8

I upgraded my server installation form 11.04 to 11.10, then to 12.04 over ssh. All seems almost ok - but there is a small issue with glibc, which is messing up my apt.

I tried sudo apt-get install -f but it does not get what it needs. I am running in a OpenVZ virtual machine.

How can I fix my apt dependencies?

sysadmin@svr:~$ sudo apt-get update 
Ign http://archive.canonical.com precise InRelease
Ign http://archive.ubuntu.com precise InRelease
Ign http://archive.ubuntu.com precise-updates InRelease
Ign http://archive.ubuntu.com precise-security InRelease
Get:1 http://archive.ubuntu.com precise Release.gpg [198 B]
Hit http://archive.canonical.com precise Release.gpg 
Get:2 http://archive.ubuntu.com precise-updates Release.gpg [198 B]
Hit http://archive.canonical.com precise Release      
Get:3 http://archive.ubuntu.com precise-security Release.gpg [198 B]
Hit http://archive.canonical.com precise/partner i386 Packages
Get:4 http://archive.ubuntu.com precise Release [49.6 kB]
Ign http://archive.canonical.com precise/partner TranslationIndex
Get:5 http://archive.ubuntu.com precise-updates Release [49.6 kB]
Get:6 http://archive.ubuntu.com precise-security Release [49.6 kB]               
Get:7 http://archive.ubuntu.com precise/main i386 Packages [1274 kB]            
Ign http://archive.canonical.com precise/partner Translation-en                  
Get:8 http://archive.ubuntu.com precise/restricted i386 Packages [8431 B]
Get:9 http://archive.ubuntu.com precise/universe i386 Packages [4796 kB]
Hit http://archive.ubuntu.com precise/main TranslationIndex                                                                                                                       
Hit http://archive.ubuntu.com precise/restricted TranslationIndex                                                                                                                 
Hit http://archive.ubuntu.com precise/universe TranslationIndex                                                                                                                   
Get:10 http://archive.ubuntu.com precise-updates/main i386 Packages [20.2 kB]                                                                                                     
Get:11 http://archive.ubuntu.com precise-updates/restricted i386 Packages [770 B]                                                                                                 
Get:12 http://archive.ubuntu.com precise-updates/universe i386 Packages [2258 B]                                                                                                  
Get:13 http://archive.ubuntu.com precise-updates/main TranslationIndex [72 B]                                                                                                     
Get:14 http://archive.ubuntu.com precise-updates/restricted TranslationIndex [71 B]                                                                                               
Get:15 http://archive.ubuntu.com precise-updates/universe TranslationIndex [72 B]                                                                                                 
Get:16 http://archive.ubuntu.com precise-security/main i386 Packages [11.8 kB]                                                                                                    
Get:17 http://archive.ubuntu.com precise-security/restricted i386 Packages [14 B]                                                                                                 
Get:18 http://archive.ubuntu.com precise-security/universe i386 Packages [1357 B]                                                                                                 
Get:19 http://archive.ubuntu.com precise-security/main TranslationIndex [72 B]                                                                                                    
Get:20 http://archive.ubuntu.com precise-security/restricted TranslationIndex [70 B]                                                                                              
Get:21 http://archive.ubuntu.com precise-security/universe TranslationIndex [71 B]                                                                                                
Hit http://archive.ubuntu.com precise/main Translation-en                                                                                                                         
Hit http://archive.ubuntu.com precise/restricted Translation-en                                                                                                                   
Hit http://archive.ubuntu.com precise/universe Translation-en                                                                                                                     
Get:22 http://archive.ubuntu.com precise-updates/main Translation-en [9145 B]                                                                                                     
Hit http://archive.ubuntu.com precise-updates/restricted Translation-en                                                                                                           
Get:23 http://archive.ubuntu.com precise-updates/universe Translation-en [1344 B]                                                                                                 
Get:24 http://archive.ubuntu.com precise-security/main Translation-en [3549 B]                                                                                                    
Hit http://archive.ubuntu.com precise-security/restricted Translation-en                                                                                                          
Get:25 http://archive.ubuntu.com precise-security/universe Translation-en [760 B]                                                                                                 
Fetched 6279 kB in 57s (109 kB/s)                                                                                                                                                 
Reading package lists... Done
sysadmin@svr:~$ sudo apt-get ugrade
E: Invalid operation ugrade
sysadmin@svr:~$ 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:
 libc6 : Depends: libc-bin (= 2.13-20ubuntu5.1) but 2.15-0ubuntu10 is installed
 libncurses5 : Depends: libtinfo5 (= 5.9-1ubuntu5) but 5.9-4 is installed
 libnih-dbus1 : Depends: libnih1 (= 1.0.3-4ubuntu9) but 1.0.3-4ubuntu2 is installed
E: Unmet dependencies. Try using -f.
sysadmin@svr:~$ sudo apt-get install -f
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
  libswscale0 libavutil50 python-support g++-4.5 libboost-program-options1.42.0 librpmio1 libpostproc51 libavformat52 libstdc++6-4.5-dev libavfilter1 libavcodec52
  libboost-filesystem1.42.0 libboost-system1.42.0 libavdevice52
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
  libc-dev-bin libc6 libc6-dev libncurses5 libnih1
Suggested packages:
  glibc-doc
The following packages will be upgraded:
  libc-dev-bin libc6 libc6-dev libncurses5 libnih1
5 upgraded, 0 newly installed, 0 to remove and 335 not upgraded.
2 not fully installed or removed.
Need to get 0 B/9099 kB of archives.
After this operation, 1618 kB disk space will be freed.
Do you want to continue [Y/n]? 
locale: /lib/i386-linux-gnu/libc.so.6: version `GLIBC_2.15' not found (required by locale)
Preconfiguring packages ...
Setting up libc-bin (2.15-0ubuntu10) ...
(Reading database ... 31190 files and directories currently installed.)
Preparing to replace libc6-dev 2.13-20ubuntu5.1 (using .../libc6-dev_2.15-0ubuntu10_i386.deb) ...
Unpacking replacement libc6-dev ...
Preparing to replace libc-dev-bin 2.13-20ubuntu5.1 (using .../libc-dev-bin_2.15-0ubuntu10_i386.deb) ...
Unpacking replacement libc-dev-bin ...
Preparing to replace libc6 2.13-20ubuntu5.1 (using .../libc6_2.15-0ubuntu10_i386.deb) ...
locale: /lib/i386-linux-gnu/libc.so.6: version `GLIBC_2.15' not found (required by locale)
Checking for services that may need to be restarted...
Checking init scripts...
runlevel:/var/run/utmp: No such file or directory
Checking for services that may need to be restarted...
Checking init scripts...
runlevel:/var/run/utmp: No such file or directory
WARNING: init script for samba not found.
Stopping some services possibly affected by the upgrade (will be restarted later):
  cron: stopping...done.

