Error timeout was reached linux

Symptoms

Segmentation fault (core dumped) with apt-get and python3 related scripts

This appears especially when trying to install/install -f «update-notifier-common» software, for example (sorry for the French):

% sudo apt-get install -f
Lecture des listes de paquets… Fait
Construction de l’arbre des dépendances      
Lecture des informations d’état… Fait
0 mis à jour, 0 nouvellement installés, 0 à enlever et 0 non mis à jour.
1 partiellement installés ou enlevés.
Après cette opération, 0 o d’espace disque supplémentaires seront utilisés.
Paramétrage de update-notifier-common (0.154.1) …
Segmentation fault (core dumped)
dpkg: error processing package update-notifier-common (—configure):
 le sous-processus script post-installation installé a retourné une erreur de sortie d’état 139
Des erreurs ont été rencontrées pendant l’exécution :
 update-notifier-common
Error: Timeout was reached
E: Sub-process /usr/bin/dpkg returned an error code (1)

The other aspect of that problem was that any Python3 related errors lead to a stack trace like that:


% python3
Python 3.4.0 (default, Apr 11 2014, 13:05:11)
[GCC 4.8.2] on linux
Type «help», «copyright», «credits» or «license» for more information.
>>> foo                                                                                                                                                                                                     
Traceback (most recent call last):
  File «», line 1, in
NameError: name ‘foo’ is not defined
Error in sys.excepthook:
Traceback (most recent call last):
  File «/usr/lib/python3/dist-packages/apport_python_hook.py», line 63, in apport_excepthook
    from apport.fileutils import likely_packaged, get_recent_crashes
  File «/usr/lib/python3/dist-packages/apport/__init__.py», line 5, in
    from apport.report import Report
  File «/usr/lib/python3/dist-packages/apport/report.py», line 30, in
    import apport.fileutils
  File «/usr/lib/python3/dist-packages/apport/fileutils.py», line 23, in
    from apport.packaging_impl import impl as packaging
  File «/usr/lib/python3/dist-packages/apport/packaging_impl.py», line 20, in
    import apt
  File «/usr/lib/python3/dist-packages/apt/__init__.py», line 23, in
    import apt_pkg
ImportError: /usr/lib/python3/dist-packages/apt_pkg.cpython-34m-x86_64-linux-gnu.so: undefined symbol: _ZN13pkgTagSectionC1Ev

Original exception was:
Traceback (most recent call last):
  File «

«, line 1, in
NameError: name ‘foo’ is not defined

Error: Timeout was reached

The second main symptom was that when using apt-* tools, I was getting an error message «Error: Timeout was reached» just at the end of the process. Nonetheless, everything seemed to be correctly installed/removed/etc.

Bug tracking, short version

That led me to some bug about a timeout to short for packagekit:

/usr/bin/test -e /usr/share/dbus-1/system-services/org.freedesktop.PackageKit.service && /usr/bin/test -S /var/run/dbus/system_bus_socket && /usr/bin/gdbus call —system —dest org.freedesktop.PackageKit —object-path /org/freedesktop/PackageKit —timeout 4 —method org.freedesktop.PackageKit.StateHasChanged cache-update

So I tested with a really big number, and got:


/usr/bin/gdbus call —system —dest org.freedesktop.PackageKit —object-path /org/freedesktop/PackageKit —timeout 300 —method org.freedesktop.PackageKit.StateHasChanged cache-update

Error: GDBus.Error:org.freedesktop.DBus.Error.TimedOut: Activation of org.freedesktop.PackageKit timed out

What lead to testing packagkit itself:

