Update problem [solved]

Hello Folks,

I’m having a problem with system updates. I keep being told not all updates can be installed, and to run a partial upgrade.

Problem is, when I try that, the upgrade threatens to uninstall Virtualbox 6, which I rely on. Therefore I keep cancelling the upgrade.

Any help much appreciated.

Mike

Xubuntu 18.04
Virtualbox 6.0

What’s the output from:

sudo apt-get update

and

cat /etc/apt/sources.list; for X in /etc/apt/sources.list.d/*; do echo; echo; echo "** $X:"; echo; cat $X; done

Hello Mark,

outputs as follows

mike@xubuntu:~$ sudo apt-get update
[sudo] password for mike:
Hit:1 Index of /ubuntu bionic InRelease
Get:2 Index of /ubuntu bionic-security InRelease [88.7 kB]
Hit:3 Index of /ubuntu bionic InRelease
Get:4 Index of /ubuntu bionic-updates InRelease [88.7 kB]
Ign:5 http://dl.google.com/linux/chrome/deb stable InRelease
Get:6 http://dl.google.com/linux/chrome/deb stable Release [943 B]
Get:7 http://dl.google.com/linux/chrome/deb stable Release.gpg [819 B]
Get:8 Index of /ubuntu bionic-security/main i386 Packages [382 kB]
Get:9 Index of /ubuntu bionic-security/main amd64 Packages [530 kB]
Get:10 Index of /ubuntu bionic-updates/main i386 Packages [597 kB]
Get:11 Index of /ubuntu bionic-security/main amd64 DEP-11 Metadata [38.5 kB]
Get:12 Index of /ubuntu bionic-security/main DEP-11 48x48 Icons [17.6 kB]
Get:13 Index of /ubuntu bionic-updates/main amd64 Packages [763 kB]
Get:14 http://dl.google.com/linux/chrome/deb stable/main amd64 Packages [1,109 B]
Get:15 Index of /ubuntu bionic-security/main DEP-11 64x64 Icons [41.5 kB]
Get:16 Index of /ubuntu bionic-security/universe i386 Packages [594 kB]
Get:17 Index of /ubuntu bionic-updates/main Translation-en [273 kB]
Get:18 Index of /ubuntu bionic-security/universe amd64 Packages [614 kB]
Get:19 Index of /ubuntu bionic-updates/main amd64 DEP-11 Metadata [295 kB]
Get:20 Index of /ubuntu bionic-security/universe Translation-en [205 kB]
Get:21 Index of /ubuntu bionic-updates/main DEP-11 48x48 Icons [73.8 kB]
Get:22 Index of /ubuntu bionic-security/universe amd64 DEP-11 Metadata [42.0 kB]
Get:23 Index of /ubuntu bionic-updates/main DEP-11 64x64 Icons [143 kB]
Get:24 Index of /ubuntu bionic-security/universe DEP-11 48x48 Icons [16.4 kB]
Get:25 Index of /ubuntu bionic-security/universe DEP-11 64x64 Icons [116 kB]
Get:26 Index of /ubuntu bionic-updates/restricted amd64 Packages [16.6 kB]
Get:27 Index of /ubuntu bionic-updates/restricted Translation-en [5,120 B]
Get:28 Index of /ubuntu bionic-security/multiverse amd64 DEP-11 Metadata [2,464 B]
Get:29 Index of /ubuntu bionic-updates/universe i386 Packages [982 kB]
Get:30 Index of /ubuntu bionic-updates/universe amd64 Packages [1,014 kB]
Get:31 Index of /ubuntu bionic-updates/universe Translation-en [312 kB]
Get:32 Index of /ubuntu bionic-updates/universe amd64 DEP-11 Metadata [254 kB]
Get:33 Index of /ubuntu bionic-updates/universe DEP-11 48x48 Icons [201 kB]
Get:34 Index of /ubuntu bionic-updates/universe DEP-11 64x64 Icons [442 kB]
Get:35 Index of /ubuntu bionic-updates/multiverse amd64 DEP-11 Metadata [2,468 B]
Fetched 8,153 kB in 3s (2,780 kB/s)
Reading package lists… Done

mike@xubuntu:~$ cat /etc/apt/sources.list; for X in /etc/apt/sources.list.d/*; do echo; echo; echo “** $X:”; echo; cat $X; done

deb Index of /ubuntu xenial main restricted

deb Index of /ubuntu xenial-updates main restricted

deb Index of /ubuntu xenial-security main restricted

See UpgradeNotes - Community Help Wiki for how to upgrade to

newer versions of the distribution.

