Can't upgrade libc6 on Debian Wheezy

holms asked:

I tried to upgrade few packages and then it’s failed on libc upgrade. And now it’s impossible to upgrade anything at all. here’s things I’ve done:

# apt-get dist-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 (= 2.13-37) but 2.13-38 is installed
E: Unmet dependencies. Try using -f.

root@pagalbadaiktais:~# apt-get -f install
Reading package lists... Done
Building dependency tree
Reading state information... Done
Correcting dependencies... Done
The following extra packages will be installed:
  libc6
Suggested packages:
  glibc-doc
The following packages will be upgraded:
  libc6
1 upgraded, 0 newly installed, 0 to remove and 71 not upgraded.
Need to get 4339 kB of archives.
After this operation, 1024 B of additional disk space will be used.
Do you want to continue [Y/n]? Y
Get:1 http://ftp.lt.debian.org/debian/ testing/main libc6 amd64 2.13-38 [4339 kB]
Fetched 4339 kB in 0s (30.5 MB/s)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
Preconfiguring packages ...
dpkg: warning: files list file for package 'libc6:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'gcc-4.7-base:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'liblzma5:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libgcc1:amd64' missing; assuming package has no files currently installed
(Reading database ... 26345 files and directories currently installed.)
Preparing to replace libc6:amd64 2.13-37 (using .../libc6_2.13-38_amd64.deb) ...

A copy of the C library was found in an unexpected directory:
  '/lib/x86_64-linux-gnu/libc-2.13.so'
It is not safe to upgrade the C library in this situation;
please remove that copy of the C library or get it out of
'/lib/x86_64-linux-gnu' and try again.

dpkg: error processing /var/cache/apt/archives/libc6_2.13-38_amd64.deb (--unpack):
 subprocess new pre-installation script returned error exit status 1
Errors were encountered while processing:
 /var/cache/apt/archives/libc6_2.13-38_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

I’ve googled for this problem so much.. people who tried to solve this problem, after restarting machine, ended up reinstalling whole disto – which is not an option for me, because this project is quite highly loaded to have a downtime.

Some additional info from irc help:

