Dist-upgrade potential issues

Created:

2016-11-16 12:49:37 UTC

Modified:

2017-05-19 07:30:48 UTC

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Dist-upgrade potential issues

Applicable to:

  • Plesk 12.5 for Linux
  • Plesk 12.0 for Linux

Dist-upgrade is not a simple process. To go through it you must have considerable experience in the system administration, the knowledge of the system and its components.
During or after dist-upgrade there might be some issues that can be solved with the help of this article.

Before starting dist-upgrade procedure make sure that you have read instructions provided in the documentation by the OS vendor:
Debian 6 to Debian 7
Debian 7 to Debian 8
Ubuntu 12 to Ubuntu 14

To avoid any potential problems follow the steps provided in the article #213410369 .

Table of contents

General errors during dist-upgrade

  • Plymouth package has unmet dependencies

    Dist-upgrade failed with the following error:

        # apt-get dist-upgrade 
    Reading package lists...
    Done Building dependency tree
    Reading state information...
    Done Calculating upgrade... Failed
    The following packages have unmet dependencies:
    udev : Breaks: plymouth (< 0.9.0-7) but 0.8.5.1-5 is to be installed
    E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.

    'plymouth' package has unmet dependencies.
    Remove this package and run dist-upgrade again.

  • Could not perform immediate configuration

    Dist-upgrade failed with the following error:

    E: Could not perform immediate configuration on...

    Run:

    # apt-get dist-upgrade -o APT::Immediate-Configure=0
  • Failed to get D-Bus connection

    After dist-upgrade some services are failing to start with error:

    Failed to get D-Bus connection: Unknown error -1
    Switching to 'systemd' system initialization service was not completed:

    # ps -p 1 -o comm=
    init
    1. Remove file /etc/apt/preferences.d/local-pin-init and install 'systemd-sysv' package:

      # rm -f /etc/apt/preferences.d/local-pin-init
      # apt-get install systemd-sysv
    2. Reboot your server.

    3. Repair Plesk services:

      # plesk repair installation
    4. Note: systemd should be installed on Ubuntu 14.04
  • There is no public key available

    #apt-get update command shows warnings:

    N: Ignoring file '50sw_autoinstaller.list.saved_by_plesk_distupgrade' in directory '/etc/apt/sources.list.d/' as it has an invalid filename extension
    W: There is no public key available for the following key IDs:
    9D6D8F6BC857C906
    W: There is no public key available for the following key IDs:
    7638D0442B90D010

    You may safely ignore them, but in case you want to get rid of them, install keyring:

    # apt-get install debian-archive-keyring
  • initscripts : Breaks: nfs-common

    Dist-upgrade command fails with error if nfs-common is installed:

    # apt-get dist-upgrade
    Calculating upgrade... Failed
    The following packages have unmet dependencies:
    initscripts : Breaks: nfs-common (< 1:1.2.5-3) but 1:1.2.2-4squeeze2 is to be installed
    E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.

    Remove nfs-common package to proceeed with an upgrade:

    #apt-get remove nfs-common
  • Could not perform immediate configuration on mysql-server-5.5

    Dist-upgrade command fails with error:

    E: Could not perform immediate configuration on 'mysql-server-5.5'. Please see man 5 apt.conf under APT::Immediate-Configure for details. (2)

    It fails if libc6-dev package is installed, but mysql-server requires gcc-4.4 . Install missing packages to proceed with an upgrade:

    # apt-get install gcc-4.4
    # apt-get install mysql-server-5.5
  • Unable to access Horde webmail

    Horde webmail shows error after authentication:

    Call to a member function write() on NULL

    In /var/log/maillog records like:

    Dec 18 22:03:23 testpar1 courier-imapd: Connection, ip=[::ffff:127.0.0.1]
    Dec 18 22:03:23 testpar1 courier-imapd: authdaemon: s_connect() failed: No such file or directory
    Dec 18 22:03:24 testpar1 courier-imapd: LOGIN FAILED, method=PLAIN, ip=[::ffff:127.0.0.1]
    Dec 18 22:03:24 testpar1 courier-imapd: authentication error: No such file or directory

    Repair the mail server configuration:

    # plesk repair mail
  • Plesk pre-upgrade script returns that package is not up-to-date

    Plesk pre-upgrade script from Debian 7 to Debian 8 returns the following message:

    The following packages are not up-to-date:
    db4.8-util
    You should install the latest updates before performing dist-upgrade

    Update package db4.8-util manually:

    # apt-get install --only-upgrade db4.8-util
  • Restarting SpamAssassin Mail Filter Daemon: Can't locate NetAddr/IP.pm

    Dist-upgrade failed with SpamAssassin error:

    Restarting SpamAssassin Mail Filter Daemon: Can't locate NetAddr/IP.pm in
    @INC (you may need to install the NetAddr::IP module) (@INC contains:
    /usr/share/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.20.2
    /usr/local/share/perl/5.20.2 /usr/lib/x86_64-linux-gnu/perl5/5.20
    /usr/lib/x86_64-linux-gnu/perl/5.20 /usr/share/perl/5.20
    /usr/local/lib/site_perl) at /usr/share/perl5/Mail/SpamAssassin/NetSet.pm
    line 25.

