Debian apt dependency mismatch (libc6)

Sean Gordon asked:

Earlier, I tried to install package via apt-get (cython), but it failed with the Errors were encountered while processing: message, and since then, apt is refusing to install anything. apt-get check output below:

root@dix:~# apt-get check
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 (= 2.11.3-2) but 2.11.3-4 is installed
 libc6-dev : Depends: libc6 (= 2.11.3-4) but 2.11.3-2 is installed
 libc6-i386 : Depends: libc6 (= 2.11.3-4) but 2.11.3-2 is installed
E: Unmet dependencies. Try using -f.

Apt/aptitude don’t seem to be able to fix this dependency issue, and I don’t know what to do.

Edit: Running apt-get -f install results in no change, and my sources are all squeeze. Running apt-get update then apt-get dist-upgrade show no change either.

Edit 2: I went back to try this again in a new terminal and apt-get -f install gives this error:

dpkg: error processing /var/cache/apt/archives/libc6_2.11.3-4_amd64.deb (--unpack):
 subprocess new pre-installation script killed by signal (Aborted)
configured to not write apport reports
                                      Errors were encountered while processing:
 /var/cache/apt/archives/libc6_2.11.3-4_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

Edit 3: Using apt-get clean first, then the previous commands, results in the first error again. Using apt-get -f dist-upgrade gives the below.

