Resolved HELP! Update stuck with Plesk Onyx 17.8.11#1

[frdho]

I'm having the same issue, but with 208 updates.

For me, it was related to this topic: Resolved - Plesk Onyx & CentOS 7.4 compatible?

Apparently, auto-updates in plesk caused some yum issues, in turn causing duplicate packages and updating errors.

Removing these errors and updating the packages resulted in apache & nginx failure to start (as described in the topic).

I was forced to restore a backup twice. Now I'm stuck with this.

 

[Sergio Manzi]

Hello @frdho and thanks for the info.

I've (very quickly) read the article you cited, but I think it doesn't apply to the current situation: I was already on CentOS 7.4 with 17.5.3 and never had any issue before...

I have the strong feeling that the problem might be elsewere: in PHP Settings I had disabled "5.4.16 by OS vendor FPM application (Outdated)" because: A) as rightly indicated by Plesk itself, it is an outdated version, B) I don't have any use for it, C) I'm offered the possibility and thus "I can".

The stuck service that globally blocked the update is exactly the one relative to that outdated PHP FPM interface.

Have you disabled that PHP interface too?

Now I'm stuck between a rock and an hard place:

• In the control panel I'm still offered those 23 updates
• If I retry (having duly activated "5.4.16 by OS vendor FPM application (Outdated)"), I'm told that "All the selected packages are up-to-date." (but continue to be listed as available).
• yum is unhappy:

# yum history
ID     | Login user               | Date and time    | Action(s)      | Altered
-------------------------------------------------------------------------------
   158 | System <unset>           | 2018-03-09 04:11 | Update         |   23 **
   157 | System <unset>           | 2018-03-07 04:47 | Update         |   42 EE
   156 | System <unset>           | 2018-03-07 04:47 | I, U           |    2
   155 | root <root>              | 2018-03-06 00:23 | Update         |   51
   154 | root <root>              | 2018-02-17 04:17 | Install        |    1  <
   153 | root <root>              | 2018-02-13 23:57 | E, I, O, U     |   75 >E
   152 | root <root>              | 2018-02-13 23:57 | I, U           |    8
   151 | System <unset>           | 2018-02-07 12:31 | Update         |    1
   150 | System <unset>           | 2018-02-06 03:16 | Update         |   29
   149 | root <root>              | 2018-02-05 03:36 | I, O, U        |   33
   148 | root <root>              | 2018-02-04 23:52 | Erase          |    1 EE
   147 | System <unset>           | 2018-02-02 23:39 | Install        |    1
   146 | System <unset>           | 2018-02-02 04:17 | Update         |    4
   145 | System <unset>           | 2018-02-01 00:41 | Erase          |   29 EE
   144 | System <unset>           | 2018-02-01 00:40 | Update         |    3
   143 | System <unset>           | 2018-01-31 04:49 | Update         |    2
   142 | root <root>              | 2018-01-31 03:15 | Update         |    1
   141 | System <unset>           | 2018-01-28 01:11 | Update         |   25
   140 | System <unset>           | 2018-01-20 03:26 | Update         |   52
   139 | System <unset>           | 2018-01-08 21:39 | Update         |    5
Warning: RPMDB altered outside of yum.
** Found 23 pre-existing rpmdb problem(s), 'yum check' output follows:
cloud-init-0.7.9-9.el7.centos.6.x86_64 is a duplicate with cloud-init-0.7.9-9.el7.centos.2.x86_64
iptables-1.4.21-18.3.el7_4.x86_64 is a duplicate with iptables-1.4.21-18.2.el7_4.x86_64
libgcc-4.8.5-16.el7_4.2.x86_64 is a duplicate with libgcc-4.8.5-16.el7_4.1.x86_64
libgomp-4.8.5-16.el7_4.2.x86_64 is a duplicate with libgomp-4.8.5-16.el7_4.1.x86_64
libgudev1-219-42.el7_4.10.x86_64 is a duplicate with libgudev1-219-42.el7_4.7.x86_64
libstdc++-4.8.5-16.el7_4.2.x86_64 is a duplicate with libstdc++-4.8.5-16.el7_4.1.x86_64
libteam-1.25-6.el7_4.3.x86_64 is a duplicate with libteam-1.25-5.el7.x86_64
php-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-5.4.16-43.el7_4.x86_64
php-cli-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-cli-5.4.16-43.el7_4.x86_64
php-common-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-common-5.4.16-43.el7_4.x86_64
php-fpm-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-fpm-5.4.16-43.el7_4.x86_64
php-gd-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-gd-5.4.16-43.el7_4.x86_64
php-mbstring-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-mbstring-5.4.16-43.el7_4.x86_64
php-mysql-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-mysql-5.4.16-43.el7_4.x86_64
php-pdo-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-pdo-5.4.16-43.el7_4.x86_64
php-xml-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-xml-5.4.16-43.el7_4.x86_64
python-perf-3.10.0-693.21.1.el7.x86_64 is a duplicate with python-perf-3.10.0-693.17.1.el7.x86_64
selinux-policy-3.13.1-166.el7_4.9.noarch is a duplicate with selinux-policy-3.13.1-166.el7_4.7.noarch
selinux-policy-targeted-3.13.1-166.el7_4.9.noarch is a duplicate with selinux-policy-targeted-3.13.1-166.el7_4.7.noarch
systemd-219-42.el7_4.10.x86_64 is a duplicate with systemd-219-42.el7_4.7.x86_64
systemd-libs-219-42.el7_4.10.x86_64 is a duplicate with systemd-libs-219-42.el7_4.7.x86_64
systemd-sysv-219-42.el7_4.10.x86_64 is a duplicate with systemd-sysv-219-42.el7_4.7.x86_64
teamd-1.25-6.el7_4.3.x86_64 is a duplicate with teamd-1.25-5.el7.x86_64
history list