deb Index of /ubuntu bionic main restricted

deb-src Index of /ubuntu xenial main restricted

Major bug fix updates produced after the final release of the

distribution.

deb Index of /ubuntu bionic-updates main restricted

deb-src Index of /ubuntu xenial-updates main restricted

N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu

team. Also, please note that software in universe WILL NOT receive any

review or updates from the Ubuntu security team.

deb Index of /ubuntu bionic universe

deb-src Index of /ubuntu xenial universe

deb Index of /ubuntu bionic-updates universe

deb-src Index of /ubuntu xenial-updates universe

N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu

team, and may not be under a free licence. Please satisfy yourself as to

your rights to use the software. Also, please note that software in

multiverse WILL NOT receive any review or updates from the Ubuntu

security team.

deb Index of /ubuntu bionic multiverse

deb-src Index of /ubuntu xenial multiverse

deb Index of /ubuntu bionic-updates multiverse

deb-src Index of /ubuntu xenial-updates multiverse

N.B. software from this repository may not have been tested as

extensively as that contained in the main release, although it includes

newer versions of some applications which may provide useful features.

Also, please note that software in backports WILL NOT receive any review

or updates from the Ubuntu security team.

deb-src Index of /ubuntu xenial-backports main restricted universe multiverse

Uncomment the following two lines to add software from Canonical’s

‘partner’ repository.

This software is not part of Ubuntu, but is offered by Canonical and the

respective vendors as a service to Ubuntu users.

deb Index of /ubuntu bionic partner

deb-src Index of /ubuntu xenial partner

deb Index of /ubuntu bionic-security main restricted

deb-src Index of /ubuntu xenial-security main restricted

deb Index of /ubuntu bionic-security universe

deb-src Index of /ubuntu xenial-security universe

deb Index of /ubuntu bionic-security multiverse

deb-src Index of /ubuntu xenial-security multiverse

Oracle VirtualBox repo

deb [arch=amd64] http://download.virtualbox.org/virtualbox/debian bionic contrib # disabled on upgrade to bionic

** /etc/apt/sources.list.d/google-chrome.list:

THIS FILE IS AUTOMATICALLY CONFIGURED

You may comment out this entry, but any other modifications may be lost.

deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main

** /etc/apt/sources.list.d/google-chrome.list.distUpgrade:

THIS FILE IS AUTOMATICALLY CONFIGURED

You may comment out this entry, but any other modifications may be lost.

deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main

** /etc/apt/sources.list.d/google-chrome.list.save:

THIS FILE IS AUTOMATICALLY CONFIGURED

You may comment out this entry, but any other modifications may be lost.

deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main
mike@xubuntu:~$

I freely admit to being a bit baffled…

Can you run:

mousepad /etc/apt/sources.list

and post the contents of the file that opens back here.
(I’m pretty sure the contents are listed above, but just wanna make 100% sure of the formatting)

deb Index of /ubuntu xenial main restricted

deb Index of /ubuntu xenial-updates main restricted

deb Index of /ubuntu xenial-security main restricted

See UpgradeNotes - Community Help Wiki for how to upgrade to

newer versions of the distribution.

deb Index of /ubuntu bionic main restricted

deb-src Index of /ubuntu xenial main restricted

Major bug fix updates produced after the final release of the

distribution.

deb Index of /ubuntu bionic-updates main restricted

deb-src Index of /ubuntu xenial-updates main restricted

N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu

team. Also, please note that software in universe WILL NOT receive any

review or updates from the Ubuntu security team.

deb Index of /ubuntu bionic universe

deb-src Index of /ubuntu xenial universe

deb Index of /ubuntu bionic-updates universe

deb-src Index of /ubuntu xenial-updates universe

N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu

team, and may not be under a free licence. Please satisfy yourself as to

your rights to use the software. Also, please note that software in

multiverse WILL NOT receive any review or updates from the Ubuntu

security team.

deb Index of /ubuntu bionic multiverse

deb-src Index of /ubuntu xenial multiverse

deb Index of /ubuntu bionic-updates multiverse

deb-src Index of /ubuntu xenial-updates multiverse

N.B. software from this repository may not have been tested as

extensively as that contained in the main release, although it includes

newer versions of some applications which may provide useful features.