    Complete installation of packages using this command:

    # apt-get -f install

    Continue dist-upgrade:

    # apt-get dist-upgrade
  • Dist-upgrade failed due to udev package

    Dist-upgrade failed with message that udev package can not be upgraded due to not upgraded kernel.

    Complete installation of packages using this command:

    # apt-get -f install

    Continue dist-upgrade:

    # apt-get dist-upgrade

    Repeat apt-get -f install and apt-get dist-upgrade to that moment when only 'udev' package will be marked for upgrade.

    Perform server reboot.Finish dist-upgrade:

    # apt-get dist-upgrade
  • Some of essential Plesk components are not upgraded: panel

    After dist-upgrade from Debian 7 to Debian 8 post-upgrade script /opt/psa/bin/distupgrade.helper.deb7-deb8_post.x64.sh finishes with message:

    Some of essential Plesk components are not upgraded: panel
    You may either upgrade them manually upgrade them or rerun utility with option --skip-check-latest
    Some error during dist-upgrade post stage occurs.

    Also Horde package got removed.

    Before executing post-upgrade script /opt/psa/bin/distupgrade.helper.deb7-deb8_post.x64.sh run the following command:

    # apt-get install psa-phpfpm-configurator
  • Unmet dependencies for libmyodbc

    During upgrade from Debian 6 to Debian 7 the following dependencies issue appears:

    # apt-get dist-upgrade
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    Calculating upgrade... Failed
    The following packages have unmet dependencies:
    odbcinst1debian2 : Breaks: libmyodbc (< 5.1.6-2) but 5.1.6-1 is to be installed
    pp12.5.30-bootstrapper : Depends: plesk-mysql-server (>= 12.5.30) but it is not going to be installed
    E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.

    The solution is to install package odbcinst1debian2 and continue dist-upgrade:

    # apt-get install odbcinst1debian2
    ...
    # apt-get dist-upgrade
  • Failed to set up sasl2-bin

    During dist-upgrade the following error might appear:

    Setting up sasl2-bin (2.1.25.dfsg1-6+deb7u1) ...
    saslpasswd2: user not found
    dpkg: error processing sasl2-bin (--configure):
    subprocess installed post-installation script returned error exit status 20
    Errors were encountered while processing:
    sasl2-bin
    E: Sub-process /usr/bin/dpkg returned an error code (1)

    To solve it run sasldbconverter2 utility and press Enter when prompted. Then run:

    # apt-get install -f

    Once package sasl2-bin has been configured, continue the dist-upgrade.

  • Rsyslog is unable to start

    # /etc/init.d/rsyslog restart
    [....] Starting enhanced syslogd: rsyslogd rsyslogd: [origin software="rsyslogd" swVersion="5.8.11" x-pid="1973" x-info="http://www.rsyslog.com"] start rsyslogd-2013:CONFIG ERROR: could not interpret master config file '/etc/rsyslog.conf'. [try http://www.rsyslog.com/e/2013 ] rsyslogd:EMERGENCY CONFIGURATION ACTIVATED - fix rsyslog config file!. ok

Replace the rsyslog configuration with preupgrade one and restart the service:

    # mv /etc/rsyslog.conf.saved_by_plesk_distupgrade /etc/rsyslog.conf
# /etc/init.d/rsyslog restart
[ ok ] Stopping enhanced syslogd: rsyslogd.
[ ok ] Starting enhanced syslogd: rsyslogd.

Apache errors on dist-upgrade

If dist-upgrade failed without any errors, only information that it failed on installing apache packages, run packages installation again using this command to see the error or to continue dist-upgrade after fixing the issue:

# apt-get install -f
  • Config file dir.conf not properly enabled

    Command apt-get install -f showed error for apache service:

    Config file dir.conf not properly enabled: /etc/apache2/mods-enabled/dir.conf is a real file, not touching it.

