LinuxQuestions.org - Please help me to solve sudo apt-get upgrade error

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Please help me to solve sudo apt-get upgrade error

I am not able to open software centre or any system setting in Linux mint. I have tried all the suggestions posted by experts but none of them is working. While running "sudo apt-get upgrade" or installing any aother software am getting this:

Code:

sumit@sumit ~ $ sudo apt-get upgrade 

Reading package lists... Done

Building dependency tree      

Reading state information... Done

You might want to run 'apt-get -f install' to correct these.

The following packages have unmet dependencies:

 python : PreDepends: python-minimal (= 2.7.11-1) but 2.7.12-1~16.04 is installed

          Depends: libpython-stdlib (= 2.7.11-1) but 2.7.12-1~16.04 is installed

E: Unmet dependencies. Try using -f.

Hi: & Welcome to LQ.

I'm assuming you're running Ubuntu 16.04:-

To fix the problem you need to run:

Code:

sudo apt-get -f install

Those umet dependencies won't go away you will need to satisfy them. The -f means to force.

What are you trying to install?

I am using Mint. At first I was trying to install gnuplot, but later I found that am facing same problem with almost every installation.This is what am getting:

Code:

sumit@sumit ~ $ sudo apt-get -f install

[sudo] password for sumit: 

Reading package lists... Done

Building dependency tree      

Reading state information... Done

Correcting dependencies... Done

The following additional packages will be installed:

  python

Suggested packages:

  python-doc python-tk

The following packages will be upgraded:

  python

1 upgraded, 0 newly installed, 0 to remove and 181 not upgraded.

1 not fully installed or removed.

Need to get 0 B/137 kB of archives.

After this operation, 0 B of additional disk space will be used.

Do you want to continue? [Y/n] Y

Setting up python-minimal (2.7.12-1~16.04) ...

Bus error (core dumped)

dpkg: error processing package python-minimal (--configure):

 subprocess installed post-installation script returned error exit status 135

Errors were encountered while processing:

 python-minimal

E: Sub-process /usr/bin/dpkg returned an error code (1)

My Gnuplot installation error is as following:

Code:

sumit@sumit ~ $ sudo apt-get install gnuplot

Reading package lists... Done

Building dependency tree      

Reading state information... Done

You might want to run 'apt-get -f install' to correct these:

The following packages have unmet dependencies:

 gnuplot : Depends: gnuplot5-qt but it is not going to be installed or

                    gnuplot5-x11 but it is not going to be installed or

                    gnuplot5-nox

 python : PreDepends: python-minimal (= 2.7.11-1) but 2.7.12-1~16.04 is to be installed

          Depends: libpython-stdlib (= 2.7.11-1) but 2.7.12-1~16.04 is to be installed

E: Unmet dependencies. Try 'apt-get -f install' with no packages (or specify a solution).

Been messing about with your sources.list?
Your python package is out of sync with it's dependencies.

I had installed the XCrysDen software and it replaced the original bashrc file. I restored it but since then am facing this issue. Please tell me how can I fix this?

That bus error message is not a good sign.
How did you install XcrySDen (exactly)?

I have downloaded the package from the home site and then run the configuration file.

this is not an exact description. What did you download exactly? How did you run which configuration file. But the most important: did you make it as root or as regular user?

This is the content of XCrysDen configuration file. I run this executable only to install the XCrysden.

Code:

#!/bin/sh



InstallError () {

    echo "

*************************************************

An ERROR occured during configuration of XCrySDen



Code: $1

Exit 1

"

    exit 1

}



#

# Usage: xcConfigure [topdir]

#



if test "$#" -lt 1 ; then

    XCRYSDEN_TOPDIR=`pwd`

    if test \( "$0" != "./xcConfigure.sh" \) -a \( "$0" != "./xcConfigure" \)

    then

        echo "

    Please goto XCrySDen toplevel (root) directory and execute the xcConfigure

    as \"./xcConfigure\" or from any other place as \"xcConfigure topdir\"