I don't have the slightest idea how to get out from here... (yum clean? but "clean what?": rpmdb? dbcache? expire-cache? all?)

 

[frdho]

Hello,

Seems we are in a similar situation. I have '5.4.16 by OS vendor FPM application' disabled in services management as well.

The yum error list seems very similar, only is mine a lot longer.

I've tried yum clean and deleting dupes and everything, but when I do that, I get corrupt apache & nginx, so no solution...

I hope someone of Plesk team jumps in to help, I'm getting desperate...

 

[Sergio Manzi]

I hope someone of Plesk team jumps in to help, I'm getting desperate...

... pinging @IgorG ... Sorry, Igor but it seems we definitely need your help here...

In the meanwhile I did the following:

# yum clean all
# rm -f /var/lib/rpm/__db*
# rpm --rebuilddb
# yum update

the above seems to have fixed yum (and installed a kernel update that yesterday was not offered...):

# yum history
Loaded plugins: fastestmirror
ID     | Login user               | Date and time    | Action(s)      | Altered
-------------------------------------------------------------------------------
   159 | root <root>              | 2018-03-09 12:52 | I, U           |    5 PP
   158 | System <unset>           | 2018-03-09 04:11 | Update         |   23 **
   157 | System <unset>           | 2018-03-07 04:47 | Update         |   42 EE
   156 | System <unset>           | 2018-03-07 04:47 | I, U           |    2
   155 | root <root>              | 2018-03-06 00:23 | Update         |   51
   154 | root <root>              | 2018-02-17 04:17 | Install        |    1  <
   153 | root <root>              | 2018-02-13 23:57 | E, I, O, U     |   75 >E
   152 | root <root>              | 2018-02-13 23:57 | I, U           |    8
   151 | System <unset>           | 2018-02-07 12:31 | Update         |    1
   150 | System <unset>           | 2018-02-06 03:16 | Update         |   29
   149 | root <root>              | 2018-02-05 03:36 | I, O, U        |   33
   148 | root <root>              | 2018-02-04 23:52 | Erase          |    1 EE
   147 | System <unset>           | 2018-02-02 23:39 | Install        |    1
   146 | System <unset>           | 2018-02-02 04:17 | Update         |    4
   145 | System <unset>           | 2018-02-01 00:41 | Erase          |   29 EE
   144 | System <unset>           | 2018-02-01 00:40 | Update         |    3
   143 | System <unset>           | 2018-01-31 04:49 | Update         |    2
   142 | root <root>              | 2018-01-31 03:15 | Update         |    1
   141 | System <unset>           | 2018-01-28 01:11 | Update         |   25
   140 | System <unset>           | 2018-01-20 03:26 | Update         |   52

