at the end of your log:
ImportError: libgfortran.so.3: cannot open shared object file: No such
file or directory
Are you using system's gfortran? (you should)
On Wed, Jan 8, 2020 at 4:42 PM Malcolm MacCallum
<m.a.h.maccal...@qmul.ac.uk> wrote:
>
> This is from Ubuntu 18.04 Linux 64-bit
> Sage built from source. The build had an error as follows
> =================
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all-start'):
>
> * package: r-3.6.2
> log file: /usr/local/CA/sage-9.0/logs/pkgs/r-3.6.2.log
> build directory: /usr/local/CA/sage-9.0/local/var/tmp/sage/build/r-3.6.2
>
> 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.
>
> Makefile:31: recipe for target 'all-start' failed
> make[1]: *** [all-start] Error 1
> make[1]: Leaving directory '/usr/local/CA/sage-9.0'
> Makefile:13: recipe for target 'all' failed
>
> I then tried to run sage, getting the following error log.
>
> ***************************************************************************
>
> IPython post-mortem report
>
> {'commit_hash': u'033ab93c7',
> 'commit_source': 'installation',
> 'default_encoding': 'UTF-8',
> 'ipython_path':
> '/usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/IPython',
> 'ipython_version': '5.8.0',
> 'os_name': 'posix',
> 'platform': 'Linux-5.0.0-37-generic-x86_64-with-debian-buster-sid',
> 'sys_executable': '/usr/local/CA/sage-8.8/local/bin/python2',
> 'sys_platform': 'linux2',
> 'sys_version': '2.7.15 (default, Sep 4 2019, 11:48:34) \n[GCC 4.8.5
> 20150623 (Red Hat 4.8.5-39)]'}
>
> ***************************************************************************
>
>
>
> ***************************************************************************
>
> Crash traceback:
>
> ---------------------------------------------------------------------------
> ---------------------------------------------------------------------------
> ImportError Python 2.7.15: /usr/local/CA/sage-8.8/local/bin/python2
> Wed Jan 8 16:34:13 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.
> /usr/local/CA/sage-8.8/src/bin/sage-ipython in <module>()
> 1 #!/usr/bin/env sage-python23
> 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 SageTerminalApp.initialize of
> <sage.repl.interpreter.SageTerminalApp object at 0x7f2348145c50>>
> 16 app.start()
>
> <decorator-gen-110> in initialize(self=<sage.repl.interpreter.SageTerminalApp
> object>, argv=None)
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/traitlets/config/application.pyc
> in catch_config_error(method=<function 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 initialize at 0x7f2342cc56e0>
> app = <sage.repl.interpreter.SageTerminalApp object at 0x7f2348145c50>
> 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
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/IPython/terminal/ipapp.pyc
> 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 0x7f2348145c50>>
> 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,
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/repl/interpreter.pyc
> in init_shell(self=<sage.repl.interpreter.SageTerminalApp object>)
> 743 self.shell.has_sage_extensions = SAGE_EXTENSION in
> self.extensions
> 744
> 745 # Load the %lprun extension if available
> 746 try:
> 747 import line_profiler
> 748 except ImportError:
> 749 pass
> 750 else:
> 751 self.extensions.append('line_profiler')
> 752
> 753 if self.shell.has_sage_extensions:
> 754 self.extensions.remove(SAGE_EXTENSION)
> 755
> 756 # load sage extension here to get a crash if
> 757 # something is wrong with the sage library
> --> 758
> 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 0x7f2340066710>>
> global SAGE_EXTENSION = 'sage'
> 759
> 760
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/IPython/core/extensions.pyc
> 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 0x7f2340066710>>
> mod = <module 'sage' from
> '/usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/__init__.pyc'>
> 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:
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/IPython/core/extensions.pyc
> in
> _call_load_ipython_extension(self=<IPython.core.extensions.ExtensionManager
> object>, mod=<module 'sage' from
> '/usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/__init__.pyc'>)
> 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
> 0x7f234aa0e8c0>
> self.shell = <sage.repl.interpreter.SageTerminalInteractiveShell
> object at 0x7f2342cea4d0>
> 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.
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/__init__.pyc 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 0x7f2333521578>
> args = (<sage.repl.interpreter.SageTerminalInteractiveShell object at
> 0x7f2342cea4d0>,)
> 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)
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/repl/ipython_extension.pyc
> in wrapper(*args=(<sage.repl.interpreter.SageTerminalInteractiveShell
> object>,), **kwargs={})
> 547 ....: if work:
> 548 ....: return 'foo worked'
> 549 ....: raise RuntimeError("foo didn't work")
> 550 sage: foo(False)
> 551 Traceback (most recent call last):
> 552 ...
