update manager error due to gvfs-bin error

Asked by Judith Stockem

I am trying to update my system via Update Manager. Fails every time and this is the error message:
Package operation failed

The installation or removal of a software package failed.

installArchives() failed: (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%dpkg: unrecoverable fatal error, aborting:
 failed to read on buffer copy for files list for package `gvfs-bin': Input/output error

Same happens when I do an update via Terminal. I cannot open gvfs-bin, it's corrupted. I cannot reinstall it, as I get the same error message for anything I try to install. When I try to reinstall it via the synaptic package manager the spm freezes and then closes itself.

Not sure if this is going to be of any help, but I ran this diagnostic https://help.ubuntu.com/community/PackageManagerTroubleshootingProcedure :

judith@judith-laptop:~$ cat /etc/lsb-release

DISTRIB_ID=Ubuntu

DISTRIB_RELEASE=10.10

DISTRIB_CODENAME=maverick

DISTRIB_DESCRIPTION="Ubuntu 10.10"

judith@judith-laptop:~$ uname -a

Linux judith-laptop 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21 17:40:48 UTC 2011 i686 GNU/Linux

judith@judith-laptop:~$ sudo rm /var/lib/apt/lists/lock

judith@judith-laptop:~$ sudo cp -arf /var/lib/dpkg /var/lib/dpkg.backup

sudo cp /var/lib/dpkg/status-old /var/lib/dpkg/statuscp: reading `/var/lib/dpkg/info/gvfs-bin.list': Input/output error

judith@judith-laptop:~$ sudo cp /var/lib/dpkg/status-old /var/lib/dpkg/status

judith@judith-laptop:~$ sudo cp /var/lib/dpkg/available-old /var/lib/dpkg/available

judith@judith-laptop:~$ sudo rm -rf /var/lib/dpkg/updates/*

judith@judith-laptop:~$ sudo rm -rf /var/lib/apt/lists

judith@judith-laptop:~$ sudo rm /var/cache/apt/*.bin

judith@judith-laptop:~$ sudo mkdir /var/lib/apt/lists

judith@judith-laptop:~$ sudo mkdir /var/lib/apt/lists/partial

judith@judith-laptop:~$ LANG=C;sudo apt-get clean

judith@judith-laptop:~$ LANG=C;sudo apt-get autoclean

Reading package lists... Done

Building dependency tree

Reading state information... Done

judith@judith-laptop:~$ LANG=C;sudo apt-get --purge autoremove

Reading package lists... Done

Building dependency tree

Reading state information... Done

The following packages will be REMOVED:

  linux-headers-2.6.35-23* linux-headers-2.6.35-23-generic* python-bugbuddy*

  python-evince* python-evolution* python-gnomedesktop* python-gtop*

  python-mediaprofiles* python-metacity* python-totem-plparser*

0 upgraded, 0 newly installed, 10 to remove and 0 not upgraded.

After this operation, 91.3MB disk space will be freed.

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

(Reading database ... 65%dpkg: unrecoverable fatal error, aborting:

 failed to read on buffer copy for files list for package `gvfs-bin': Input/output error

E: Sub-process /usr/bin/dpkg returned an error code (2)

judith@judith-laptop:~$ LANG=C;sudo apt-get update -o APT::Cache-Limit=25165824

Get:1 http://extras.ubuntu.com maverick Release.gpg [72B]

Ign http://extras.ubuntu.com/ubuntu/ maverick/main Translation-en

Get:2 http://ppa.launchpad.net maverick Release.gpg [316B]

Ign http://ppa.launchpad.net/thp/gpodder/ubuntu/ maverick/main Translation-en

Get:3 http://archive.ubuntu.com maverick Release.gpg [198B]

Ign http://archive.ubuntu.com/ubuntu/ maverick/main Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick/multiverse Translation-en

Get:4 http://extras.ubuntu.com maverick Release [9762B]

Ign http://archive.ubuntu.com/ubuntu/ maverick/restricted Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick/universe Translation-en

