir object at 0x105fa5be0>, 'ipython_dir': '/Users/wdj/.sage/ipython-5.0.0'}
520 self.init_prompt_toolkit_cli()
521 self.init_term_title()
522 self.keep_running = True
523
524 self.debugger_history = InMemoryHistory()
525
526 def ask_exit(self):
527 self.keep_running = False
528
529 rl_next_input = None
530
531 def interact(self, display_banner=DISPLAY_BANNER_DEPRECATED):
532
533 if display_banner is not DISPLAY_BANNER_DEPRECATED:
534 warn('interact `display_banner` argument is deprecated since IPython 5.0. Call `show_banner()` if needed.', DeprecationWarning, stacklevel=2)
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/IPython/core/interactiveshell.py in __init__(self=<sage.repl.interpreter.SageTerminalInteractiveShell object>, ipython_dir='/Users/wdj/.sage/ipython-5.0.0', profile_dir=<IPython.core.profiledir.ProfileDir object>, user_module=None, user_ns=None, custom_exceptions=((), None), **kwargs={'config': {'TerminalIPythonApp': {'display_banner': False,...']}, 'SageTerminalApp': {'force_interact': True}}, 'parent': <sage.repl.interpreter.SageTerminalApp object>})
668 self.init_pushd_popd_magic()
669 self.init_user_ns()
670 self.init_logger()
671 self.init_builtins()
672
673 # The following was in post_config_initialization
674 self.init_inspector()
675 self.raw_input_original = input
676 self.init_completer()
677 # TODO: init_io() needs to happen before init_traceback handlers
678 # because the traceback handlers hardcode the stdout/stderr streams.
679 # This logic in in debugger.Pdb and should eventually be changed.
680 self.init_io()
681 self.init_traceback_handlers(custom_exceptions)
682 self.init_prompts()
--> 683 self.init_display_formatter()
self.init_display_formatter = <bound method SageTerminalInteractiveShell.init_display_formatter of <sage.repl.interpreter.SageTerminalInteractiveShell object at 0x105fa5dc0>>
684 self.init_display_pub()
685 self.init_data_pub()
686 self.init_displayhook()
687 self.init_magics()
688 self.init_alias()
689 self.init_logstart()
690 self.init_pdb()
691 self.init_extension_manager()
692 self.init_payload()
693 self.init_deprecation_warnings()
694 self.hooks.late_startup_hook()
695 self.events.trigger('shell_initialized', self)
696 atexit.register(self.atexit_operations)
697
698 # The trio runner is used for running Trio in the foreground thread. It
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/sage/repl/interpreter.py in init_display_formatter(self=<sage.repl.interpreter.SageTerminalInteractiveShell object>)
281
282 sage: from sage.repl.interpreter import SageTerminalInteractiveShell
283 sage: SageTerminalInteractiveShell() # not tested
284 <sage.repl.interpreter.SageNotebookInteractiveShell object at 0x...>
285 """
286
287 def init_display_formatter(self):
288 """
289 Switch to the Sage IPython commandline rich output backend
290
291 EXAMPLES::
292
293 sage: from sage.repl.interpreter import SageTerminalInteractiveShell
294 sage: SageTerminalInteractiveShell().init_display_formatter() # not tested
295 """
--> 296 from sage.repl.rich_output.backend_ipython import BackendIPythonCommandline
global sage.repl.rich_output.backend_ipython = undefined
BackendIPythonCommandline = undefined
297 backend = BackendIPythonCommandline()
298 backend.get_display_manager().switch_backend(backend, shell=self)
299
300
301 class SageTestShell(SageShellOverride, TerminalInteractiveShell):
302 """
303 Test Shell
304
305 Care must be taken in these doctests to quit the test shell in
306 order to switch back the rich output display backend to the
307 doctest backend.
308
309 EXAMPLES::
310
311 sage: from sage.repl.interpreter import get_test_shell
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/sage/repl/rich_output/__init__.py in <module>
1 # -*- encoding: utf-8 -*-
2
----> 3 from .display_manager import get_display_manager
global display_manager = undefined
global get_display_manager = undefined
4 from .pretty_print import pretty_print
5
6
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/sage/repl/rich_output/display_manager.py in <module>
24 The Sage display manager using the doctest backend
25 """
26
27 # ****************************************************************************
28 # Copyright (C) 2015 Volker Braun <vbrau...@gmail.com>
29 #
30 # Distributed under the terms of the GNU General Public License (GPL)
31 # as published by the Free Software Foundation; either version 2 of
32 # the License, or (at your option) any later version.