% sudo /usr/lib/packagekit/packagekitd —verbose
11:12:57        PackageKit          Verbose debugging enabled (on console 1)
11:12:57        PackageKit          keep_environment: 0
11:12:57        PackageKit          using config file ‘/etc/PackageKit/PackageKit.conf’
11:12:57        PackageKit          syslog fucntionality disabled
11:12:57        PackageKit          Log all transactions: 1
11:12:57        PackageKit          daemon shutdown set to 300 seconds
11:12:57        PackageKit          clearing download cache at /var/cache/PackageKit/downloads
11:12:57        PackageKit          destination eth0 is valid
11:12:57        PackageKit          setting config file watch on /etc/PackageKit/PackageKit.conf
11:12:57        PackageKit          ProxyHTTP read error: Key file does not have key ‘ProxyHTTP’
11:12:57        PackageKit          searching for plugins in /usr/lib/x86_64-linux-gnu/packagekit-plugins
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-systemd-updates.so: A plugin to write the prepared-updates file
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-clear-firmware-requests.so: Clears firmware requests
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-check-shared-libraries-in-use.so: checks for any shared libraries in use after a security update
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-scan-desktop-files.so: Scans desktop files on refresh and adds them to a database
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-update-check-processes.so: Checks for running processes during update for session restarts
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-no-update-process.so: Updates the package lists after refresh
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-update-package-cache.so: Maintains a database of all packages for fast read-only access to package information
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin_scripts.so: Runs external scrips
11:12:57        PackageKit          opened plugin /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-require-restart.so: A dummy plugin that doesn’t do anything
11:12:57        PackageKit          run pk_plugin_initialize on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-check-shared-libraries-in-use.so
11:12:57        PackageKit          finished pk_plugin_initialize
11:12:57        PackageKit          run pk_plugin_initialize on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-scan-desktop-files.so
11:12:57        PackageKit          finished pk_plugin_initialize
11:12:57        PackageKit          run pk_plugin_initialize on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-update-check-processes.so
11:12:57        PackageKit          finished pk_plugin_initialize
11:12:57        PackageKit          run pk_plugin_initialize on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-no-update-process.so
11:12:57        PackageKit          finished pk_plugin_initialize
11:12:57        PackageKit          run pk_plugin_initialize on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-update-package-cache.so
11:12:57        PackageKit          finished pk_plugin_initialize
11:12:57        PackageKit          run pk_plugin_initialize on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-require-restart.so
11:12:57        PackageKit          finished pk_plugin_initialize
11:12:57        PackageKit          Trying to load : aptcc
11:12:57        PackageKit          dlopening ‘/usr/lib/x86_64-linux-gnu/packagekit-backend/libpk_backend_aptcc.so’
Failed to load the backend: opening module aptcc failed : /usr/lib/x86_64-linux-gnu/packagekit-backend/libpk_backend_aptcc.so: undefined symbol: _ZN13pkgTagSectionC1Ev11:12:57 PackageKit          run pk_plugin_destroy on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-check-shared-libraries-in-use.so
11:12:57        PackageKit          finished pk_plugin_destroy
11:12:57        PackageKit          run pk_plugin_destroy on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-scan-desktop-files.so
11:12:57        PackageKit          finished pk_plugin_destroy
11:12:57        PackageKit          run pk_plugin_destroy on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-update-check-processes.so
11:12:57        PackageKit          finished pk_plugin_destroy
11:12:57        PackageKit          run pk_plugin_destroy on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-no-update-process.so
11:12:57        PackageKit          finished pk_plugin_destroy
11:12:57        PackageKit          run pk_plugin_destroy on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-update-package-cache.so
11:12:57        PackageKit          finished pk_plugin_destroy
11:12:57        PackageKit          run pk_plugin_destroy on /usr/lib/x86_64-linux-gnu/packagekit-plugins/libpk_plugin-require-restart.so
11:12:57        PackageKit          finished pk_plugin_destroy
11:12:57        PackageKit          already closed (nonfatal)
11:12:57        PackageKit          parent_class->finalize

HooooOOoo… What about Aptitude ?

% aptitude
aptitude: symbol lookup error: aptitude: undefined symbol: _ZN3APT11CacheFilter39PackageArchitectureMatchesSpecificationC1ERKSsb

Solution

The problem was that somehow, I get a bad version of libapt-pkg4.12. So anything related to apt in some way had a chance to end badly.

Reinstalling the correct version of them (the one provided with my distribution) corrected all the problems:

sudo apt-get install libapt-pkg4.12=1.1.1bodhi1 apt=1.1.1bodhi1 apt-transport-https=1.1.1bodhi1 apt-utils=1.1.1bodhi1

Hope it helps !

I’m in a difficult situation.

Using Debian Jessie / Stretch, apt-get -f install fails.