Also, please note that software in backports WILL NOT receive any review

or updates from the Ubuntu security team.

deb-src Index of /ubuntu xenial-backports main restricted universe multiverse

Uncomment the following two lines to add software from Canonical’s

‘partner’ repository.

This software is not part of Ubuntu, but is offered by Canonical and the

respective vendors as a service to Ubuntu users.

deb Index of /ubuntu bionic partner

deb-src Index of /ubuntu xenial partner

deb Index of /ubuntu bionic-security main restricted

deb-src Index of /ubuntu xenial-security main restricted

deb Index of /ubuntu bionic-security universe

deb-src Index of /ubuntu xenial-security universe

deb Index of /ubuntu bionic-security multiverse

deb-src Index of /ubuntu xenial-security multiverse

Oracle VirtualBox repo

deb [arch=amd64] Index of http://download.virtualbox.org/virtualbox/debian bionic contrib # disabled on upgrade to bionic

Okay, first let’s backup that file before editing it … run:

sudo cp -v /etc/apt/sources.list /etc/apt/sources.list.backup

now open the file for editing

sudo mousepad /etc/apt/sources.list

and make it read

# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://archive.ubuntu.com/ubuntu/ bionic restricted universe main

## Major bug fix updates produced after the final release of the
## distribution.
deb http://archive.ubuntu.com/ubuntu/ bionic-updates restricted universe main

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
# deb-src http://gb.archive.ubuntu.com/ubuntu/ bionic universe
# deb-src http://gb.archive.ubuntu.com/ubuntu/ bionic-updates universe

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu 
## team, and may not be under a free licence. Please satisfy yourself as to 
## your rights to use the software. Also, please note that software in 
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://archive.ubuntu.com/ubuntu/ bionic multiverse
# deb-src http://gb.archive.ubuntu.com/ubuntu/ bionic multiverse
deb http://archive.ubuntu.com/ubuntu/ bionic-updates multiverse
# deb-src http://gb.archive.ubuntu.com/ubuntu/ bionic-updates multiverse

## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://archive.ubuntu.com/ubuntu/ bionic-backports restricted multiverse universe main

## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
deb http://archive.canonical.com/ubuntu bionic partner
deb-src http://archive.canonical.com/ubuntu bionic partner

deb http://archive.ubuntu.com/ubuntu/ bionic-security restricted universe main
# deb-src http://security.ubuntu.com/ubuntu bionic-security universe
deb http://archive.ubuntu.com/ubuntu/ bionic-security multiverse
# deb-src http://security.ubuntu.com/ubuntu bionic-security multiverse

## Oracle VirtualBox repo [BEGIN]
deb [arch=amd64] https://download.virtualbox.org/virtualbox/debian bionic contrib
## Oracle VirtualBox repo [END]


(MAKE SURE YOU GET ALL OF THAT, IT SCROLLS)

SAVE the file and exit mousepad.

Back in the terminal run:

sudo apt-get update

if you get NO errors, try running

sudo apt-get upgrade

and (before accepting any changes) see if it still says it wants to uninstall virtualbox ?

I did get errors Mark - see below.

To add to the fun, my internet connection keeps dropping out then coming back. I assume either BT or my ISP is working on it as I type, since the router seems to be quite happy and claims to be connected. I re-booted it to be on the safe side. Maybe the drop-outs explain some of the problems below (I’m thinking of the last five lines in particular)?

Thanks for your help, as always. Forgive me if I don’t respond tonight. I may not be able to…

mike@xubuntu:~$ sudo mousepad /etc/apt/sources.list

(mousepad:4417): Gtk-WARNING **: 22:49:38.368: Theme parsing error: :2:29: The style property GtkButton:default-border is deprecated and shouldn’t be used anymore. It will be removed in a future version

(mousepad:4417): Gtk-WARNING **: 22:49:38.368: Theme parsing error: :3:37: The style property GtkButton:default-outside-border is deprecated and shouldn’t be used anymore. It will be removed in a future version

(mousepad:4417): Gtk-WARNING **: 22:49:38.368: Theme parsing error: :4:27: The style property GtkButton:inner-border is deprecated and shouldn’t be used anymore. It will be removed in a future version