33 # http://www.gnu.org/licenses/
34 # ****************************************************************************
35
36
37 import warnings
38
---> 39 from sage.structure.sage_object import SageObject
global sage.structure.sage_object = undefined
global SageObject = undefined
40 from sage.repl.rich_output.output_basic import (
41 OutputPlainText, OutputAsciiArt, OutputUnicodeArt, OutputLatex,
42 )
43 from sage.repl.rich_output.preferences import DisplayPreferences
44
45
46 class DisplayException(Exception):
47 """
48 Base exception for all rich output-related exceptions.
49
50 EXAMPLES::
51
52 sage: from sage.repl.rich_output.display_manager import DisplayException
53 sage: raise DisplayException('foo')
54 Traceback (most recent call last):
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/sage/structure/__init__.py in <module>
1 # Resolve a cyclic import
----> 2 import sage.structure.element
global sage.structure.element = undefined
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/sage/structure/element.pyx in init sage.structure.element (build/cythonized/sage/structure/element.c:35676)()
----> 1 # Compile this with -Os because it works around a bug with
2 # GCC-4.7.3 + Cython 0.19 on Itanium, see Trac #14452. Moreover, it
3 # actually results in faster code than -O3.
4 #
5 # distutils: extra_compile_args = -Os
6
7 r"""
8 Elements
9
10 AUTHORS:
11
12 - David Harvey (2006-10-16): changed CommutativeAlgebraElement to
13 derive from CommutativeRingElement instead of AlgebraElement
14
15 - David Harvey (2006-10-29): implementation and documentation of new
16 arithmetic architecture
17
18 - William Stein (2006-11): arithmetic architecture -- pushing it
19 through to completion.
20
21 - Gonzalo Tornaria (2007-06): recursive base extend for coercion --
22 lots of tests
23
24 - Robert Bradshaw (2007-2010): arithmetic operators and coercion
25
26 - Maarten Derickx (2010-07): added architecture for is_square and sqrt
27
28 - Jeroen Demeyer (2016-08): moved all coercion to the base class
29 :class:`Element`, see :trac:`20767`
30
31 The Abstract Element Class Hierarchy
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/sage/structure/sage_object.pyx in init sage.structure.sage_object (build/cythonized/sage/structure/sage_object.c:11967)()
1 # -*- encoding: utf-8 -*-
2 r"""
3 Abstract base class for Sage objects
4 """
5
----> 6 from sage.misc.persist import (_base_dumps, _base_save,
global sage.misc.persist = undefined
global _base_dumps = undefined
global _base_save = undefined
global register_unpickle_override = undefined
global make_None = undefined
7 register_unpickle_override, make_None)
8
9 from sage.misc.lazy_import import LazyImport
10
11 # NOTE: These imports are just for backwards-compatibility
12 loads = LazyImport('sage.misc.persist', 'loads', deprecation=25153)
13 dumps = LazyImport('sage.misc.persist', 'dumps', deprecation=25153)
14 save = LazyImport('sage.misc.persist', 'save', deprecation=25153)
15 load = LazyImport('sage.misc.persist', 'load', deprecation=25153)
16 unpickle_all = LazyImport('sage.misc.persist', 'unpickle_all',
17 deprecation=25153)
18 unpickle_global = LazyImport('sage.misc.persist', 'unpickle_global',
19 deprecation=25153)
20 unpickle_override = LazyImport('sage.misc.persist', 'unpickle_override',
21 deprecation=25153)
22
23
24 # Generators is no longer used (#21382)
25 register_unpickle_override('sage.structure.generators', 'make_list_gens',
26 make_None)
27
28
29 __all__ = ['SageObject']
30
31
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/site-packages/sage/misc/persist.pyx in init sage.misc.persist (build/cythonized/sage/misc/persist.c:11955)()
25 correctly or work correctly.
26
27 - Objects are zlib compressed for space efficiency.
28 """
29
30 import io
31 import os
32 import pickle
33 import sys
34
35 from textwrap import dedent
36
37 # change to import zlib to use zlib instead; but this
38 # slows down loading any data stored in the other format
39 import zlib; comp = zlib
---> 40 import bz2; comp_other = bz2
global bz2 = undefined
global comp_other = undefined
41
42 from .misc import SAGE_DB
43 from .sage_unittest import TestSuite
44
45
46 cdef _normalize_filename(s):
47 """
48 Append the .sobj extension to a filename if it doesn't already have it.
49 """
50 if s[-5:] != '.sobj':
51 return s + '.sobj'
52
53 return s
54
55
~/sagefiles/sage-9.2.rc0/local/lib/python3.8/bz2.py in <module>
4 (de)compression, and functions for one-shot (de)compression.