> 553 RuntimeError: foo didn't work
> 554 sage: foo(True)
> 555 'foo worked'
> 556 sage: foo(False)
> 557 sage: foo(True)
> 558 """
> 559 @wraps(func)
> 560 def wrapper(*args, **kwargs):
> 561 if not wrapper.has_run:
> --> 562 result = func(*args, **kwargs)
> result = undefined
> global func = undefined
> args = (<sage.repl.interpreter.SageTerminalInteractiveShell object at
> 0x7f2342cea4d0>,)
> kwargs = {}
> 563 wrapper.has_run = True
> 564 return result
> 565 wrapper.has_run = False
> 566 return wrapper
> 567
> 568
> 569 @run_once
> 570 def load_ipython_extension(ip):
> 571 """
> 572 Load the extension in IPython.
> 573 """
> 574 # this modifies ip
> 575 SageCustomizations(shell=ip)
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/repl/ipython_extension.pyc
> in
> load_ipython_extension(ip=<sage.repl.interpreter.SageTerminalInteractiveShell
> object>)
> 560 def wrapper(*args, **kwargs):
> 561 if not wrapper.has_run:
> 562 result = func(*args, **kwargs)
> 563 wrapper.has_run = True
> 564 return result
> 565 wrapper.has_run = False
> 566 return wrapper
> 567
> 568
> 569 @run_once
> 570 def load_ipython_extension(ip):
> 571 """
> 572 Load the extension in IPython.
> 573 """
> 574 # this modifies ip
> --> 575 SageCustomizations(shell=ip)
> global SageCustomizations = <class
> 'sage.repl.ipython_extension.SageCustomizations'>
> global shell = undefined
> ip = <sage.repl.interpreter.SageTerminalInteractiveShell object at
> 0x7f2342cea4d0>
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/repl/ipython_extension.pyc
> in __init__(self=<sage.repl.ipython_extension.SageCustomizations object>,
> shell=<sage.repl.interpreter.SageTerminalInteractiveShell object>)
> 418 def __init__(self, shell=None):
> 419 """
> 420 Initialize the Sage plugin.
> 421 """
> 422 self.shell = shell
> 423
> 424 self.auto_magics = SageMagics(shell)
> 425 self.shell.register_magics(self.auto_magics)
> 426
> 427 import sage.misc.edit_module as edit_module
> 428 self.shell.set_hook('editor', edit_module.edit_devel)
> 429
> 430 self.init_inspector()
> 431 self.init_line_transforms()
> 432
> --> 433 import sage.all # until sage's import hell is fixed
> sage.all = undefined
> 434
> 435 self.shell.verbose_quit = True
> 436 self.set_quit_hook()
> 437
> 438 self.register_interface_magics()
> 439
> 440 if SAGE_IMPORTALL == 'yes':
> 441 self.init_environment()
> 442
> 443 def register_interface_magics(self):
> 444 """
> 445 Register magics for each of the Sage interfaces
> 446 """
> 447 from sage.repl.interface_magic import InterfaceMagic
> 448 InterfaceMagic.register_all(self.shell)
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/all.py in
> <module>()
> 69 import math
> 70
> 71 from sage.env import SAGE_ROOT, SAGE_SRC, SAGE_DOC_SRC, SAGE_LOCAL,
> DOT_SAGE, SAGE_ENV
> 72
> 73
> 74 ###################################################################
> 75
> 76 # This import also sets up the interrupt handler
> 77 from cysignals.signals import (AlarmInterrupt, SignalError,
> 78 sig_on_reset as sig_on_count)
> 79
> 80 from time import sleep
> 81 from functools import reduce # in order to keep reduce in python3
> 82
> 83 import sage.misc.lazy_import
> ---> 84 from sage.misc.all import * # takes a while
> global sage.misc.all = undefined
> 85 from sage.typeset.all import *
> 86 from sage.repl.all import *
> 87
> 88 from sage.misc.sh import sh
> 89
> 90 from sage.libs.all import *
> 91 from sage.data_structures.all import *
> 92 from sage.doctest.all import *
> 93
> 94 from sage.structure.all import *
> 95 from sage.rings.all import *
> 96 from sage.arith.all import *
> 97 from sage.matrix.all import *
> 98
> 99 from sage.symbolic.all import *
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/misc/all.py in
> <module>()
> 69
> 70 from .defaults import (set_default_variable_name,
> 71 series_precision, set_series_precision)
> 72
> 73 from .sage_eval import sage_eval, sageobj
> 74
> 75 from .sage_input import sage_input
> 76
> 77 lazy_import("sage.misc.cython", ["cython_lambda",
> "cython_create_local_so"])
> 78 lazy_import("sage.misc.cython", "cython_compile", "cython")
> 79
> 80 from .persist import save, load, dumps, loads, db, db_save
> 81