Reading package lists...
Building dependency tree...
Reading state information...
Correcting dependencies... Done
The following packages will be upgraded:
  apache2 apache2-mpm-prefork apache2-utils apache2.2-bin apache2.2-common at
  automake base-files bind9 bind9-doc bind9-host bind9utils
  debian-archive-keyring dnsutils dpkg-dev file host initscripts
  isc-dhcp-client isc-dhcp-common krb5-multidev libapr1 libbind9-60 libc6
  libdns69 libdpkg-perl libexpat1 libexpat1-dev libgc1c2 libgssapi-krb5-2
  libgssrpc4 libisc62 libisccc60 libisccfg62 libk5crypto3 libkadm5clnt-mit7
  libkadm5srv-mit7 libkdb5-4 libkrb5-3 libkrb5-dev libkrb5support0 liblwres60
  libmagic1 libmysqlclient16 libnss3-1d libssl-dev libssl0.9.8 libtiff4
  libtiff4-dev libtiffxx0c2 libxi6 libxml2 linux-libc-dev lwresd
  mysql-client-5.1 mysql-common mysql-server mysql-server-5.1
  mysql-server-core-5.1 openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib
  openssh-client openssh-server openssl procps python python-crypto
  python-minimal sudo sysv-rc sysvinit sysvinit-utils tzdata tzdata-java
75 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
5 not fully installed or removed.
Need to get 0 B/79.9 MB of archives.
After this operation, 1,411 kB of additional disk space will be used.
(Reading database ... 52241 files and directories currently installed.)
Preparing to replace libc6 2.11.3-2 (using .../libc6_2.11.3-4_amd64.deb) ...
*** stack smashing detected ***: /usr/bin/perl terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x37)[0x7fdaad9b9f87]
/lib/libc.so.6(__fortify_fail+0x0)[0x7fdaad9b9f50]
/usr/lib/libperl.so.5.10(Perl_yylex+0x5896)[0x7fdaae343346]
[0x8e83a0]
======= Memory map: ========
00400000-00402000 r-xp 00000000 08:01 525338                             /usr/bin/perl
00601000-00602000 rw-p 00001000 08:01 525338                             /usr/bin/perl
00602000-0091f000 rw-p 00000000 00:00 0                                  [heap]
7fdaaca54000-7fdaaca6a000 r-xp 00000000 08:01 393818                     /lib/libgcc_s.so.1
7fdaaca6a000-7fdaacc69000 ---p 00016000 08:01 393818                     /lib/libgcc_s.so.1
7fdaacc69000-7fdaacc6a000 rw-p 00015000 08:01 393818                     /lib/libgcc_s.so.1
7fdaacc6a000-7fdaacc6f000 r-xp 00000000 08:01 524949                     /usr/lib/perl5/auto/Locale/gettext/gettext.so
7fdaacc6f000-7fdaace6e000 ---p 00005000 08:01 524949                     /usr/lib/perl5/auto/Locale/gettext/gettext.so
7fdaace6e000-7fdaace6f000 rw-p 00004000 08:01 524949                     /usr/lib/perl5/auto/Locale/gettext/gettext.so
7fdaace6f000-7fdaace79000 r-xp 00000000 08:01 532753                     /usr/lib/perl/5.10.1/auto/Encode/Encode.so
7fdaace79000-7fdaad078000 ---p 0000a000 08:01 532753                     /usr/lib/perl/5.10.1/auto/Encode/Encode.so
7fdaad078000-7fdaad079000 rw-p 00009000 08:01 532753                     /usr/lib/perl/5.10.1/auto/Encode/Encode.so
7fdaad079000-7fdaad07e000 r-xp 00000000 08:01 525444                     /usr/lib/perl/5.10.1/auto/IO/IO.so
7fdaad07e000-7fdaad27d000 ---p 00005000 08:01 525444                     /usr/lib/perl/5.10.1/auto/IO/IO.so
7fdaad27d000-7fdaad27e000 rw-p 00004000 08:01 525444                     /usr/lib/perl/5.10.1/auto/IO/IO.so
7fdaad27e000-7fdaad299000 r-xp 00000000 08:01 525450                     /usr/lib/perl/5.10.1/auto/POSIX/POSIX.so
7fdaad299000-7fdaad498000 ---p 0001b000 08:01 525450                     /usr/lib/perl/5.10.1/auto/POSIX/POSIX.so
7fdaad498000-7fdaad49b000 rw-p 0001a000 08:01 525450                     /usr/lib/perl/5.10.1/auto/POSIX/POSIX.so
7fdaad49b000-7fdaad49e000 r-xp 00000000 08:01 525436                     /usr/lib/perl/5.10.1/auto/Fcntl/Fcntl.so
7fdaad49e000-7fdaad69e000 ---p 00003000 08:01 525436                     /usr/lib/perl/5.10.1/auto/Fcntl/Fcntl.so
7fdaad69e000-7fdaad69f000 rw-p 00003000 08:01 525436                     /usr/lib/perl/5.10.1/auto/Fcntl/Fcntl.so
7fdaad69f000-7fdaad6a7000 r-xp 00000000 08:01 393824                     /lib/libcrypt-2.11.3.so
7fdaad6a7000-7fdaad8a6000 ---p 00008000 08:01 393824                     /lib/libcrypt-2.11.3.so
7fdaad8a6000-7fdaad8a7000 r--p 00007000 08:01 393824                     /lib/libcrypt-2.11.3.so
7fdaad8a7000-7fdaad8a8000 rw-p 00008000 08:01 393824                     /lib/libcrypt-2.11.3.so
7fdaad8a8000-7fdaad8d6000 rw-p 00000000 00:00 0
7fdaad8d6000-7fdaada2f000 r-xp 00000000 08:01 393822                     /lib/libc-2.11.3.so
7fdaada2f000-7fdaadc2e000 ---p 00159000 08:01 393822                     /lib/libc-2.11.3.so
7fdaadc2e000-7fdaadc32000 r--p 00158000 08:01 393822                     /lib/libc-2.11.3.so
7fdaadc32000-7fdaadc33000 rw-p 0015c000 08:01 393822                     /lib/libc-2.11.3.so
7fdaadc33000-7fdaadc38000 rw-p 00000000 00:00 0
7fdaadc38000-7fdaadc4f000 r-xp 00000000 08:01 393248                     /lib/libpthread-2.11.3.so
7fdaadc4f000-7fdaade4e000 ---p 00017000 08:01 393248                     /lib/libpthread-2.11.3.so
7fdaade4e000-7fdaade4f000 r--p 00016000 08:01 393248                     /lib/libpthread-2.11.3.so
7fdaade4f000-7fdaade50000 rw-p 00017000 08:01 393248                     /lib/libpthread-2.11.3.so
7fdaade50000-7fdaade54000 rw-p 00000000 00:00 0
7fdaade54000-7fdaaded4000 r-xp 00000000 08:01 393826                     /lib/libm-2.11.3.so
7fdaaded4000-7fdaae0d4000 ---p 00080000 08:01 393826                     /lib/libm-2.11.3.so
7fdaae0d4000-7fdaae0d5000 r--p 00080000 08:01 393826                     /lib/libm-2.11.3.so
7fdaae0d5000-7fdaae0d6000 rw-p 00081000 08:01 393826                     /lib/libm-2.11.3.so
7fdaae0d6000-7fdaae0d8000 r-xp 00000000 08:01 393825                     /lib/libdl-2.11.3.so
7fdaae0d8000-7fdaae2d8000 ---p 00002000 08:01 393825                     /lib/libdl-2.11.3.so
7fdaae2d8000-7fdaae2d9000 r--p 00002000 08:01 393825                     /lib/libdl-2.11.3.so
7fdaae2d9000-7fdaae2da000 rw-p 00003000 08:01 393825                     /lib/libdl-2.11.3.so
7fdaae2da000-7fdaae43f000 r-xp 00000000 08:01 525387                     /usr/lib/libperl.so.5.10.1
7fdaae43f000-7fdaae63e000 ---p 00165000 08:01 525387                     /usr/lib/libperl.so.5.10.1
7fdaae63e000-7fdaae647000 rw-p 00164000 08:01 525387                     /usr/lib/libperl.so.5.10.1
7fdaae647000-7fdaae665000 r-xp 00000000 08:01 393819                     /lib/ld-2.11.3.so
7fdaae854000-7fdaae859000 rw-p 00000000 00:00 0
7fdaae862000-7fdaae864000 rw-p 00000000 00:00 0
7fdaae864000-7fdaae865000 r--p 0001d000 08:01 393819                     /lib/ld-2.11.3.so
7fdaae865000-7fdaae866000 rw-p 0001e000 08:01 393819                     /lib/ld-2.11.3.so
7fdaae866000-7fdaae867000 rw-p 00000000 00:00 0
7fff9616d000-7fff9618e000 rw-p 00000000 00:00 0                          [stack]
7fff961ff000-7fff96200000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r--p 00000000 00:00 0                  [vsyscall]
dpkg: error processing /var/cache/apt/archives/libc6_2.11.3-4_amd64.deb (--unpack):
 subprocess new pre-installation script killed by signal (Aborted)
Errors were encountered while processing:
 /var/cache/apt/archives/libc6_2.11.3-4_amd64.deb

My answer:


First, you do what it told you to do:

You might want to run 'apt-get -f install' to correct these.

If this doesn’t correct the problem, then do all of the following:

  1. Check /etc/apt/sources.list and make sure you are on a single version (e.g. squeeze) and haven’t tried to mix in sources from unstable/testing, etc.
  2. Run apt-get clean.
  3. Run apt-get update.
  4. Run apt-get dist-upgrade.

View the full question and answer on Server Fault.

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