[Bio-linux-list] Update error Red icon

[Tauqeer Alam]

Hi Tony
Thanks for your help. It seems like the problem is more complex than I
thought. I was trying to fix the problem, but actually I messed up lot of
things it seems. The Ubuntu Software Center icon from the side bar also
disappeared. Please see the output attached with this e-mail.

Thanks

Tauqeer



On Thu, Nov 23, 2017 at 6:09 AM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 23/11/17 02:24, Tauqeer Alam wrote:
> > Hi All
> >
> > I was trying to install python 3.6, which I think was installed without
> > problem. Now I get a "red circle with horizontal white line" in the
> > taskbar at the top, and the error message "An error occurred when
> > checking for updates". My computer works fine otherwise without a
> > problem, except that the little red circle is always there on the top. I
> > tried “sudo apt-get -f install, sudo apt-get update, sudo apt-get
> > upgrade” commands without any success. I also removed python 3.6, still
> > the error exists. Could anyone guide me how to fix this error. Here is
> > the output of the upgrade command-
>
> Hi, Tauqeer.
>
> How did you install Python 3.6?
>
> This is what you should see in Bio-linux 8 (Ubuntu 14.04.5 LTS):
>
> > apt list 'python[0-9].[0-9]'
> > Listing... Done
> > python2.7/trusty-updates,trusty-security,now 2.7.6-8ubuntu0.3 amd64
> [installed,automatic]
> > python3.4/trusty-updates,trusty-security,now 3.4.3-1ubuntu1~14.04.5
> amd64 [installed]
>
> Please post the output from:
>
> > sudo apt-cache policy 'python3'
> > sudo apt -f install
>
> I suspect that you have packages with dependencies that can't be
> installed, which gives you the red warning that mean "fix it manually".
>
> HTH,
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
> Bio-Linux-list mailing list
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>
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:~$  apt list 'python[0-9].[0-9]'

Listing... Done
python2.7/trusty-updates,trusty-security,now 2.7.6-8ubuntu0.3 amd64 [installed]
python3.4/trusty-updates,trusty-security,now 3.4.3-1ubuntu1~14.04.5 amd64 [installed]

:~$ sudo apt-cache policy 'python3'

python3:
  Installed: 3.4.0-0ubuntu2
  Candidate: 3.4.0-0ubuntu2
  Version table:
 *** 3.4.0-0ubuntu2 0
        500 http://us.archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages
        100 /var/lib/dpkg/status

:~$ sudo apt -f install

Reading package lists... Done
Building dependency tree       
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
102 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Setting up python3.4-minimal (3.4.3-1ubuntu1~14.04.5) ...
# Empty sitecustomize.py to avoid a dangling symlink
Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Fatal Python error: Py_Initialize: Unable to get the locale encoding
ImportError: No module named 'encodings'
Aborted
dpkg: error processing package python3.4-minimal (--configure):
 subprocess installed post-installation script returned error exit status 134
Setting up libc6-dev-i386 (2.19-0ubuntu6.13) ...
Setting up libc6-x32 (2.19-0ubuntu6.13) ...
Setting up libc6-dev-x32 (2.19-0ubuntu6.13) ...
Setting up libx32gcc1 (1:4.9.3-0ubuntu4) ...
Setting up lib32gomp1 (4.8.4-2ubuntu1~14.04.3) ...
Setting up libx32gomp1 (4.8.4-2ubuntu1~14.04.3) ...
Setting up lib32itm1 (4.8.4-2ubuntu1~14.04.3) ...
Setting up libx32itm1 (4.8.4-2ubuntu1~14.04.3) ...
Setting up lib32atomic1 (4.8.4-2ubuntu1~14.04.3) ...
Setting up libx32atomic1 (4.8.4-2ubuntu1~14.04.3) ...
Setting up lib32asan0 (4.8.4-2ubuntu1~14.04.3) ...
Setting up libx32asan0 (4.8.4-2ubuntu1~14.04.3) ...
Setting up lib32quadmath0 (4.8.4-2ubuntu1~14.04.3) ...
Setting up libx32quadmath0 (4.8.4-2ubuntu1~14.04.3) ...
Setting up lib32gcc-4.8-dev (4.8.4-2ubuntu1~14.04.3) ...
Setting up libx32gcc-4.8-dev (4.8.4-2ubuntu1~14.04.3) ...
Setting up gcc-4.8-multilib (4.8.4-2ubuntu1~14.04.3) ...
Setting up gcc-multilib (4:4.8.2-1ubuntu6) ...
Setting up python3-xkit (0.5.0ubuntu2) ...
/var/lib/dpkg/info/python3-xkit.postinst: 6: /var/lib/dpkg/info/python3-xkit.postinst: py3compile: not found
dpkg: error processing package python3-xkit (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of ubuntu-drivers-common:
 ubuntu-drivers-common depends on python3-xkit; however:
  Package python3-xkit is not configured yet.