"

    exit 1

    fi

else

    if test -d "$1" ; then

        XCRYSDEN_TOPDIR=$1

    else

        InstallError "XCRYSDEN_TOPDIR $1 does not exists"

    fi

fi



# check if XCRYSDEN_TOPDIR exists:

xcv=`env | grep XCRYSDEN_TOPDIR`



cd $XCRYSDEN_TOPDIR



#

# assuming user shell is csh or tcsh or sh

#



if test "`echo -n a`" = "-n a" ; then

    ECHO_n=echo

else

    ECHO_n="echo -n"

fi





if [ \( -d /tmp \) -a \( -w /tmp \) ]; then

    tempdir=/tmp

else

    # set tempdir to $HOME

    tempdir=$HOME

fi



CLEAR=$XCRYSDEN_TOPDIR/scripts/dummy.sh

MORE="cat -"

type clear > $tempdir/install.$$ 2>&1

if test "$?" -eq 0 ; then CLEAR=clear; fi

type more > $tempdir/install.$$ 2>&1

if test "$?" -eq 0 ; then MORE=more; fi



rm -f $tempdir/install.$$



date=`date`

export XCRYSDEN_TOPDIR

. $XCRYSDEN_TOPDIR/sys_utils/xcConfigure_updateProfile.sh

. $XCRYSDEN_TOPDIR/sys_utils/xcConfigure_definitions.sh



rm -f $tempdir/xcInstall-sh.$$ $tempdir/xcInstall-csh.$$;

ON running the file it gives following

Code:

  ========================================================================



      * * * *      XCRYSDEN's Configuration/Setup Utility      * * * * 



  ------------------------------------------------------------------------



                          XCRYSDEN version: 1.5.21



      PLEASE FOLLOW INSTRUCTIONS DURING THE CONFIGURATION PROCEDURE !!!

  =========================================================================

  

  Press <Enter> to continue ...





  Please specify XCRYSDEN_SCRATCH directory (default: /home/sumit/xcrys_tmp):



 Updating profile file /home/sumit/.bashrc ... OK



  The following record was inserted into /home/sumit/.bashrc:





#------------------------------------------------------------------------

# this is for XCRYSDEN 1.5.21; added by XCRYSDEN installation on

# Wed Feb 28 14:23:22 IST 2018

#------------------------------------------------------------------------

XCRYSDEN_TOPDIR=/home/sumit/Software/XCrySDen

XCRYSDEN_SCRATCH=/home/sumit/xcrys_tmp

export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH

PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util"





  I am about to create the $HOME/.xcrysden/custom-definitions file,

  which is XCRYSDEN's customization file.



  Press <Enter> to continue ... 

 Answer the following question(s) please:

  ----------------------------------------



  CRYSTAL is an electronic structure program for periodic systems.

  (http://www.crystal.unito.it/)



  Do you have a CRYSTAL package ([y]es/[n]o): n

backing-up existing custom-definitions file to /home/sumit/.xcrysden/custom-definitions.1

  

  creating new /home/sumit/.xcrysden/custom-definitions file ... OK



  Press <Enter> to continue ...

Would you like to add xcrysden icon to the desktop ([y]es/[n]o): y

  

  creating xcrysden dekstop icon via /home/sumit/Desktop/xcrysden.desktop file ... OK





  XCRYSDEN uses a few external utility programs. These are the following:



  1.) the "Open Babel" program is needed to display molecular structure from 

      Gaussian Z-matrix file.



  2.) the ImageMagick's suit of programs is used to print-to-file (PNG/JPG/GIF/...), 

      to create animated-GIFs, and to screen dump windows.



  3.) the "Mplayer's mencoder" program is used to create AVI/MPEG movies

      from the animation snapshots.



  4.) xcrysden may also use other programs such as gifsicle, xwd, ppmtompeg, ...



  Links

  --

  Open BABEL:  http://openbabel.org/

  IMAGEMAGICK: http://www.imagemagick.org/

  MENCODER:    http://www.mplayerhq.hu/



  Press <Enter> to continue ...

 Please report BUGS to Tone.Kokalj@ijs.si. 



  TERMS OF USE:

  -------------

  XCRYSDEN is released under the GNU General Public License.

  

  Whenever graphics generated by XCrySDen are used in scientific

  publications, it shall be greatly appreciated to include an

  explicit reference. The preferred form is the following:



  [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.

        Code available from http://www.xcrysden.org/.

  

      

  XCRYSDEN tips: 

                  - try: xcrysden --help



                  - occasionally clean the xcrysden scratch directory

                    (you can use the "xc_cleanscratch" utility)



  Press <Enter> to continue ...



FINAL NOTICE: before running xcrysden please load (source) your profile, i.e.:



  - for bash:          source ~/.bashrc

  - for csh or tcsh:    source ~/.cshrc

  - for sh:            . ~/.profile



Then type: xcrysden

so you did not execute it as root (as far as I see). In that case it is not related to the apt-get install -f problem.
But obviously you need to solve that.
which version of mint do you have? How /etc/apt/sources.list is set?

