Ok. It seems that the build is failing because of the PKGBUILD... nothing
to do with the package. Sorry for the post.
On Wednesday, July 30, 2014 9:57:40 AM UTC-5, Nick Paulin wrote:
>
> 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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