Get:5 http://archive.ubuntu.com maverick-updates Release.gpg [198B]

Ign http://archive.ubuntu.com/ubuntu/ maverick-updates/main Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-updates/multiverse Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-updates/restricted Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-updates/universe Translation-en

Get:6 http://ppa.launchpad.net maverick Release [9756B]

Get:7 http://archive.ubuntu.com maverick-security Release.gpg [198B]

Ign http://archive.ubuntu.com/ubuntu/ maverick-security/main Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-security/multiverse Translation-en

Get:8 http://dl.google.com stable Release.gpg [197B]

Ign http://archive.ubuntu.com/ubuntu/ maverick-security/restricted Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-security/universe Translation-en

Get:9 http://archive.ubuntu.com maverick Release [39.8kB]

Get:10 http://extras.ubuntu.com maverick/main i386 Packages [700B]

Ign http://dl.google.com/linux/chrome/deb/ stable/main Translation-en

Get:11 http://ppa.launchpad.net maverick/main Sources [723B]

Get:12 http://archive.ubuntu.com maverick-updates Release [31.4kB]

Get:13 http://dl.google.com stable Release.gpg [197B]

Get:14 http://archive.ubuntu.com maverick-security Release [31.4kB]

Get:15 http://ppa.launchpad.net maverick/main i386 Packages [747B]

Ign http://dl.google.com/linux/talkplugin/deb/ stable/main Translation-en

Get:16 http://dl.google.com stable Release [1347B]

Get:17 http://archive.ubuntu.com maverick/main Sources [829kB]

Get:18 http://dl.google.com stable Release [1347B]

Get:19 http://dl.google.com stable/main i386 Packages [1066B]

Get:20 http://dl.google.com stable/main i386 Packages [737B]

Get:21 http://archive.getdeb.net maverick-getdeb Release.gpg [836B]

Ign http://archive.getdeb.net/ubuntu/ maverick-getdeb/apps Translation-en

Get:22 http://archive.getdeb.net maverick-getdeb Release [7246B]

Get:23 http://archive.ubuntu.com maverick/restricted Sources [4370B]

Get:24 http://archive.ubuntu.com maverick/universe Sources [4179kB]

Get:25 http://archive.getdeb.net maverick-getdeb/apps i386 Packages [62.3kB]

Get:26 http://archive.ubuntu.com maverick/multiverse Sources [151kB]

Get:27 http://archive.ubuntu.com maverick/main i386 Packages [1492kB]

Get:28 http://archive.ubuntu.com maverick/restricted i386 Packages [5992B]

Get:29 http://archive.ubuntu.com maverick/universe i386 Packages [5791kB]

Get:30 http://archive.ubuntu.com maverick/multiverse i386 Packages [183kB]

Get:31 http://archive.ubuntu.com maverick-updates/main Sources [85.5kB]

Get:32 http://archive.ubuntu.com maverick-updates/restricted Sources [778B]

Get:33 http://archive.ubuntu.com maverick-updates/universe Sources [31.3kB]

Get:34 http://archive.ubuntu.com maverick-updates/multiverse Sources [1498B]

Get:35 http://archive.ubuntu.com maverick-updates/main i386 Packages [234kB]

Get:36 http://archive.ubuntu.com maverick-updates/restricted i386 Packages [1797B]

Get:37 http://archive.ubuntu.com maverick-updates/universe i386 Packages [98.6kB]

Get:38 http://archive.ubuntu.com maverick-updates/multiverse i386 Packages [2834B]

Get:39 http://archive.ubuntu.com maverick-security/main Sources [27.6kB]

Get:40 http://archive.ubuntu.com maverick-security/restricted Sources [14B]

Get:41 http://archive.ubuntu.com maverick-security/universe Sources [11.0kB]

Get:42 http://archive.ubuntu.com maverick-security/multiverse Sources [643B]

Get:43 http://archive.ubuntu.com maverick-security/main i386 Packages [93.2kB]