dpkg: error processing package ubuntu-drivers-common (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of python3.4:
 python3.4 depends on python3.4-minimal (= 3.4.3-1ubuntu1~14.04.5); however:
  Package python3.4-minimal is not configured yet.

dpkg: error processing package python3.4 (--configure):
 dependency problems - leaving unconfigured
Setting up python3-commandnotfound (0.3ubuntu12) ...
/var/lib/dpkg/info/python3-commandnotfound.postinst: 6: /var/lib/dpkg/info/python3-commandnotfound.postinst: py3compile: not found
dpkg: error processing package python3-commandnotfound (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up ufw (0.34~rc-0ubuntu2) ...
/var/lib/dpkg/info/ufw.postinst: 162: /var/lib/dpkg/info/ufw.postinst: py3compile: not found
dpkg: error processing package ufw (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up apturl-common (0.5.2ubuntu4) ...
/var/lib/dpkg/info/apturl-common.postinst: 27: /var/lib/dpkg/info/apturl-common.postinst: py3compile: not found
dpkg: error processing package apturl-common (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up python3-software-properties (0.92.37.8) ...
/var/lib/dpkg/info/python3-software-properties.postinst: 6: /var/lib/dpkg/info/python3-software-properties.postinst: py3compile: not found
dpkg: error processing package python3-software-properties (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of software-properties-common:
 software-properties-common depends on python3-software-properties (= 0.92.37.8); however:
  Package python3-software-properties is not configured yet.

dpkg: error processing package software-properties-common (--configure):
 dependency problems - leaving unconfigured
Setting up python3-aptdaemon.gtk3widgets (1.1.1-1ubuntu5.2) ...
/var/lib/dpkg/info/python3-aptdaemon.gtk3widgets.postinst: 6: /var/lib/dpkg/info/python3-aptdaemon.gtk3widgets.postinst: py3compile: not found
dpkg: error processing package python3-aptdaemon.gtk3widgets (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of software-properties-gtk:
 software-properties-gtk depends on python3-software-properties (= 0.92.37.8); however:
  Package python3-software-properties is not configured yet.
 software-properties-gtk depends on python3-aptdaemon.gtk3widgets; however:
  Package python3-aptdaemon.gtk3widgets is not configured yet.
 software-properties-gtk depends on software-properties-common; however:
  Package software-properties-common is not configured yet.
 software-properties-gtk depends on ubuntu-drivers-common (>= 1:0.2.75); however:
  Package ubuntu-drivers-common is not configured yet.

dpkg: error processing package software-properties-gtk (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of apturl:
 apturl depends on apturl-common (= 0.5.2ubuntu4); however:
  Package apturl-common is not configured yet.
 apturl depends on software-properties-gtk; however:
  Package software-properties-gtk is not configured yet.
 apturl depends on python3-aptdaemon.gtk3widgets; however:
  Package python3-aptdaemon.gtk3widgets is not configured yet.