(mousepad:4417): Gtk-WARNING **: 22:49:38.368: Theme parsing error: :5:31: The style property GtkWidget:focus-line-width is deprecated and shouldn’t be used anymore. It will be removed in a future version

(mousepad:4417): Gtk-WARNING **: 22:49:38.368: Theme parsing error: :6:28: The style property GtkWidget:focus-padding is deprecated and shouldn’t be used anymore. It will be removed in a future version

(mousepad:4417): GLib-GObject-CRITICAL **: 22:51:55.323: g_object_ref: assertion ‘G_IS_OBJECT (object)’ failed

(mousepad:4417): GLib-GObject-CRITICAL **: 22:51:55.323: g_object_ref: assertion ‘G_IS_OBJECT (object)’ failed

(mousepad:4417): GLib-GObject-CRITICAL **: 22:51:55.323: g_object_ref: assertion ‘G_IS_OBJECT (object)’ failed
mike@xubuntu:~$ sudo apt-get update
Err:1 Index of http://download.virtualbox.org/virtualbox/debian bionic InRelease
Temporary failure resolving ‘download.virtualbox.org
Err:2 http://dl.google.com/linux/chrome/deb stable InRelease
Temporary failure resolving ‘dl.google.com
Err:3 Index of /ubuntu bionic InRelease
Temporary failure resolving ‘archive.canonical.com
Err:4 Index of /ubuntu bionic InRelease
Temporary failure resolving ‘archive.ubuntu.com
Get:5 Index of /ubuntu bionic-updates InRelease [88.7 kB]
Get:6 Index of /ubuntu bionic-backports InRelease [74.6 kB]
Get:7 Index of /ubuntu bionic-security InRelease [88.7 kB]
Get:8 Index of /ubuntu bionic-updates/restricted i386 Packages [8,600 B]
Get:9 Index of /ubuntu bionic-updates/restricted amd64 Packages [16.7 kB]
Get:10 Index of /ubuntu bionic-updates/restricted Translation-en [5,144 B]
Get:11 Index of /ubuntu bionic-updates/universe amd64 Packages [1,015 kB]
Get:12 Index of /ubuntu bionic-updates/universe i386 Packages [982 kB]
Get:13 Index of /ubuntu bionic-updates/universe Translation-en [312 kB]
Get:14 Index of /ubuntu bionic-updates/universe amd64 DEP-11 Metadata [254 kB]
Get:15 Index of /ubuntu bionic-updates/universe DEP-11 48x48 Icons [202 kB]
Get:16 Index of /ubuntu bionic-updates/universe DEP-11 64x64 Icons [451 kB]
Get:17 Index of /ubuntu bionic-updates/main amd64 Packages [764 kB]
Get:18 Index of /ubuntu bionic-updates/main i386 Packages [597 kB]
Get:19 Index of /ubuntu bionic-updates/main Translation-en [273 kB]
Get:20 Index of /ubuntu bionic-updates/main amd64 DEP-11 Metadata [295 kB]
Get:21 Index of /ubuntu bionic-updates/main DEP-11 48x48 Icons [73.8 kB]
Get:22 Index of /ubuntu bionic-updates/main DEP-11 64x64 Icons [143 kB]
Get:23 Index of /ubuntu bionic-updates/multiverse i386 Packages [6,932 B]
Get:24 Index of /ubuntu bionic-updates/multiverse amd64 Packages [8,092 B]
Get:25 Index of /ubuntu bionic-updates/multiverse Translation-en [3,972 B]
Get:26 Index of /ubuntu bionic-updates/multiverse amd64 DEP-11 Metadata [2,468 B]
Get:27 Index of /ubuntu bionic-updates/multiverse DEP-11 48x48 Icons [29 B]
Get:28 Index of /ubuntu bionic-updates/multiverse DEP-11 64x64 Icons [2,638 B]
Get:29 Index of /ubuntu bionic-backports/universe i386 Packages [4,020 B]
Get:30 Index of /ubuntu bionic-backports/universe amd64 Packages [4,020 B]
Get:31 Index of /ubuntu bionic-backports/universe Translation-en [1,856 B]
Get:32 Index of /ubuntu bionic-backports/universe amd64 DEP-11 Metadata [7,916 B]
Get:33 Index of /ubuntu bionic-backports/universe DEP-11 48x48 Icons [29 B]
Get:34 Index of /ubuntu bionic-backports/universe DEP-11 64x64 Icons [29 B]
Get:35 Index of /ubuntu bionic-backports/main amd64 Packages [2,512 B]
Get:36 Index of /ubuntu bionic-backports/main i386 Packages [2,516 B]
Get:37 Index of /ubuntu bionic-backports/main Translation-en [1,644 B]