Get:44 http://archive.ubuntu.com maverick-security/restricted i386 Packages [14B]

Get:45 http://archive.ubuntu.com maverick-security/universe i386 Packages [49.0kB]

Get:46 http://archive.ubuntu.com maverick-security/multiverse i386 Packages [1659B]

Fetched 13.5MB in 21s (614kB/s)

E: dpkg was interrupted, you must manually run 'sudo dpkg --configure -a' to correct the problem.

judith@judith-laptop:~$ sudo dpkg --configure -a

judith@judith-laptop:~$ sudo dpkg --clear-avail

judith@judith-laptop:~$ sudo dpkg --configure -a

judith@judith-laptop:~$ LANG=C;sudo apt-get -f install

Reading package lists... Done

Building dependency tree

Reading state information... Done

The following packages were automatically installed and are no longer required:

  python-evince linux-headers-2.6.35-23 python-gnomedesktop python-metacity

  python-mediaprofiles python-bugbuddy python-totem-plparser python-evolution

  linux-headers-2.6.35-23-generic python-gtop

Use 'apt-get autoremove' to remove them.

0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.

judith@judith-laptop:~$ LANG=C;sudo apt-get --fix-missing install

Reading package lists... Done

Building dependency tree

Reading state information... Done

The following packages were automatically installed and are no longer required:

  python-evince linux-headers-2.6.35-23 python-gnomedesktop python-metacity

  python-mediaprofiles python-bugbuddy python-totem-plparser python-evolution

  linux-headers-2.6.35-23-generic python-gtop

Use 'apt-get autoremove' to remove them.

0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.

judith@judith-laptop:~$ LANG=C;sudo apt-get update -o APT::Cache-Limit=25165824 && sudo apt-get dist-upgrade

Hit http://ppa.launchpad.net maverick Release.gpg

Ign http://ppa.launchpad.net/thp/gpodder/ubuntu/ maverick/main Translation-en

Hit http://archive.ubuntu.com maverick Release.gpg

Ign http://archive.ubuntu.com/ubuntu/ maverick/main Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick/multiverse Translation-en

Hit http://extras.ubuntu.com maverick Release.gpg

Ign http://extras.ubuntu.com/ubuntu/ maverick/main Translation-en

Hit http://ppa.launchpad.net maverick Release

Ign http://archive.ubuntu.com/ubuntu/ maverick/restricted Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick/universe Translation-en

Hit http://archive.ubuntu.com maverick-updates Release.gpg

Ign http://archive.ubuntu.com/ubuntu/ maverick-updates/main Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-updates/multiverse Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-updates/restricted Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-updates/universe Translation-en

Hit http://extras.ubuntu.com maverick Release

Hit http://archive.ubuntu.com maverick-security Release.gpg

Ign http://archive.ubuntu.com/ubuntu/ maverick-security/main Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-security/multiverse Translation-en

Get:1 http://dl.google.com stable Release.gpg [197B]

Hit http://ppa.launchpad.net maverick/main Sources

Hit http://extras.ubuntu.com maverick/main i386 Packages

Ign http://archive.ubuntu.com/ubuntu/ maverick-security/restricted Translation-en

Ign http://archive.ubuntu.com/ubuntu/ maverick-security/universe Translation-en

Hit http://archive.ubuntu.com maverick Release

Hit http://archive.ubuntu.com maverick-updates Release

Hit http://ppa.launchpad.net maverick/main i386 Packages

Ign http://dl.google.com/linux/chrome/deb/ stable/main Translation-en

Get:2 http://dl.google.com stable Release.gpg [197B]

Ign http://dl.google.com/linux/talkplugin/deb/ stable/main Translation-en

Hit http://archive.ubuntu.com maverick-security Release

Hit http://archive.ubuntu.com maverick/main Sources

Hit http://archive.ubuntu.com maverick/restricted Sources

Get:3 http://dl.google.com stable Release [1347B]