dpkg: error processing package apturl (--configure):
 dependency problems - leaving unconfigured
Setting up gedit (3.10.4-0ubuntu4) ...
/var/lib/dpkg/info/gedit.postinst: 37: /var/lib/dpkg/info/gedit.postinst: py3compile: not found
dpkg: error processing package gedit (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up python3-xdg (0.25-4) ...
/var/lib/dpkg/info/python3-xdg.postinst: 6: /var/lib/dpkg/info/python3-xdg.postinst: py3compile: not found
dpkg: error processing package python3-xdg (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of python3-speechd:
 python3-speechd depends on python3-xdg; however:
  Package python3-xdg is not configured yet.

dpkg: error processing package python3-speechd (--configure):
 dependency problems - leaving unconfigured
Setting up python3-pyatspi (2.10.0+dfsg-1) ...
/var/lib/dpkg/info/python3-pyatspi.postinst: 6: /var/lib/dpkg/info/python3-pyatspi.postinst: py3compile: not found
dpkg: error processing package python3-pyatspi (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up python3-louis (2.5.3-2ubuntu1.2) ...
/var/lib/dpkg/info/python3-louis.postinst: 6: /var/lib/dpkg/info/python3-louis.postinst: py3compile: not found
dpkg: error processing package python3-louis (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of gnome-orca:
 gnome-orca depends on python3-speechd (>= 0.6.2); however:
  Package python3-speechd is not configured yet.
 gnome-orca depends on python3-pyatspi (>= 2.6); however:
  Package python3-pyatspi is not configured yet.
 gnome-orca depends on python3-louis (>= 1.6.2); however:
  Package python3-louis is not configured yet.

dpkg: error processing package gnome-orca (--configure):
 dependency problems - leaving unconfigured
Setting up python3-cairo (1.10.0+dfsg-3ubuntu2) ...
/var/lib/dpkg/info/python3-cairo.postinst: 6: /var/lib/dpkg/info/python3-cairo.postinst: py3compile: not found
dpkg: error processing package python3-cairo (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of python3-gi-cairo:
 python3-gi-cairo depends on python3-cairo (>= 1.10.0+dfsg-3~exp2); however:
  Package python3-cairo is not configured yet.

dpkg: error processing package python3-gi-cairo (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of gnome-sudoku:
 gnome-sudoku depends on python3-gi-cairo (>= 2.90.1); however:
  Package python3-gi-cairo is not configured yet.
 gnome-sudoku depends on python3-cairo; however:
  Package python3-cairo is not configured yet.

dpkg: error processing package gnome-sudoku (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of language-selector-gnome:
 language-selector-gnome depends on python3-aptdaemon.gtk3widgets; however:
  Package python3-aptdaemon.gtk3widgets is not configured yet.

dpkg: error processing package language-selector-gnome (--configure):
 dependency problems - leaving unconfigured
Setting up libc6-pic:amd64 (2.19-0ubuntu6.13) ...
dpkg: dependency problems prevent configuration of onboard:
 onboard depends on python3-cairo; however:
  Package python3-cairo is not configured yet.
 onboard depends on python3-gi-cairo; however:
  Package python3-gi-cairo is not configured yet.

dpkg: error processing package onboard (--configure):
 dependency problems - leaving unconfigured
Setting up python3-chardet (2.2.1-2~ubuntu1) ...
/var/lib/dpkg/info/python3-chardet.postinst: 6: /var/lib/dpkg/info/python3-chardet.postinst: py3compile: not found
dpkg: error processing package python3-chardet (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up python3-lxml (3.3.3-1ubuntu0.1) ...
/var/lib/dpkg/info/python3-lxml.postinst: 6: /var/lib/dpkg/info/python3-lxml.postinst: py3compile: not found
dpkg: error processing package python3-lxml (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of python3-plainbox:
 python3-plainbox depends on python3-lxml; however:
  Package python3-lxml is not configured yet.

dpkg: error processing package python3-plainbox (--configure):
 dependency problems - leaving unconfigured
Setting up python3-six (1.5.2-1ubuntu1) ...
/var/lib/dpkg/info/python3-six.postinst: 6: /var/lib/dpkg/info/python3-six.postinst: py3compile: not found
dpkg: error processing package python3-six (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of python3-urllib3:
 python3-urllib3 depends on python3-six; however:
  Package python3-six is not configured yet.