Code:

RELEASE=18.3

CODENAME=sylvia

EDITION="Cinnamon 64-bit"

DESCRIPTION="Linux Mint 18.3 Sylvia"

DESKTOP=Gnome

TOOLKIT=GTK

NEW_FEATURES_URL=http://www.linuxmint.com/rel_sylvia_cinnamon_whatsnew.php

RELEASE_NOTES_URL=http://www.linuxmint.com/rel_sylvia_cinnamon.php

USER_GUIDE_URL=help:linuxmint

GRUB_TITLE=Linux Mint 18.3 Cinnamon 64-bit

There is no source.list at /etc/apt/. However apt contains following folder and file

Code:

sumit@sumit ~ $ ls /etc/apt

apt.conf.d  preferences.d  sources.list.d  trusted.gpg  trusted.gpg~  trusted.gpg.d

All *.d are directory and source.list.d contains following files:

Code:

sumit@sumit ~ $ ls /etc/apt/sources.list.d/

google-chrome.list  graphics-drivers-ppa-xenial.list  official-package-repositories.list

ok, try the following:

Code:

# as root

apt-get update

apt-get upgrade

apt-get install -f

and post the full output

and output of:

Code:

apt-cache policy python python-minimal

Code:

sumit ~ # sudo apt-get update

Get:1 http://security.ubuntu.com/ubuntu xenial-security InRelease [102 kB]

Hit:2 http://archive.ubuntu.com/ubuntu xenial InRelease                                                                                                          

Ign:3 http://dl.google.com/linux/chrome/deb stable InRelease                                                                                                    

Hit:4 http://ppa.launchpad.net/graphics-drivers/ppa/ubuntu xenial InRelease                                                                

Get:5 http://archive.ubuntu.com/ubuntu xenial-updates InRelease [102 kB]                                                                    

Hit:6 http://archive.canonical.com/ubuntu xenial InRelease                                                                                  

Hit:7 http://dl.google.com/linux/chrome/deb stable Release                                                                                  

Ign:8 http://packages.linuxmint.com sylvia InRelease                                                    

Get:9 http://archive.ubuntu.com/ubuntu xenial-backports InRelease [102 kB]                              

Hit:10 http://packages.linuxmint.com sylvia Release                                                      

Fetched 306 kB in 2s (119 kB/s)                  

Reading package lists... Done

Code:

sumit ~ # sudo apt-get upgrade

Reading package lists... Done

Building dependency tree      

Reading state information... Done

You might want to run 'apt-get -f install' to correct these.

The following packages have unmet dependencies:

 python : PreDepends: python-minimal (= 2.7.11-1) but 2.7.12-1~16.04 is installed

          Depends: libpython-stdlib (= 2.7.11-1) but 2.7.12-1~16.04 is installed

E: Unmet dependencies. Try using -f.

Code:

sumit ~ # sudo apt-get install -f

Reading package lists... Done

Building dependency tree      

Reading state information... Done

Correcting dependencies... Done

The following additional packages will be installed:

  python

Suggested packages:

  python-doc python-tk

The following packages will be upgraded:

  python

1 upgraded, 0 newly installed, 0 to remove and 181 not upgraded.

1 not fully installed or removed.

Need to get 0 B/137 kB of archives.

After this operation, 0 B of additional disk space will be used.

Do you want to continue? [Y/n] Y

Setting up python-minimal (2.7.12-1~16.04) ...

Bus error (core dumped)

dpkg: error processing package python-minimal (--configure):

 subprocess installed post-installation script returned error exit status 135

Errors were encountered while processing:

 python-minimal

E: Sub-process /usr/bin/dpkg returned an error code (1)

Code:

sumit ~ # apt-cache policy python python-minimal

python:

  Installed: 2.7.11-1

  Candidate: 2.7.12-1~16.04

  Version table:

    2.7.12-1~16.04 1001

      1001 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages

 *** 2.7.11-1 1001

      1001 http://archive.ubuntu.com/ubuntu xenial/main amd64 Packages

        100 /var/lib/dpkg/status

python-minimal:

  Installed: 2.7.12-1~16.04

  Candidate: 2.7.12-1~16.04

  Version table:

 *** 2.7.12-1~16.04 1001

      1001 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages

        100 /var/lib/dpkg/status

    2.7.11-1 1001

      1001 http://archive.ubuntu.com/ubuntu xenial/main amd64 Packages

looks like it is a conflict because of libpython-stdlib (at least I think so).
I would try:

Code:

apt-get install python-minimal=2.7.11-1