> 82 from .func_persist import func_persist
> 83
> ---> 84 from .functional import (additive_order,
> global functional = undefined
> global additive_order = undefined
> global base_ring = undefined
> global base_field = undefined
> global basis = undefined
> global category = undefined
> global charpoly = undefined
> global characteristic_polynomial = undefined
> global coerce = undefined
> global cyclotomic_polynomial = undefined
> global decomposition = undefined
> global denominator = undefined
> global det = undefined
> global dimension = undefined
> global dim = undefined
> global discriminant = undefined
> global disc = undefined
> global eta = undefined
> global fcp = undefined
> global gen = undefined
> global gens = undefined
> global hecke_operator = undefined
> global image = undefined
> global integral = undefined
> global integrate = undefined
> global integral_closure = undefined
> global interval = undefined
> global xinterval = undefined
> global is_commutative = undefined
> global is_even = undefined
> global is_integrally_closed = undefined
> global is_field = undefined
> global is_odd = undefined
> global kernel = undefined
> global krull_dimension = undefined
> global lift = undefined
> global log = undefined
> global log_b = undefined
> global minimal_polynomial = undefined
> global minpoly = undefined
> global multiplicative_order = undefined
> global ngens = undefined
> global norm = undefined
> global numerator = undefined
> global numerical_approx = undefined
> global n = undefined
> global N = undefined
> global objgens = undefined
> global objgen = undefined
> global order = undefined
> global rank = undefined
> global regulator = undefined
> global round = undefined
> global quotient = undefined
> global quo = undefined
> global isqrt = undefined
> global squarefree_part = undefined
> global symbolic_sum = undefined
> global sum = undefined
> global symbolic_prod = undefined
> global product = undefined
> global transpose = undefined
> 85 base_ring,
> 86 base_field,
> 87 basis,
> 88 category,
> 89 charpoly,
> 90 characteristic_polynomial,
> 91 coerce,
> 92 cyclotomic_polynomial,
> 93 decomposition,
> 94 denominator,
> 95 det,
> 96 dimension,
> 97 dim,
> 98 discriminant,
> 99 disc,
>
> /usr/local/CA/sage-8.8/local/lib/python2.7/site-packages/sage/misc/functional.py
> in <module>()
> 12 - David Joyner (2005-12-20): More Examples
> 13 """
> 14
> #*****************************************************************************
> 15 # Copyright (C) 2004 William Stein <wst...@gmail.com>
> 16 #
> 17 # This program is free software: you can redistribute it and/or modify
> 18 # it under the terms of the GNU General Public License as published by
> 19 # the Free Software Foundation, either version 2 of the License, or
> 20 # (at your option) any later version.
> 21 # http://www.gnu.org/licenses/
> 22
> #*****************************************************************************
> 23 from __future__ import absolute_import
> 24 from six.moves import range, builtins
> 25 from six import integer_types
> 26
> ---> 27 from sage.rings.complex_double import CDF
> global sage.rings.complex_double = undefined
> global CDF = undefined
> 28 from sage.rings.real_double import RDF, RealDoubleElement
> 29 from sage.rings.integer_ring import ZZ
> 30 from sage.rings.integer import Integer
> 31 from sage.misc.superseded import deprecation
> 32
> 33
> ##############################################################################
> 34 # There are many functions on elements of a ring, which mathematicians
> 35 # usually write f(x), e.g., it is weird to write x.log() and natural
> 36 # to write log(x). The functions below allow for the more familiar
> syntax.
> 37
> ##############################################################################
> 38
> 39
> 40 def additive_order(x):
> 41 """
> 42 Return the additive order of ``x``.
>
> ImportError: libgfortran.so.3: cannot open shared object file: No such file
> or directory
>
> ***************************************************************************
>
> History of session input:
> *** Last line of input (may not be in above history):
>
> --
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