apt-get locked

[jdimatteo]

Apt-get fails to install software, e.g.

jdm@tod:~$ sudo apt-get install csh
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  libdrm2:i386 linux-image-3.13.0-34-generic
  linux-image-extra-3.13.0-34-generic
Use 'apt-get autoremove' to remove them.
The following NEW packages will be installed:
  csh
0 upgraded, 1 newly installed, 0 to remove and 132 not upgraded.
5 not fully installed or removed.
E: Could not get lock /var/cache/apt/archives/lock - open (11: Resource temporarily unavailable)
E: Unable to lock directory /var/cache/apt/archives/
jdm@tod:~$ 

[jdimatteo]

Same error February 22nd, and I didn't fix it then either:

jdm@tod:~$ sudo apt-get install autoconf-archive
...
E: Could not get lock /var/cache/apt/archives/lock - open (11: Resource temporarily unavailable)
E: Unable to lock directory /var/cache/apt/archives/

[jdimatteo]

It appears that apt-get is stuck:

jdm@tod:~$ ps aux | grep "apt\|PID"
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
root     13159  0.0  0.0 238004  2164 ?        S    Feb09   0:00 sudo apt-get upgrade bedtools
root     13161  0.0  0.0  97576  1256 ?        S    Feb09   0:14 apt-get upgrade bedtools
jdm      23462  0.0  0.0  11748   916 pts/34   S+   23:34   0:00 grep --color=auto apt\|PID
jdm@tod:~$ 

lsof never returned after 5 minutes:

jdm@tod:~$ sudo lsof /var/lib/dpkg/lock -n

[jdimatteo]

I tried sending SIGINT to the two processes, but that had no effect. SIGTERM killed it.

jdm@tod:~$ sudo kill -s SIGTERM 13161
jdm@tod:~$ ps aux | grep "apt\|PID"
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
jdm      27028  0.0  0.0  11748   916 pts/14   S+   23:52   0:00 grep --color=auto apt\|PID
jdm@tod:~$ 

[charlesylin]

Do we need to upgrade/restart?

-Charles

On Mar 25, 2015, at 11:44 PM, John DiMatteo notifications@github.com wrote:

I tried sending SIGINT to the two processes, but that had no effect. SIGTERM killed it.

jdm@tod:~$ sudo kill -s SIGTERM 13161 jdm@tod:~$ ps aux | grep "apt|PID" USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND jdm 27028 0.0 0.0 11748 916 pts/14 S+ 23:52 0:00 grep --color=auto apt|PID jdm@tod:~$ — Reply to this email directly or view it on GitHub.

[jdimatteo]

@bradnerComputation I was trying to work on other things since you are on a retreat!

[jdimatteo]

@bradnerComputation I mean, I didn't mean to interrupt your retreat :)

[charlesylin]

No worries. We are still up. Just hard to work on tod.

-Charles

On Mar 25, 2015, at 11:50 PM, John DiMatteo notifications@github.com wrote:

@bradnerComputation I mean, I didn't mean to interrupt your retreat :)

— Reply to this email directly or view it on GitHub.

[jdimatteo]

@bradnerComputation apt-get on tod seems pretty messed up. I'm going to try running sudo apt-get update , sudo apt-get upgrade

[jdimatteo]

after apt-get update && apt-get upgrade , apt-get remained in a bad state with errors like http://paste.ubuntu.com/10682050/

I'm giving up for the night. I guess this is some remaining stuff that never got upgraded successfully from 12.04 to 14.04. Maybe someone else can have better luck. Maybe my Linux system admin skills are too rusty and I should just stop. This was the last thing I tried:

jdm@tod:~$ sudo dpkg --configure -a
Setting up libpam-winbind:amd64 (2:4.1.6+dfsg-1ubuntu2.14.04.7) ...
Can't locate Debconf/Client/ConfModule.pm in @INC (you may need to install the Debconf::Client::ConfModule module) (@INC contains: /usr/local/lib/perl5/site_perl/5.18.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.18.1 /usr/local/lib/perl5/5.18.1/x86_64-linux /usr/local/lib/perl5/5.18.1 .) at /usr/sbin/pam-auth-update line 28.
BEGIN failed--compilation aborted at /usr/sbin/pam-auth-update line 28.
dpkg: error processing package libpam-winbind:amd64 (--configure):
 subprocess installed post-installation script returned error exit status 2
Setting up libpam-smbpass:amd64 (2:4.1.6+dfsg-1ubuntu2.14.04.7) ...
Can't locate Debconf/Client/ConfModule.pm in @INC (you may need to install the Debconf::Client::ConfModule module) (@INC contains: /usr/local/lib/perl5/site_perl/5.18.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.18.1 /usr/local/lib/perl5/5.18.1/x86_64-linux /usr/local/lib/perl5/5.18.1 .) at /usr/sbin/pam-auth-update line 28.
BEGIN failed--compilation aborted at /usr/sbin/pam-auth-update line 28.
dpkg: error processing package libpam-smbpass:amd64 (--configure):
 subprocess installed post-installation script returned error exit status 2
Setting up libpam-systemd:amd64 (204-5ubuntu20.10) ...
Can't locate Debconf/Client/ConfModule.pm in @INC (you may need to install the Debconf::Client::ConfModule module) (@INC contains: /usr/local/lib/perl5/site_perl/5.18.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.18.1 /usr/local/lib/perl5/5.18.1/x86_64-linux /usr/local/lib/perl5/5.18.1 .) at /usr/sbin/pam-auth-update line 28.
BEGIN failed--compilation aborted at /usr/sbin/pam-auth-update line 28.
dpkg: error processing package libpam-systemd:amd64 (--configure):
 subprocess installed post-installation script returned error exit status 2
dpkg: dependency problems prevent configuration of pulseaudio:
 pulseaudio depends on libpam-systemd; however:
  Package libpam-systemd:amd64 is not configured yet.