Get:38 Index of /ubuntu bionic-security/restricted amd64 Packages [9,856 B]
Get:39 Index of /ubuntu bionic-security/restricted i386 Packages [4,280 B]
Get:40 Index of /ubuntu bionic-security/restricted Translation-en [3,480 B]
Get:41 Index of /ubuntu bionic-security/universe amd64 Packages [616 kB]
Get:42 Index of /ubuntu bionic-security/universe i386 Packages [594 kB]
Get:43 Index of /ubuntu bionic-security/universe Translation-en [205 kB]
Get:44 Index of /ubuntu bionic-security/universe amd64 DEP-11 Metadata [42.2 kB]
Get:45 Index of /ubuntu bionic-security/universe DEP-11 48x48 Icons [16.4 kB]
Get:46 Index of /ubuntu bionic-security/universe DEP-11 64x64 Icons [116 kB]
Get:47 Index of /ubuntu bionic-security/main i386 Packages [386 kB]
Get:48 Index of /ubuntu bionic-security/main amd64 Packages [541 kB]
Get:49 Index of /ubuntu bionic-security/main Translation-en [180 kB]
Get:50 Index of /ubuntu bionic-security/main amd64 DEP-11 Metadata [38.5 kB]
Get:51 Index of /ubuntu bionic-security/main DEP-11 48x48 Icons [17.6 kB]
Get:52 Index of /ubuntu bionic-security/main DEP-11 64x64 Icons [41.5 kB]
Get:53 Index of /ubuntu bionic-security/multiverse amd64 Packages [5,476 B]
Get:54 Index of /ubuntu bionic-security/multiverse i386 Packages [4,288 B]
Get:55 Index of /ubuntu bionic-security/multiverse Translation-en [2,500 B]
Get:56 Index of /ubuntu bionic-security/multiverse amd64 DEP-11 Metadata [2,464 B]
Get:57 Index of /ubuntu bionic-security/multiverse DEP-11 48x48 Icons [29 B]
Get:58 Index of /ubuntu bionic-security/multiverse DEP-11 64x64 Icons [2,638 B]
Fetched 8,524 kB in 35s (247 kB/s)
Reading package lists… Done
W: Failed to fetch http://archive.ubuntu.com/ubuntu/dists/bionic/InRelease Temporary failure resolving ‘archive.ubuntu.com
W: Failed to fetch http://archive.canonical.com/ubuntu/dists/bionic/InRelease Temporary failure resolving ‘archive.canonical.com
W: Failed to fetch https://download.virtualbox.org/virtualbox/debian/dists/bionic/InRelease Temporary failure resolving ‘download.virtualbox.org
W: Failed to fetch http://dl.google.com/linux/chrome/deb/dists/stable/InRelease Temporary failure resolving ‘dl.google.com
W: Some index files failed to download. They have been ignored, or old ones used instead.
mike@xubuntu:~$

Can you try

sudo apt-get update

again and see if you still get errors ? … because I think those errors may have been due to an internet dropout

Thanks Mark,

My connection seems fine tonight, and the software updater has popped up saying that updated software is available. No mention of partial upgrades.

Virtualbox is listed under “install or remove” and the technical description says
Installed version: 6.0.8-130520~Ubuntu~xenial
Available version: 6.0.14-133895~Ubuntu~bionic.

Which course of action would you think is safer? Running the software updater, or not?

Let it upgrade Virtualbox:-

a) it’s a newer version (6.0.14)
and
b) it’s the right version for your updated system (ie. bionic rather than xenial)

Will do Mark,

Sorry for the lack of response. Bit busy this end.

I’ll report back once I’ve done it.

M

Ok, I’m now running the new version and it seems to be fine.

It’s a bit odd though. I deliberately unticked Virtualbox from the list of updates, as I had problems once before with upgrading it and wanted to postpone any possible problems until I have a bit more time on my hands. However, software updater blithely ignored my choice and upgraded anyway. Luckily it seems to have worked, but it’s a bit cavalier in my view. Almost like having a referendum and then blatently ignoring the result… :o

Thanks again Mark. I’ll call this solved now.

You’re not kidding…