Hello,
I've been having crashes with sagemath (5.8) on Chakra Linux lately.
Crash report
***************************************************************************
IPython post-mortem report
{'commit_hash': 'ca3d98b',
'commit_source': 'installation',
'default_encoding': 'UTF-8',
'ipython_path': '/opt/sage/local/lib/python2.7/site-packages/IPython',
'ipython_version': '0.13.1',
'os_name': 'posix',
'platform': 'Linux-3.15.5-1-CHAKRA-x86_64-with-glibc2.2.5',
'sys_executable': '/opt/sage/local/bin/python',
'sys_platform': 'linux2',
'sys_version': '2.7.3 (default, Mar 23 2013, 19:30:10) \n[GCC 4.7.2]'}
***************************************************************************
***************************************************************************
Crash traceback:
---------------------------------------------------------------------------
ImportError Python 2.7.3: /opt/sage/local/bin/python
Wed Jul 30 07:34:33 2014
A problem occured executing Python code. Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.
/opt/sage/local/bin/sage-ipython in <module>()
1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3 """
4 Sage IPython startup script.
5 """
6 from sage.misc.interpreter import SageTerminalApp
7
8 # Make sure we're using the Sage profile if one isn't specified.
9 import sys
10 if '--profile' not in sys.argv:
11 sys.argv.extend(['--profile', 'sage'])
12
13 app = SageTerminalApp.instance()
---> 14 app.initialize()
global app.initialize = <bound method SageTerminalApp.initialize of
<sage.misc.interpreter.SageTerminalApp object at 0x7fc1c3d454d0>>
15 app.start()
/opt/sage/local/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.pyc
in initialize(self=<sage.misc.interpreter.SageTerminalApp object>,
argv=None)
/opt/sage/local/lib/python2.7/site-packages/IPython/config/application.pyc
in catch_config_error(method=<function initialize>,
app=<sage.misc.interpreter.SageTerminalApp object>, *args=(None,),
**kwargs={})
69
70
#-----------------------------------------------------------------------------
71 # Application class
72
#-----------------------------------------------------------------------------
73
74 @decorator
75 def catch_config_error(method, app, *args, **kwargs):
76 """Method decorator for catching invalid config
(Trait/ArgumentErrors) during init.
77
78 On a TraitError (generally caused by bad config), this will
print the trait's
79 message, and exit the app.
80
81 For use on init methods, to prevent invoking excepthook on
invalid input.
82 """
83 try:
---> 84 return method(app, *args, **kwargs)
method = <function initialize at 0x16887d0>
app = <sage.misc.interpreter.SageTerminalApp object at
0x7fc1c3d454d0>
args = (None,)
kwargs = {}
85 except (TraitError, ArgumentError) as e:
86 app.print_description()
87 app.print_help()
88 app.print_examples()
89 app.log.fatal("Bad config encountered during
initialization:")
90 app.log.fatal(str(e))
91 app.log.debug("Config at the time: %s", app.config)
92 app.exit(1)
93
94
95 class ApplicationError(Exception):
96 pass
97
98
99 class Application(SingletonConfigurable):
/opt/sage/local/lib/python2.7/site-packages/IPython/frontend/terminal/ipapp.pyc
in initialize(self=<sage.misc.interpreter.SageTerminalApp object>,
argv=None)
309
310 @catch_config_error
311 def initialize(self, argv=None):
312 """Do actions after construct, but before starting the
app."""
313 super(TerminalIPythonApp, self).initialize(argv)
314 if self.subapp is not None:
315 # don't bother initializing further, starting subapp
316 return
317 if not self.ignore_old_config:
318 check_for_old_config(self.ipython_dir)
319 # print self.extra_args
320 if self.extra_args and not self.something_to_run:
321 self.file_to_run = self.extra_args[0]
322 self.init_path()
323 # create the shell
--> 324 self.init_shell()
self.init_shell = <bound method SageTerminalApp.init_shell of
<sage.misc.interpreter.SageTerminalApp object at 0x7fc1c3d454d0>>
325 # and draw the banner
326 self.init_banner()
327 # Now a variety of things that happen after the banner is
printed.
328 self.init_gui_pylab()
329 self.init_extensions()
330 self.init_code()
331
332 def init_shell(self):
333 """initialize the InteractiveShell instance"""
334 # Create an InteractiveShell instance.
335 # shell.display_banner should always be False for the
terminal
336 # based app, because we call shell.show_banner() by hand
below
337 # so the banner shows *before* all extension loading stuff.