dpkg: error processing package pulseaudio (--configure):
 dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of pulseaudio-module-x11:
 pulseaudio-module-x11 depends on pulseaudio; however:
  Package pulseaudio is not configured yet.

dpkg: error processing package pulseaudio-module-x11 (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 libpam-winbind:amd64
 libpam-smbpass:amd64
 libpam-systemd:amd64
 pulseaudio
 pulseaudio-module-x11
jdm@tod:~$ 

[charlesylin]

Thanks for trying to fix this John,

I've got to physically move tod on Monday so will do a restart and try to ungunk it.

-Charles

Charles Y. Lin, Ph.D. Dana-Farber Cancer Institute Department of Medical Oncology charles_lin@dfci.harvard.edumailto:charles_lin@dfci.harvard.edu http://bradnerlab.com

On Thu, Mar 26, 2015 at 1:58 AM, John DiMatteo notifications@github.com wrote:

after apt-get update && apt-get upgrade , apt-get remained in a bad state with errors like http://paste.ubuntu.com/10682050/ and http://paste.ubuntu.com/10682121/

I'm giving up for the night. I guess this is some remaining stuff that never got upgraded successfully from 12.04 to 14.04. Maybe someone else can have better luck. This was the last thing I tried:

jdm@tod:~$ sudo dpkg --configure -a Setting up libpam-winbind:amd64 (2:4.1.6+dfsg-1ubuntu2.14.04.7) ... Can't locate Debconf/Client/ConfModule.pm in @INC (you may need to install the Debconf::Client::ConfModule module) (@INC contains: /usr/local/lib/perl5/site_perl/5.18.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.18.1 /usr/local/lib/perl5/5.18.1/x86_64-linux /usr/local/lib/perl5/5.18.1 .) at /usr/sbin/pam-auth-update line 28. BEGIN failed--compilation aborted at /usr/sbin/pam-auth-update line 28. dpkg: error processing package libpam-winbind:amd64 (--configure): subprocess installed post-installation script returned error exit status 2 Setting up libpam-smbpass:amd64 (2:4.1.6+dfsg-1ubuntu2.14.04.7) ... Can't locate Debconf/Client/ConfModule.pm in @INC (you may need to install the Debconf::Client::ConfModule module) (@INC contains: /usr/local/lib/perl5/site_perl/5.18.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.18.1 /usr/local/lib/perl5/5.18.1/x86_64-linux /usr/local/lib/perl5/5.18.1 .) at /usr/sbin/pam-auth-update line 28. BEGIN failed--compilation aborted at /usr/sbin/pam-auth-update line 28. dpkg: error processing package libpam-smbpass:amd64 (--configure): subprocess installed post-installation script returned error exit status 2 Setting up libpam-systemd:amd64 (204-5ubuntu20.10) ... Can't locate Debconf/Client/ConfModule.pm in @INC (you may need to install the Debconf::Client::ConfModule module) (@INC contains: /usr/local/lib/perl5/site_perl/5.18.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.18.1 /usr/local/lib/perl5/5.18.1/x86_64-linux /usr/local/lib/perl5/5.18.1 .) at /usr/sbin/pam-auth-update line 28. BEGIN failed--compilation aborted at /usr/sbin/pam-auth-update line 28. dpkg: error processing package libpam-systemd:amd64 (--configure): subprocess installed post-installation script returned error exit status 2 dpkg: dependency problems prevent configuration of pulseaudio: pulseaudio depends on libpam-systemd; however: Package libpam-systemd:amd64 is not configured yet.

dpkg: error processing package pulseaudio (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of pulseaudio-module-x11: pulseaudio-module-x11 depends on pulseaudio; however: Package pulseaudio is not configured yet.

dpkg: error processing package pulseaudio-module-x11 (--configure): dependency problems - leaving unconfigured Errors were encountered while processing: libpam-winbind:amd64 libpam-smbpass:amd64 libpam-systemd:amd64 pulseaudio pulseaudio-module-x11 jdm@tod:~$

— Reply to this email directly or view it on GitHub https://github.com/BradnerLab/SystemAdmin/issues/12#issuecomment-86355209 .