# dpkg -S /lib/x86_64-linux-gnu/libc-2.13.so
dpkg-query: warning: files list file for package 'libc6:amd64' missing; assuming package has no files currently installed
dpkg-query: warning: files list file for package 'gcc-4.7-base:amd64' missing; assuming package has no files currently installed
dpkg-query: warning: files list file for package 'liblzma5:amd64' missing; assuming package has no files currently installed
dpkg-query: warning: files list file for package 'libgcc1:amd64' missing; assuming package has no files currently installed
dpkg-query: no path found matching pattern /lib/x86_64-linux-gnu/libc-2.13.so
# ls -l /var/lib/dpkg/info/libc*
-rw-r--r-- 1 root root     87 Dec 30 17:36 /var/lib/dpkg/info/libc-bin.conffiles
-rw-r--r-- 1 root root   1790 Mar  8 22:06 /var/lib/dpkg/info/libc-bin.list
-rw-r--r-- 1 root root   2874 Dec 30 17:36 /var/lib/dpkg/info/libc-bin.md5sums
-rwxr-xr-x 1 root root    246 Dec 30 17:36 /var/lib/dpkg/info/libc-bin.postinst
-rw-r--r-- 1 root root     40 Nov 19 01:07 /var/lib/dpkg/info/libc6.conffiles
-rw-r--r-- 1 root root  13341 Feb  1 15:45 /var/lib/dpkg/info/libc6.list
-rw-r--r-- 1 root root  21675 Nov 19 01:07 /var/lib/dpkg/info/libc6.md5sums
-rwxr-xr-x 1 root root  10114 Nov 19 01:07 /var/lib/dpkg/info/libc6.postinst
-rwxr-xr-x 1 root root   1117 Nov 19 01:07 /var/lib/dpkg/info/libc6.postrm
-rwxr-xr-x 1 root root  17327 Nov 19 01:07 /var/lib/dpkg/info/libc6.preinst
-rwxr-xr-x 1 root root   2015 Nov 19 01:07 /var/lib/dpkg/info/libc6.prerm
-rw-r--r-- 1 root root    996 Nov 19 01:07 /var/lib/dpkg/info/libc6.shlibs
-rw-r--r-- 1 root root 106948 Nov 19 01:07 /var/lib/dpkg/info/libc6.symbols
-rw-r--r-- 1 root root  64982 Nov 19 01:07 /var/lib/dpkg/info/libc6.templates
-rw-r--r-- 1 root root    267 Feb  1 15:47 /var/lib/dpkg/info/libcap2:amd64.list
-rw-r--r-- 1 root root    281 Aug 11  2012 /var/lib/dpkg/info/libcap2:amd64.md5sums
-rwxr-xr-x 1 root root    135 Aug 11  2012 /var/lib/dpkg/info/libcap2:amd64.postinst
-rwxr-xr-x 1 root root    132 Aug 11  2012 /var/lib/dpkg/info/libcap2:amd64.postrm
-rw-r--r-- 1 root root     27 Aug 11  2012 /var/lib/dpkg/info/libcap2:amd64.shlibs
-rw-r--r-- 1 root root    338 Feb  1 15:47 /var/lib/dpkg/info/libck-connector0:amd64.list
-rw-r--r-- 1 root root    322 Jul 30  2012 /var/lib/dpkg/info/libck-connector0:amd64.md5sums
-rwxr-xr-x 1 root root    135 Jul 30  2012 /var/lib/dpkg/info/libck-connector0:amd64.postinst
-rwxr-xr-x 1 root root    132 Jul 30  2012 /var/lib/dpkg/info/libck-connector0:amd64.postrm
-rw-r--r-- 1 root root     35 Jul 30  2012 /var/lib/dpkg/info/libck-connector0:amd64.shlibs
-rw-r--r-- 1 root root    350 Jul 30  2012 /var/lib/dpkg/info/libck-connector0:amd64.symbols
-rw-r--r-- 1 root root    395 Feb  1 15:46 /var/lib/dpkg/info/libclass-isa-perl.list
-rw-r--r-- 1 root root    451 Nov 24  2011 /var/lib/dpkg/info/libclass-isa-perl.md5sums
-rw-r--r-- 1 root root    247 Feb  1 15:47 /var/lib/dpkg/info/libcomerr2:amd64.list
-rw-r--r-- 1 root root    221 Jul 31  2012 /var/lib/dpkg/info/libcomerr2:amd64.md5sums
-rwxr-xr-x 1 root root    253 Jul 31  2012 /var/lib/dpkg/info/libcomerr2:amd64.postinst
-rwxr-xr-x 1 root root    247 Jul 31  2012 /var/lib/dpkg/info/libcomerr2:amd64.postrm
-rw-r--r-- 1 root root     82 Jul 31  2012 /var/lib/dpkg/info/libcomerr2:amd64.shlibs
-rw-r--r-- 1 root root    574 Jul 31  2012 /var/lib/dpkg/info/libcomerr2:amd64.symbols
-rw-r--r-- 1 root root   1553 Feb  1 15:46 /var/lib/dpkg/info/libconsole.list
-rw-r--r-- 1 root root   1556 Feb 18  2011 /var/lib/dpkg/info/libconsole.md5sums