dpkg: error processing package python3-urllib3 (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of python3-requests:
 python3-requests depends on python3-chardet; however:
  Package python3-chardet is not configured yet.
 python3-requests depends on python3-urllib3 (>= 1.5); however:
  Package python3-urllib3 is not configured yet.

dpkg: error processing package python3-requests (--configure):
 dependency problems - leaving unconfigured
Setting up python3-pyparsing (2.0.1+dfsg1-1build1) ...
/var/lib/dpkg/info/python3-pyparsing.postinst: 6: /var/lib/dpkg/info/python3-pyparsing.postinst: py3compile: not found
dpkg: error processing package python3-pyparsing (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of python3-checkbox-support:
 python3-checkbox-support depends on python3-pyparsing; however:
  Package python3-pyparsing is not configured yet.

dpkg: error processing package python3-checkbox-support (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of python3-checkbox-ng:
 python3-checkbox-ng depends on python3-plainbox (>= 0.5.3); however:
  Package python3-plainbox is not configured yet.
 python3-checkbox-ng depends on python3-requests (>= 1.0); however:
  Package python3-requests is not configured yet.
 python3-checkbox-ng depends on python3-checkbox-support; however:
  Package python3-checkbox-support is not configured yet.

dpkg: error processing package python3-checkbox-ng (--configure):
 dependency problems - leaving unconfigured
Setting up python3-crypto (2.6.1-4ubuntu0.2) ...
/var/lib/dpkg/info/python3-crypto.postinst: 6: /var/lib/dpkg/info/python3-crypto.postinst: py3compile: not found
dpkg: error processing package python3-crypto (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of python3-debian:
 python3-debian depends on python3-chardet; however:
  Package python3-chardet is not configured yet.
 python3-debian depends on python3-six; however:
  Package python3-six is not configured yet.

dpkg: error processing package python3-debian (--configure):
 dependency problems - leaving unconfigured
Setting up python3-feedparser (5.1.3-2) ...
/var/lib/dpkg/info/python3-feedparser.postinst: 6: /var/lib/dpkg/info/python3-feedparser.postinst: py3compile: not found
dpkg: error processing package python3-feedparser (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up python3-httplib2 (0.8-2build1) ...
/var/lib/dpkg/info/python3-httplib2.postinst: 6: /var/lib/dpkg/info/python3-httplib2.postinst: py3compile: not found
dpkg: error processing package python3-httplib2 (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up python3-markupsafe (0.18-1build2) ...
/var/lib/dpkg/info/python3-markupsafe.postinst: 6: /var/lib/dpkg/info/python3-markupsafe.postinst: py3compile: not found
dpkg: error processing package python3-markupsafe (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of python3-mako:
 python3-mako depends on python3-markupsafe; however:
  Package python3-markupsafe is not configured yet.

dpkg: error processing package python3-mako (--configure):
 dependency problems - leaving unconfigured
Setting up python3-natsort (3.5.1-1ubuntu1) ...
/var/lib/dpkg/info/python3-natsort.postinst: 6: /var/lib/dpkg/info/python3-natsort.postinst: py3compile: not found
dpkg: error processing package python3-natsort (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of python3-oauthlib:
 python3-oauthlib depends on python3-crypto; however:
  Package python3-crypto is not configured yet.

dpkg: error processing package python3-oauthlib (--configure):
 dependency problems - leaving unconfigured
Setting up python3-problem-report (2.14.1-0ubuntu3.27) ...
/var/lib/dpkg/info/python3-problem-report.postinst: 6: /var/lib/dpkg/info/python3-problem-report.postinst: py3compile: not found
dpkg: error processing package python3-problem-report (--configure):
 subprocess installed post-installation script returned error exit status 127
Setting up python3-uno (1:4.2.8-0ubuntu5.2) ...
/var/lib/dpkg/info/python3-uno.postinst: 6: /var/lib/dpkg/info/python3-uno.postinst: py3compile: not found
dpkg: error processing package python3-uno (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of rhythmbox:
 rhythmbox depends on python3.4; however:
  Package python3.4 is not configured yet.