The system is effectively stuck. I’ve sshed in now. As far as login terminals, only one was becoming available. (Namely, only alt-ctrl-F1 brought up a login terminal on the actual machine, alt-ctrl-f[2-5] failed).

It seems to be related to the bug listed here. Though there are multiple problems: krb-kdc doesn’t unpack because PolicyKit timeout was reached (g-io-error-quark, 24), then errors unpacking krb5-admin-server, the an error message that LDAP must be enabled (though it is and connects fine).

Namely, there are multiple time-outs with apt-get (to PolicyKit bits it seems). As far as the network, I’ve set the timeout time to 1200, with no seeming effect.
The full error message:

The following extra packages will be installed:
  krb5-admin-server krb5-kdc
Suggested packages:
  openbsd-inetd inet-superserver krb5-kdc-ldap
The following packages will be upgraded:
  krb5-admin-server krb5-kdc
2 upgraded, 0 newly installed, 0 to remove and 73 not upgraded.
9 not fully installed or removed.
Need to get 0 B/320 kB of archives.
After this operation, 115 kB disk space will be freed.
Do you want to continue? [Y/n]
Reading changelogs... Done
Preconfiguring packages ...
(Reading database ... 296869 files and directories currently installed.)
Preparing to unpack .../krb5-kdc_1.13.2+dfsg-2_amd64.deb ...
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to execute operation: Connection timed out
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to stop krb5-kdc.service: Connection timed out
Failed to get load state of krb5-kdc.service: Connection timed out
invoke-rc.d: initscript krb5-kdc, action "stop" failed.
failed to stop krb5-kdc
dpkg: warning: subprocess old pre-removal script returned error exit status 1
dpkg: trying script from the new package instead ...
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to execute operation: Connection timed out
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to stop krb5-kdc.service: Connection timed out
Failed to get load state of krb5-kdc.service: Connection timed out
invoke-rc.d: initscript krb5-kdc, action "stop" failed.
failed to stop krb5-kdc
dpkg: error processing archive /var/cache/apt/archives/krb5-kdc_1.13.2+dfsg-2_amd64.deb (--unpack):
 subprocess new pre-removal script returned error exit status 1
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to execute operation: Connection timed out
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to execute operation: Connection timed out
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to start krb5-kdc.service: Connection timed out
invoke-rc.d: initscript krb5-kdc, action "start" failed.
Preparing to unpack .../krb5-admin-server_1.13.2+dfsg-2_amd64.deb ...
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to execute operation: Connection timed out
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to stop krb5-admin-server.service: Connection timed out
Failed to get load state of krb5-admin-server.service: Connection timed out
invoke-rc.d: initscript krb5-admin-server, action "stop" failed.
dpkg: warning: subprocess old pre-removal script returned error exit status 1
dpkg: trying script from the new package instead ...
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: Timeout was reached (g-io-error-quark, 24)
Failed to execute operation: Connection timed out
Error getting authority: Error initializing authority: Error calling StartServiceByName for org.freedesktop.PolicyKit1: GDBus.Error:org.freedesktop.DBus.Error.TimedOut: Activation of org.freedesktop.PolicyKit1 timed out (g-dbus-error-quark, 20)
Failed to stop krb5-admin-server.service: Connection timed out
Failed to get load state of krb5-admin-server.service: Connection timed out
invoke-rc.d: initscript krb5-admin-server, action "stop" failed.
dpkg: error processing archive /var/cache/apt/archives/krb5-admin-server_1.13.2+dfsg-2_amd64.deb (--unpack):
 subprocess new pre-removal script returned error exit status 1
insserv: Service ldap has to be enabled to start service krb5-admin-server
insserv: exiting now!
update-rc.d: error: insserv rejected the script header
dpkg: error while cleaning up:
 subprocess installed post-installation script returned error exit status 1
Errors were encountered while processing:
 /var/cache/apt/archives/krb5-kdc_1.13.2+dfsg-2_amd64.deb
 /var/cache/apt/archives/krb5-admin-server_1.13.2+dfsg-2_amd64.deb
Error: Timeout was reached
E: Sub-process /usr/bin/dpkg returned an error code (1)

Questions:

1. What else can I do to force apt-get -f install?
2. Would it help to force a roll-back to Jessie?