Sudden problem when upgrading

Question

I am running XUbuntu 14.04 and today I issued sudo apt-get upgrade on my system and the output was

Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n]
Setting up sagemath-upstream-binary (6.7ppa7) ...
Running Sage once as root to set paths
┌────────────────────────────────────────────────────────────────────┐
│ SageMath Version 6.7, Release Date: 2015-05-17                     │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘
Traceback (most recent call last):
File "/usr/lib/sagemath/src/bin/sage-ipython", line 7, in <module>
from sage.repl.interpreter import SageTerminalApp
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/sage/__init__.py", line 3, in <module>
from sage.repl.ipython_extension import load_ipython_extension
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/sage/repl/ipython_extension.py", line 59, in <module>
from IPython.core.magic import Magics, magics_class, line_magic
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/__init__.py", line 45, in <module>
from .config.loader import Config
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/config/__init__.py", line 6, in <module>
from .application import *
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/config/application.py", line 9, in <module>
import json
File "/usr/lib/sagemath/local/lib/python/json/__init__.py", line 108, in <module>
from .decoder import JSONDecoder
File "/usr/lib/sagemath/local/lib/python/json/decoder.py", line 5, in <module>
import struct
File "/usr/lib/sagemath/local/lib/python/struct.py", line 1, in <module>
from _struct import *
ImportError: No module named _struct
dpkg: error processing package sagemath-upstream-binary (--configure):
subprocess installed post-installation script returned error exit status 1
Errors were encountered while processing:
sagemath-upstream-binary
E: Sub-process /usr/bin/dpkg returned an error code (1)

It appears that there is something wrong with sage and indeed issuing sage returns

┌────────────────────────────────────────────────────────────────────┐
│ SageMath Version 6.7, Release Date: 2015-05-17                     │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘
Traceback (most recent call last):
File "/usr/lib/sagemath/src/bin/sage-ipython", line 7, in <module>
from sage.repl.interpreter import SageTerminalApp
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/sage/__init__.py", line 3, in <module>
from sage.repl.ipython_extension import load_ipython_extension
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/sage/repl/ipython_extension.py", line 59, in <module>
from IPython.core.magic import Magics, magics_class, line_magic
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/__init__.py", line 45, in <module>
from .config.loader import Config
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/config/__init__.py", line 6, in <module>
from .application import *
File "/usr/lib/sagemath/local/lib/python2.7/site-packages/IPython/config/application.py", line 9, in <module>
import json
File "/usr/lib/sagemath/local/lib/python/json/__init__.py", line 108, in <module>
from .decoder import JSONDecoder
File "/usr/lib/sagemath/local/lib/python/json/decoder.py", line 5, in <module>
import struct
File "/usr/lib/sagemath/local/lib/python/struct.py", line 1, in <module>
from _struct import *
ImportError: No module named _struct

Does anyone have an idea what is wrong with my system? If so, how can I fix it?

Answer 1

It looks like there is a problem in the build uploaded to the mirror. They are trying to fix it. A temporary fix is to revert back to a previous version by using the following command

sudo apt-get install sagemath-upstream-binary=6.6ppa1
sudo apt-mark hold sagemath-upstream-binary 

For more information about it go to This link. You can also follow the discussion there as they will post the fix when it is done.

Answer 2

Well it appears a single application is causing this problem from lack of dependencies and/or broken packages. This can happen from time to time.

As a possible fix you can try copying and executing the script below to see if it re-mediates your problem. Since the script does not pass control back to the command-line-interface, as running individual commands does, the package manager should build and fix the dependencies as the script is executed with out having broken packages.

#! /bin/bash

sudo apt-get update

sudo apt-get -f install -y

sudo updatedb

sudo apt-get -f upgrade -y

sudo apt-get -f install -y 

sudo updatedb

exit

Copy the script into gedit and save it. Then from command line, change the mode of access to executable and execute the script using the sudo command:

:~$ chmod +x scriptname.sh

:~$ sudo ./scriptname.sh

If this does not re-mediate your problem, purge sage and it will remove all your dependencies for the application. Then reinstall sage.

:~$ sudo apt-get purge sage

:~$ sudo apt-get autoremove -y

:~$ sudo apt-get install sage

NOTICE: I did not put the -y flag on the apt-get purge sequence because sage could be linked to ubuntu-desktop package which inturn will take your whole desktop environment. To avoid this you will be prompted with a (Yes/No) option. If you see *XUbuntu-desktop as one of the packages to be removed then enter no as the option.

If this not successful re-post and the Ubuntu Universe will help you with another work around!

Good Luck and Go Ubuntu!