WARNING: this version of the GNU libc requires kernel version
2.6.24 or later. Please upgrade your kernel before installing
glibc.

The installation of a 2.6 kernel _could_ ask you to install a new libc
first, this is NOT a bug, and should *NOT* be reported. In that case,
please add lenny sources to your /etc/apt/sources.list and run:
  apt-get install -t lenny linux-image-2.6
Then reboot into this new kernel, and proceed with your upgrade
dpkg: error processing /var/cache/apt/archives/libc6_2.15-0ubuntu10_i386.deb (--unpack):
 subprocess new pre-installation script returned error exit status 1
No apport report written because MaxReports is reached already
                                                              Processing triggers for man-db ...
locale: /lib/i386-linux-gnu/libc.so.6: version `GLIBC_2.15' not found (required by locale)
Errors were encountered while processing:
 /var/cache/apt/archives/libc6_2.15-0ubuntu10_i386.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
sysadmin@svr:~$ 
  • I decided to wait a while until I update, hoping that the issue would be resolved without further effort. I have had to re-install the system a couple of times already. I suspect the top answer might hold the key to the problem, but have not tested it yet. I will tick it once verified - which I will endeavor to do soon. – Billy Moon Jun 8 '12 at 17:16
  • Thanks Billy - please comment on the answer if you have any more questions/problems! – ish Jun 16 '12 at 10:48
11

First the explanation, then a solution :)

This happens because your host is almost certainly running OpenVZ on a 2.6.18 kernel (all OpenVZ containers share the host kernel). The reason can range from stability to just plain laziness. The problem is that the libc 2.15 included with Precise requires a minimum 2.6.24 kernel to function. Sometimes this will cause the release-upgrade to fail, but it is possible to complete and get into a partially upgraded neither-here-not-there situation like you have.

Fear not though, the libc requirement is a compile-time option, and it can be set lower (in which case the library includes workarounds for older kernels). I guess setting the minimum to .24 is one way to drag folks into 2012 :)

I've set up a PPA containing a recompiled libc which will work on 2.6.18 or newer (please check uname -r!), and it should override the current libc provided by Precise. Just add ppa:izx/ovz-libc, update, and it should let you get past this. Specifically, something like this:

apt-add-repository ppa:izx/ovz-libc
apt-get update
apt-get -f install
do-release-upgrade

and continue on until the upgrade completes successfully. I highly recommend NOT replacing any changed or non-existent config files.

I will be keeping the ppa updated as and when libc is updated upstream. If you want to avoid a similar error when that happens, you may want to pin libc-bin to my PPA with a high priority, so it won't update until the "fixed" version is available from the PPA.

Hope this helps, and please post here if anyone has any questions or other feedback.

  • Could you explain how you were able to make this change? I've tried poking around the libc6 source, but can't find it. I'm stuck in a semi-upgraded state on an OpenVZ VPS running 2.6.18, but the packages require libc6 2.17, not 2.15. Any help would be much appreciated. – red_sky Jan 29 '14 at 21:14
3

Try this command. You can open a terminal with Alt+Ctrl+T:

sudo apt-get -o APT::Immediate-Configure=0 -f install

After you can do a sudo apt-get upgrade.

I've had the same problem .... using Ubuntu server ... strange isn't it ?
Hope it'll work for you.

1

For everybody stuck in the do-dist-upgrade and not being able to run

apt-add-repository ppa:izx/ovz-libc

Just add following line manually to /etc/apt/sources.list:

deb http://ppa.launchpad.net/izx/ovz-libc/ubuntu lucid main
  • This doesn't work for me with Virtuzzo containers. I use a template from 10.04 and fails. But from Debian 6.0 with a more updated kernel it works for Virtuozzo 4.6 – shakaran Aug 15 '13 at 10:40
0

I don't know if there exists another way but I had important files on my desktop that I did not back up when Ubuntu crashed on me in that exact fashion, I just so happened to have on hand the Ubuntu 11.10 Boot Multi-Option install CD and so I rebooted with the CD and then picked "Upgrade from 12.04 LTS to 11.10" and after how much time it spent re-installing 11.10 I am finally up and running again with my important files intact.

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