5 """
6
7 __all__ = ["BZ2File", "BZ2Compressor", "BZ2Decompressor",
8 "open", "compress", "decompress"]
9
10 __author__ = "Nadeem Vawda <nadeem...@gmail.com>"
11
12 from builtins import open as _builtin_open
13 import io
14 import os
15 import warnings
16 import _compression
17 from threading import RLock
18
---> 19 from _bz2 import BZ2Compressor, BZ2Decompressor
global _bz2 = undefined
global BZ2Compressor = undefined
global BZ2Decompressor = undefined
20
21
22 _MODE_CLOSED = 0
23 _MODE_READ = 1
24 # Value 2 no longer used
25 _MODE_WRITE = 3
26
27 _sentinel = object()
28
29
30 class BZ2File(_compression.BaseStream):
31
32 """A file object providing transparent bzip2 (de)compression.
33
34 A BZ2File can act as a wrapper for an existing file object, or refer
ModuleNotFoundError: No module named '_bz2'
**********************************************************************
Oops, Sage crashed. We do our best to make it stable, but...
A crash report was automatically generated with the following information:
- A verbatim copy of the crash traceback.
- A copy of your input history during this session.
- Data on your current Sage configuration.
It was left in the file named:
'/Users/wdj/.sage/ipython-5.0.0/Sage_crash_report.txt'
If you can email this file to the developers, the information in it will help
them in understanding and correcting the problem.
You can mail it to: sage-support at sage-s...@googlegroups.com
with the subject 'Sage Crash Report'.
If you want to do it now, the following command will work (under Unix):
mail -s 'Sage Crash Report' sage-s...@googlegroups.com < /Users/wdj/.sage/ipython-5.0.0/Sage_crash_report.txt
In your email, please also include information about:
- The operating system under which the crash happened: Linux, macOS, Windows,
other, and which exact version (for example: Ubuntu 16.04.3, macOS 10.13.2,
Windows 10 Pro), and whether it is 32-bit or 64-bit;
- How Sage was installed: using pip or conda, from GitHub, as part of
a Docker container, or other, providing more detail if possible;
- How to reproduce the crash: what exact sequence of instructions can one
input to get the same crash? Ideally, find a minimal yet complete sequence
of instructions that yields the crash.
To ensure accurate tracking of this issue, please file a report about it at:
wdj@jeeves sage-9.2.rc0 % ./sage -python3
Python 3.8.5 (default, Oct 7 2020, 13:59:53)
[Clang 12.0.0 (clang-1200.0.32.2)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 2+3
5
It seems very close to compiling. Does that make sense?
- David
wdj@jeeves sage-9.2.rc0 % brew list --versions
autoconf 2.69
automake 1.16.1_1
bdw-gc 8.0.4
boost 1.71.0
cmake 3.15.5
fontconfig 2.13.1
freetype 2.10.1
gcc 9.2.0_1
gd 2.2.5
gettext 0.20.1 0.21
gmp 6.2.0 6.1.2_2
gnutls 3.6.15
gpatch 2.7.6
guile 3.0.4
icu4c 64.2
isl 0.22.1 0.21
jpeg 9c
libde265 1.0.3
libdvdcss 1.4.2
libevent 2.1.12
libffi 3.3 3.2.1
libidn2 2.3.0 2.2.0_1
libmpc 1.1.0 1.2.0
libomp 9.0.0
libpng 1.6.37
libtasn1 4.14 4.16.0
libtiff 4.0.10_1
libtool 2.4.6_1 2.4.6_2
libunistring 0.9.10
libyaml 0.2.5
mpfi 1.5.3
mpfr 4.1.0 4.0.2
nettle 3.4.1 3.6
ntl 11.4.1
openssl 1.0.2t
openssl@1.1 1.1.1g 1.1.1d
p11-kit 0.23.21 0.23.18.1
pari 2.11.4
pkg-config 0.29.2_3 0.29.2
readline 8.0.4
ruby 2.7.1_2
sqlite 3.33.0
unbound 1.11.0
webp 1.0.3
xz 5.2.4
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David Joyner
2020-10-07 21:09:18 UTC, John H Palmieri:>> including details of which homebrew packages you've installed.To get your installed homebrew packages listed in a file:```$ brew list --versions > brew-list-versions.txt```
Or to add the date to the filename:```$ brew list --versions > brew-list-versions-`date "+%Y-%m-%d"`.txt```
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slelievre
David Joyner
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Mike Lensi
Dima Pasechnik
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