-rwxr-xr-x 1 root root    135 Feb 18  2011 /var/lib/dpkg/info/libconsole.postinst
-rwxr-xr-x 1 root root    132 Feb 18  2011 /var/lib/dpkg/info/libconsole.postrm
-rw-r--r-- 1 root root    124 Feb 18  2011 /var/lib/dpkg/info/libconsole.shlibs
-rw-r--r-- 1 root root   3889 Feb  1 15:48 /var/lib/dpkg/info/libcrack2.list
-rw-r--r-- 1 root root   3226 Dec 13 00:00 /var/lib/dpkg/info/libcrack2.md5sums
-rwxr-xr-x 1 root root    135 Dec 13 00:00 /var/lib/dpkg/info/libcrack2.postinst
-rwxr-xr-x 1 root root    132 Dec 13 00:00 /var/lib/dpkg/info/libcrack2.postrm
-rw-r--r-- 1 root root     21 Dec 13 00:00 /var/lib/dpkg/info/libcrack2.shlibs
-rw-r--r-- 1 root root    703 Dec 13 00:00 /var/lib/dpkg/info/libcrack2.symbols
-rw-r--r-- 1 root root    432 Feb  1 15:47 /var/lib/dpkg/info/libcroco3:amd64.list
-rw-r--r-- 1 root root    558 Nov 26 15:53 /var/lib/dpkg/info/libcroco3:amd64.md5sums
-rwxr-xr-x 1 root root    135 Nov 26 15:53 /var/lib/dpkg/info/libcroco3:amd64.postinst
-rwxr-xr-x 1 root root    132 Nov 26 15:53 /var/lib/dpkg/info/libcroco3:amd64.postrm
-rw-r--r-- 1 root root     25 Nov 26 15:53 /var/lib/dpkg/info/libcroco3:amd64.shlibs
-rw-r--r-- 1 root root  15081 Nov 26 15:53 /var/lib/dpkg/info/libcroco3:amd64.symbols
-rw-r--r-- 1 root root    366 Feb  1 15:47 /var/lib/dpkg/info/libcups2:amd64.list
-rw-r--r-- 1 root root    438 Jan 11 11:57 /var/lib/dpkg/info/libcups2:amd64.md5sums
-rwxr-xr-x 1 root root    135 Jan 11 11:55 /var/lib/dpkg/info/libcups2:amd64.postinst
-rwxr-xr-x 1 root root    132 Jan 11 11:55 /var/lib/dpkg/info/libcups2:amd64.postrm
-rw-r--r-- 1 root root     19 Jan 11 11:55 /var/lib/dpkg/info/libcups2:amd64.shlibs
-rw-r--r-- 1 root root  11545 Jan 11 11:55 /var/lib/dpkg/info/libcups2:amd64.symbols
-rw-r--r-- 1 root root    834 Feb  5 12:12 /var/lib/dpkg/info/libcurl3-gnutls:amd64.list
-rw-r--r-- 1 root root   1056 May 25  2012 /var/lib/dpkg/info/libcurl3-gnutls:amd64.md5sums
-rwxr-xr-x 1 root root    135 May 25  2012 /var/lib/dpkg/info/libcurl3-gnutls:amd64.postinst
-rwxr-xr-x 1 root root    132 May 25  2012 /var/lib/dpkg/info/libcurl3-gnutls:amd64.postrm
-rw-r--r-- 1 root root     33 May 25  2012 /var/lib/dpkg/info/libcurl3-gnutls:amd64.shlibs
-rw-r--r-- 1 root root   2390 May 25  2012 /var/lib/dpkg/info/libcurl3-gnutls:amd64.symbols
-rw-r--r-- 1 root root   4336 Feb  1 15:46 /var/lib/dpkg/info/libcwidget3.list
-rw-r--r-- 1 root root   3462 Jun 17  2012 /var/lib/dpkg/info/libcwidget3.md5sums
-rwxr-xr-x 1 root root    135 Jun 17  2012 /var/lib/dpkg/info/libcwidget3.postinst
-rwxr-xr-x 1 root root    132 Jun 17  2012 /var/lib/dpkg/info/libcwidget3.postrm
-rw-r--r-- 1 root root     25 Jun 17  2012 /var/lib/dpkg/info/libcwidget3.shlibs
#  apt-cache policy libc6
libc6:
  Installed: 2.13-37
  Candidate: 2.13-38
  Version table:
     2.13-38 0
        500 http://ftp.lt.debian.org/debian/ testing/main amd64 Packages
 *** 2.13-37 0
        100 /var/lib/dpkg/status

In conclusion from IRC help it’s multiarch problem. Would be nice stick to 64bit packages.

My answer:


First, you do what it told you to do.

A copy of the C library was found in an unexpected directory:
  '/lib/x86_64-linux-gnu/libc-2.13.so'
It is not safe to upgrade the C library in this situation;
please remove that copy of the C library or get it out of
'/lib/x86_64-linux-gnu' and try again.

Maybe that will fix everything. But you still have enough going on there that you should have a maintenance period and reinstall the system.


View the full question and answer on Server Fault.

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