dpkg: error processing package rhythmbox (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of rhythmbox-plugin-magnatune:
 rhythmbox-plugin-magnatune depends on rhythmbox (= 3.0.2-0ubuntu2); however:
  Package rhythmbox is not configured yet.

dpkg: error processing package rhythmbox-plugin-magnatune (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of rhythmbox-plugins:
 rhythmbox-plugins depends on python3.4; however:
  Package python3.4 is not configured yet.
 rhythmbox-plugins depends on rhythmbox (= 3.0.2-0ubuntu2); however:
  Package rhythmbox is not configured yet.
 rhythmbox-plugins depends on python3-mako; however:
  Package python3-mako is not configured yet.

dpkg: error processing package rhythmbox-plugins (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of rhythmbox-plugin-zeitgeist:
 rhythmbox-plugin-zeitgeist depends on rhythmbox (>= 3.0); however:
  Package rhythmbox is not configured yet.
 rhythmbox-plugin-zeitgeist depends on rhythmbox (<< 3.1); however:
  Package rhythmbox is not configured yet.

dpkg: error processing package rhythmbox-plugin-zeitgeist (--configure):
 dependency problems - leaving unconfigured
Setting up software-center-aptdaemon-plugins (0.1.6build1) ...
/var/lib/dpkg/info/software-center-aptdaemon-plugins.postinst: 13: /var/lib/dpkg/info/software-center-aptdaemon-plugins.postinst: py3compile: not found
dpkg: error processing package software-center-aptdaemon-plugins (--configure):
 subprocess installed post-installation script returned error exit status 127
dpkg: dependency problems prevent configuration of usb-creator-common:
 usb-creator-common depends on python3-debian; however:
  Package python3-debian is not configured yet.

dpkg: error processing package usb-creator-common (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of usb-creator-gtk:
 usb-creator-gtk depends on usb-creator-common (= 0.2.56.3ubuntu0.1); however:
  Package usb-creator-common is not configured yet.

dpkg: error processing package usb-creator-gtk (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of friends-dispatcher:
 friends-dispatcher depends on python3-oauthlib; however:
  Package python3-oauthlib is not configured yet.

dpkg: error processing package friends-dispatcher (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of friends:
 friends depends on friends-dispatcher; however:
  Package friends-dispatcher is not configured yet.

dpkg: error processing package friends (--configure):
 dependency problems - leaving unconfigured
dpkg: too many errors, stopping
Processing triggers for libc-bin (2.19-0ubuntu6.13) ...
Processing triggers for menu (2.1.46ubuntu1) ...
Errors were encountered while processing:
 python3.4-minimal
 python3-xkit
 ubuntu-drivers-common
 python3.4
 python3-commandnotfound
 ufw
 apturl-common
 python3-software-properties
 software-properties-common
 python3-aptdaemon.gtk3widgets
 software-properties-gtk
 apturl
 gedit
 python3-xdg
 python3-speechd
 python3-pyatspi
 python3-louis
 gnome-orca
 python3-cairo
 python3-gi-cairo
 gnome-sudoku
 language-selector-gnome
 onboard
 python3-chardet
 python3-lxml
 python3-plainbox
 python3-six
 python3-urllib3
 python3-requests
 python3-pyparsing
 python3-checkbox-support
 python3-checkbox-ng
 python3-crypto
 python3-debian
 python3-feedparser
 python3-httplib2
 python3-markupsafe
 python3-mako
 python3-natsort
 python3-oauthlib
 python3-problem-report
 python3-uno
 rhythmbox
 rhythmbox-plugin-magnatune
 rhythmbox-plugins
 rhythmbox-plugin-zeitgeist
 software-center-aptdaemon-plugins
 usb-creator-common
 usb-creator-gtk
 friends-dispatcher
 friends
Processing was halted because there were too many errors.
E: Sub-process /usr/bin/dpkg returned an error code (1)