    Replace 'dir.conf' with symlink and continue upgrade if apache can be started:

    # ln -sf ../mods-available/dir.conf /etc/apache2/mods-enabled/dir.conf
  • API module structure 1aclr_module1 is garbled

    Upgrade failed on:

    API module structure 1aclr_module1 in file /usr/lib/apache2/modules/mod_aclr.so is garbled - expected signature 4 1503234 but saw 41503232 - perhaps this is not an Apache module DSO, or was compiled for a different Apache version?

    'aclr' module was not properly upgraded. The same issue may be with 'fcgi' module. Disable it and try to start apache:

    # a2dismod aclr
    Module aclr disabled

    Disable 'fcgi' using the same command if it is required. Continue upgrade if apache can be started.

  • No matches for the wildcard '*.conf'

    apache startup failed on:

    apache2: Syntax error on line 234 of /etc/apache2/apache2.conf: Syntax error on line 5 of /etc/apache2/conf.d/zz010_psa_httpd.conf: Syntax error on line 72 of /etc/apache2/plesk.conf.d/server.conf: No matches for the wildcard '*.conf' in '/etc/apache2/plesk.conf.d/ip_default', failing (use IncludeOptional if required)
    Action 'configtest' failed.
    The Apache error log may have more information.

    Use solution from article [KB213944365]After upgrade Apache from 2.2 to 2.4, Apache is not starting and continue upgrade if apache can be started.

  • Could not open configuration file /etc/apache2/sites-enabled/000-default: No such file or directory

    apache startup failed on:

    apache2: Syntax error on line 268 of /etc/apache2/apache2.conf: Could not open configuration file /etc/apache2/sites-enabled/000-default: No such file or directory

    Remove symlink and continue upgrade if apache can be started:

    # rm /etc/apache2/sites-enabled/000-default
  • Invalid command 'LockFile'

    apache startup failed on:

    Invalid command 'LockFile', perhaps misspelled or defined by a module not included in the server configuration Action 'configtest' failed.
    The Apache error log may have more information.

    'LockFile' directive doesn't exist in apache 2.4, replace it with 'Mutex' directive in /etc/apache2/apache2.conf :

    LockFile ${APACHE_LOCK_DIR}/accept.lock

    with

    Mutex file:${APACHE_LOCK_DIR} default

    Also replace 'SSLMutex' with 'Mutex' in /etc/apache2/mods-enabled/ssl.conf and continue upgrade if apache can be started.

  • SSLSessionCache: 'shmcb1' session cache not supported

    apache startup failed on:

    SSLSessionCache: 'shmcb1' session cache not supported (known names: ). 
    Maybe you need to load the appropriate socache module (mod_socache_shmcb?).

    Comment 'SSLSessionCache' in /etc/apache2/mods-enabled/ssl.conf and continue upgrade if apache can be started.

  • Invalid command 'Order'

    apache startup failed on:

    Invalid command 'Order', perhaps misspelled or defined by a module not included in the server configuration.

    Remove 'Order..' and 'Allow..', add 'Require all granted' in /etc/apache2/plesk.conf.d/server.conf for all sections, as on example:

    <Directоry "/var/www/vhosts/default/cgi-bin">
    AllowOverride None
    Options None
    - Order allow,deny
    - Allow from all
    + Require all granted
    </Directory>

    Continue upgrade if apache can be started.

  • Apache started with no sites

    Apache is starting properly, however there is no sites are loaded.
    apache2ctl -S output shows only default site.

    Create a symlink from /etc/apache2/conf.d/zz010_psa_httpd.conf to /etc/apache2/conf-enabled/zz010_psa_httpd.conf

    # ln -s /etc/apache2/conf.d/zz010_psa_httpd.conf /etc/apache2/conf-enabled/zz010_psa_httpd.conf
  • Port conflict with nginx

    Apache web server does not start after upgrade to Debian 8 with the following message:

    root@dist-upgrade:~# apache2ctl start
    (98)Address already in use: AH00072: make_sock: could not bind to address [::]:80
    (98)Address already in use: AH00072: make_sock: could not bind to address 0.0.0.0:80
    no listening sockets available, shutting down
    AH00015: Unable to open logs
    Action 'start' failed.
    The Apache error log may have more information.

    This means that file /etc/apache2/ports.conf was overwritten by the package maintainer's version and uses ports 80 and 443 for http and https respectively. However, nginx is also running and uses the same ports.

    To reconfigure Apache to use proper ports, disable and enable nginx reverse proxy server:

    # plesk sbin nginxmng --disable
    # plesk sbin nginxmng --enable

    Then, run plesk repair web and continue dist-upgrade.

Note : Do not forget to run Plesk autoinstaller to install all available Plesk updates after dist-upgrade.

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