338 self.shell =
TerminalInteractiveShell.instance(config=self.config,
339 display_banner=False,
profile_dir=self.profile_dir,
/opt/sage/local/lib/python2.7/site-packages/sage/misc/interpreter.pyc in
init_shell(self=<sage.misc.interpreter.SageTerminalApp object>)
716 sage: from sage.misc.interpreter import
SageTerminalApp, DEFAULT_SAGE_CONFIG
717 sage: app = SageTerminalApp(config=DEFAULT_SAGE_CONFIG)
718 sage: app.initialize(argv=[]) # indirect doctest
719 sage: app.shell
720 <sage.misc.interpreter.SageInteractiveShell object at
0x...>
721 """
722 # We need verbose crashes for the Sage crash handler. We
set it here
723 # so that we don't overwrite the traitlet attribute
724 self.verbose_crash = True
725
726 # Shell initialization
727 self.shell =
SageInteractiveShell.instance(config=self.config,
728 display_banner=False,
profile_dir=self.profile_dir,
729 ipython_dir=self.ipython_dir)
730 self.shell.configurables.append(self)
--> 731
self.shell.extension_manager.load_extension('sage.misc.sage_extension')
self.shell.extension_manager.load_extension = <bound method
ExtensionManager.load_extension of
<IPython.core.extensions.ExtensionManager object at 0x16b9d50>>
/opt/sage/local/lib/python2.7/site-packages/IPython/core/extensions.pyc in
load_extension(self=<IPython.core.extensions.ExtensionManager object>,
module_str='sage.misc.sage_extension')
75
76 def _on_ipython_dir_changed(self):
77 if not os.path.isdir(self.ipython_extension_dir):
78 os.makedirs(self.ipython_extension_dir, mode = 0777)
79
80 def load_extension(self, module_str):
81 """Load an IPython extension by its module name.
82
83 If :func:`load_ipython_extension` returns anything, this
function
84 will return that object.
85 """
86 from IPython.utils.syspathcontext import
prepended_to_syspath
87
88 if module_str not in sys.modules:
89 with prepended_to_syspath(self.ipython_extension_dir):
---> 90 __import__(module_str)
global __import__ = undefined
module_str = 'sage.misc.sage_extension'
91 mod = sys.modules[module_str]
92 return self._call_load_ipython_extension(mod)
93
94 def unload_extension(self, module_str):
95 """Unload an IPython extension by its module name.
96
97 This function looks up the extension's name in
``sys.modules`` and
98 simply calls ``mod.unload_ipython_extension(self)``.
99 """
100 if module_str in sys.modules:
101 mod = sys.modules[module_str]
102 self._call_unload_ipython_extension(mod)
103
104 def reload_extension(self, module_str):
105 """Reload an IPython extension by calling reload.
/opt/sage/local/lib/python2.7/site-packages/sage/misc/sage_extension.py in
<module>()
35 2
36
37 In contrast, input to the ``%time`` magic command is preparsed::
38
39 sage: shell.run_cell('%time 594.factor()')
40 CPU times: user ...
41 Wall time: ...
42 2 * 3^3 * 11
43 """
44
45 from IPython.core.hooks import TryNext
46 from IPython.core.magic import Magics, magics_class, line_magic
47 import os
48 import sys
49 import sage
---> 50 import sage.all
global sage.all = undefined
51 from sage.misc.interpreter import preparser
52 from sage.misc.preparser import preparse
53
54 @magics_class
55 class SageMagics(Magics):
56
57 @line_magic
58 def runfile(self, s):
59 r"""
60 Loads the code contained in the file ``s``. This is designed
61 to be used from the command line as ``%runfile
/path/to/file``.
62
63 :param s: file to be loaded
64 :type s: string
65
/opt/sage/local/lib/python2.7/site-packages/sage/all.py in <module>()
55
56 ###################################################################
57
58 from sage.ext.c_lib import _init_csage, sig_on_count
59 _init_csage()
60
61 from time import sleep
62
63 from sage.misc.all import * # takes a while
64
65 from sage.misc.sh import sh
66
67 from sage.libs.all import *
68
69 from sage.rings.all import *
---> 70 from sage.matrix.all import *
global sage.matrix.all = undefined
71
72 # This must come before Calculus -- it initializes the Pynac
library.