Hit http://archive.ubuntu.com maverick/universe Sources

Hit http://archive.ubuntu.com maverick/multiverse Sources

Hit http://archive.ubuntu.com maverick/main i386 Packages

Hit http://archive.ubuntu.com maverick/restricted i386 Packages

Hit http://archive.ubuntu.com maverick/universe i386 Packages

Hit http://archive.ubuntu.com maverick/multiverse i386 Packages

Hit http://archive.ubuntu.com maverick-updates/main Sources

Hit http://archive.ubuntu.com maverick-updates/restricted Sources

Get:4 http://dl.google.com stable Release [1347B]

Hit http://archive.ubuntu.com maverick-updates/universe Sources

Hit http://archive.ubuntu.com maverick-updates/multiverse Sources

Hit http://archive.ubuntu.com maverick-updates/main i386 Packages

Hit http://archive.ubuntu.com maverick-updates/restricted i386 Packages

Hit http://archive.ubuntu.com maverick-updates/universe i386 Packages

Hit http://archive.ubuntu.com maverick-updates/multiverse i386 Packages

Hit http://archive.ubuntu.com maverick-security/main Sources

Hit http://archive.ubuntu.com maverick-security/restricted Sources

Get:5 http://dl.google.com stable/main i386 Packages [1066B]

Hit http://archive.ubuntu.com maverick-security/universe Sources

Hit http://archive.ubuntu.com maverick-security/multiverse Sources

Hit http://archive.ubuntu.com maverick-security/main i386 Packages

Hit http://archive.ubuntu.com maverick-security/restricted i386 Packages

Hit http://archive.ubuntu.com maverick-security/universe i386 Packages

Hit http://archive.ubuntu.com maverick-security/multiverse i386 Packages

Get:6 http://dl.google.com stable/main i386 Packages [737B]

Hit http://archive.getdeb.net maverick-getdeb Release.gpg

Ign http://archive.getdeb.net/ubuntu/ maverick-getdeb/apps Translation-en

Hit http://archive.getdeb.net maverick-getdeb Release

Hit http://archive.getdeb.net maverick-getdeb/apps i386 Packages

Fetched 4891B in 2s (2076B/s)

Reading package lists... Done

Reading package lists... Done

Building dependency tree

Reading state information... Done

Calculating upgrade... Done

The following packages will be upgraded:

  gir1.0-pango-1.0 google-chrome-beta libgssapi-krb5-2 libk5crypto3 libkrb5-3

  libkrb5support0 libpango1.0-0 libpango1.0-common libssl0.9.8 login openssl

  passwd shotwell

13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

Need to get 32.9MB of archives.

After this operation, 86.0kB of additional disk space will be used.

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

Get:1 http://archive.ubuntu.com/ubuntu/ maverick-updates/main login i386 1:4.1.4.2-1ubuntu3.2 [315kB]

Get:2 http://dl.google.com/linux/chrome/deb/ stable/main google-chrome-beta i386 9.0.597.98-r74359 [26.8MB]

Get:3 http://archive.ubuntu.com/ubuntu/ maverick-updates/main libpango1.0-common all 1.28.2-0ubuntu1 [114kB]

Get:4 http://archive.getdeb.net/ubuntu/ maverick-getdeb/apps shotwell i386 0.8.1-1~getdeb1 [2610kB]

Get:5 http://archive.ubuntu.com/ubuntu/ maverick-updates/main libpango1.0-0 i386 1.28.2-0ubuntu1 [293kB]

Get:6 http://archive.ubuntu.com/ubuntu/ maverick-updates/main libssl0.9.8 i386 0.9.8o-1ubuntu4.4 [866kB]

Get:7 http://archive.ubuntu.com/ubuntu/ maverick-updates/main passwd i386 1:4.1.4.2-1ubuntu3.2 [875kB]

Get:8 http://archive.ubuntu.com/ubuntu/ maverick-updates/main libk5crypto3 i386 1.8.1+dfsg-5ubuntu0.4 [96.3kB]

Get:9 http://archive.ubuntu.com/ubuntu/ maverick-updates/main libgssapi-krb5-2 i386 1.8.1+dfsg-5ubuntu0.4 [120kB]

Get:10 http://archive.ubuntu.com/ubuntu/ maverick-updates/main libkrb5-3 i386 1.8.1+dfsg-5ubuntu0.4 [349kB]

Get:11 http://archive.ubuntu.com/ubuntu/ maverick-updates/main libkrb5support0 i386 1.8.1+dfsg-5ubuntu0.4 [42.6kB]

Get:12 http://archive.ubuntu.com/ubuntu/ maverick-updates/main gir1.0-pango-1.0 i386 1.28.2-0ubuntu1 [86.2kB]

Get:13 http://archive.ubuntu.com/ubuntu/ maverick-updates/main openssl i386 0.9.8o-1ubuntu4.4 [400kB]

Fetched 32.9MB in 44s (734kB/s)

Preconfiguring packages ...

(Reading database ... 65%dpkg: unrecoverable fatal error, aborting:

 failed to read on buffer copy for files list for package `gvfs-bin': Input/output error

E: Sub-process /usr/bin/dpkg returned an error code (2)

I'm new to Linux, so any help will be appreciated. Really don't fancy reinstalling the whole thing. If you need more info, please let me know. But explain everything step-by-step please.

Question information

Language:
English Edit question
Status:
Solved
For:
Ubuntu update-manager Edit question
Assignee:
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Solved by:
Manfred Hampl
Solved:
Last query:
Last reply:
Revision history for this message
Manfred Hampl (m-hampl) said :
#1

The error messages
"reading `/var/lib/dpkg/info/gvfs-bin.list': Input/output error"
"failed to read on buffer copy for files list for package `gvfs-bin': Input/output error"
point towards a file system corruption regarding the file /var/lib/dpkg/info/gvfs-bin.list

You should execute a file system check. As I cannot predict the extent of the corruption (if this is really the case), and the effects that an attempted repair action will have, you should in any case make sure to have backups of your important files.

Revision history for this message
Judith Stockem (jstockem) said :
#2

Thanks for coming back!

I have backups of all my important files. At the risk of sounding stupid: How exactly do I do a file system check?

I did restart my system and forced it to check all files, but it doesn't find anything wrong. So I tried this: http://en.kioskea.net/faq/3505-ubuntu-repair-file-system-error
But might have done something wrong as nothing happened. The disk I used was for an older distro, could that be the problem?

I tried to find other sites that explained system checks, but they were over my head. Is there any thread or step-by-step guide you could direct me to so I can do a proper check and repair?

Revision history for this message
Best Manfred Hampl (m-hampl) said :
#3

A file system check can be executed only if the file system is not in use. The link you copied above shows the two ways to do it - Either force a file system check at your next boot by executing the command "sudo touch /forcefsck" or Boot from another media in a way that the file system is not mounted (e.g. by booting from the Ubuntu live disk in the mode 'try out Ubuntu').

From your previous post I conlude that you have already done "sudo touch /forcefsck" and rebooted, and no errors were shown. Is that correct?

If you have executed a file system check with no errors reported, the next steps that I would execute are:
delete the file that is listed in the error messages (/var/lib/dpkg/info/gvfs-bin.list)
execute a file system check again
and then (if there are no severe error messages) try to install or remove a package

If you feel confident enough to execute these commands alone feel free to do so (on your own risk). If you would prefer someone to provide more support please indicate so, and wait with executing commands that might change your system, but begin with some reporting commands first:
cat /var/log/fsck/checkfs
fdisk -l
df -h
ls /lost+found

Revision history for this message
Judith Stockem (jstockem) said :
#4

Thanks Manfred Hampl, that solved my question.

Revision history for this message
Judith Stockem (jstockem) said :
#5

I deleted the file and then was able to re-install the package that it was part of. Update manager is working fine now.

Thanks for the help!