73 import sage.symbolic.pynac
74
75 from sage.modules.all import *
76 from sage.monoids.all import *
77 from sage.algebras.all import *
78 from sage.modular.all import *
79 from sage.schemes.all import *
80 from sage.graphs.all import *
81 from sage.groups.all import *
82 from sage.databases.all import *
83 from sage.structure.all import *
84 from sage.categories.all import *
85 from sage.sets.all import *
/opt/sage/local/lib/python2.7/site-packages/sage/matrix/all.py in <module>()
----> 1 from matrix_space import MatrixSpace, is_MatrixSpace
global matrix_space = undefined
global MatrixSpace = undefined
global is_MatrixSpace = undefined
2 from constructor import matrix, Matrix, column_matrix,
random_matrix, diagonal_matrix, identity_matrix, block_matrix,
block_diagonal_matrix, jordan_block, zero_matrix, ones_matrix,
elementary_matrix, companion_matrix
3 from matrix import is_Matrix
4 from berlekamp_massey import berlekamp_massey
5
6
7 Mat = MatrixSpace
8
/opt/sage/local/lib/python2.7/site-packages/sage/matrix/matrix_space.pyc in
<module>()
22 sage: matrix(GF(11),2,2,sparse=True)
23 [0 0]
24 [0 0]
25 """
26
27 # System imports
28 import types
29 import weakref
30 import operator
31
32 # Sage matrix imports
33 import matrix
34 import matrix_generic_dense
35 import matrix_generic_sparse
36
---> 37 import matrix_modn_dense
global matrix_modn_dense = undefined
38 import matrix_modn_sparse
39
40 import matrix_mod2_dense
41 import matrix_mod2e_dense
42
43 import matrix_integer_dense
44 import matrix_integer_sparse
45
46 import matrix_rational_dense
47 import matrix_rational_sparse
48
49 import matrix_mpolynomial_dense
50
51 #import padics.matrix_padic_capped_relative_dense
52
/run/media/npaulin/TEMP1/sage-mathematics/matrix_modn_dense_template_header.pxi
in init sage.matrix.matrix_modn_dense
(sage/matrix/matrix_modn_dense.c:13934)()
/run/media/npaulin/TEMP1/sage-mathematics/matrix_integer_dense.pxd in init
sage.matrix.matrix_modn_dense_float
(sage/matrix/matrix_modn_dense_float.cpp:16937)()
/run/media/npaulin/TEMP1/sage-mathematics/matrix_mod2_dense.pxd in init
sage.matrix.matrix_integer_dense
(sage/matrix/matrix_integer_dense.c:43257)()
ImportError: /usr/lib/libharfbuzz.so.0: undefined symbol:
FT_Face_GetCharVariantIndex
***************************************************************************
History of session input:
*** Last line of input (may not be in above history):
So.... I tried to rebuild the sage-mathematics package myself to get back
to work. I've been hitting a problem that seems to have caused users
trouble in the past, but I'm still not able to get passed the issue. I'm
running Chakra Linux inside Virtualbox on Windows 7. I have also gotten
the same results on a native installation of Chakra for version 6.1 and 6.2.
error
****************************************************************
make[3]: Leaving directory
`/run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/local/var/tmp/sage/build/atlas-3.10.1.20140210/src/ATLAS-build'
Installed ATLAS headers
Copying
/run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/local/var/tmp/sage/build/atlas-3.10.1.20140210/patches/atlas-config
to /run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/local/bin
real 10m48.614s
user 8m55.893s
sys 0m42.173s
Successfully installed atlas-3.10.1.20140210
You can safely delete the temporary build directory
/run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/local/var/tmp/sage/build/atlas-3.10.1.20140210
Finished installing atlas-3.10.1.20140210.spkg
make[2]: Leaving directory
`/run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/build'
make[1]: *** [all] Error 2
make[1]: Leaving directory
`/run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/build'
real 10m52.793s
user 15m38.983s
sys 1m0.510s
***************************************************************
Error building Sage.
The following package(s) may have failed to build:
package: libgap-4.7.4
log file:
/run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/logs/pkgs/libgap-4.7.4.log
build directory:
/run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/local/var/tmp/sage/build/libgap-4.7.4
The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
make: *** [build] Error 1
************************************************************************************
from
/run/media/npaulin/TEMP1/sage-mathematics/src/sage-6.2/logs/pkgs/libgap-4.7.4.log
***************************************************************************
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in
`/run/media/npaulin/TEMP1/sage-mathema
tics/src/sage-6.2/local/var/tmp/sage/build/libgap-4.7.4/src':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
Error configuring libGAP.
real 0m0.430s
user 0m0.073s
sys 0m0.030s
************************************************************************
Error installing package libgap-4.7.4
************************************************************************
This is the version of gcc considered stable in Chakra.
$ gcc --version
gcc (GCC) 4.9.0 20140521 (prerelease)
Chakra has two versions of gcc available. gcc and gcc-multilib. Both gcc
builds give the same build error and are both on version 4.9.0
I'm happy to provide any other information needed.
--
Nick Paulin
--
Nick Paulin
--
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