... but in the Plesk panel I'm still offered the 23 updates (and I don't dare to try it!)

 

[frdho]

Have you rebooted your machine? Do apache & nginx still run?

 

[Sergio Manzi]

Nope, no reboot so far and I don't dare trying it until I'm reasonably sure it will work...

 

[Sergio Manzi]

... and yes, Apache and nginx are working right now, no problem!

 

[Sergio Manzi]

@frdho Your situation might be worst than mine because you had many more updates pending...

Can you publish the output of your "yum history"?

 

[Sergio Manzi]

Latest update:

Now, after some time and having done nothing beside logging out and back into the panel, in the panel's Home page I have the following message:

Warning: Information on some packages might not be actual: inconsistencies were detected in the system's package manager database. Please resolve this issue manually.​

On the other hand, in /admin/pum/updates-list I have, at the same time, the same above warning and a message stating that "All packages are up-to-date".

 

[MarkM]

Guess what I've been watching for 30+ minutes....

 

[Sergio Manzi]

Guess what I've been watching for 30+ minutes....

ahahhah!

If my theory is correct and php-fpm is not part of the updates or you have php-fpm by OS activated, you shouldn't have any problem. Otherwise... welcome to the club!

 

[Sergio Manzi]

ahhh noooo I missed the pop-up in the corner! Then... Welcome to the club, buddy!

 

[MarkM]

annnnnnnd it's dead.

Marks-MacBook-Pro:~ MarkyMark$ ping plesk.wired-solutions.net
PING plesk.wired-solutions.net (107.189.48.141): 56 data bytes
Request timeout for icmp_seq 0
Request timeout for icmp_seq 1
Request timeout for icmp_seq 2
Request timeout for icmp_seq 3
Request timeout for icmp_seq 4
Request timeout for icmp_seq 5
Request timeout for icmp_seq 6
Request timeout for icmp_seq 7
Request timeout for icmp_seq 8
Request timeout for icmp_seq 9
Request timeout for icmp_seq 10
Request timeout for icmp_seq 11

 

[Sergio Manzi]

... worst than mine... what's the stuck pum child?

EDIT: the above is a moronic question: if you can't ping it, you probably can't ssh into it neither...

 

[MarkM]

... worst than mine... what's the stuck pum child?

We shall find out soon. I'm about to mount the data to another server.

 

[MarkM]

Alright that was strange. I was able to get the VM going by switching to a different kernel, so that's unrelated to the issue and YES, php-fpm packages were part of the update. (I didn't realize I had a Package Update Manager notification chillin' in my inbox) Logging into Plesk after I recovered it said 31 updates completed when it originally said 5 but a yum update shows no packages marked for update. I'm fixed.

 

[Sergio Manzi]

... but you had php-fpm (OS version) enabled in your "PHP Settings", right?

 

[MarkM]

Negative, disabled all outdated.

 

[Sergio Manzi]

... and it got stuck: I'd say that on update (1) it tries to re-start the service (2) the service cannot start as it is not correctly configured, (3) goto 1

But in your case yum is in a merry state, while mine is feeling a little bit sick:

# yum check
Loaded plugins: fastestmirror
cloud-init-0.7.9-9.el7.centos.6.x86_64 is a duplicate with cloud-init-0.7.9-9.el7.centos.2.x86_64
iptables-1.4.21-18.3.el7_4.x86_64 is a duplicate with iptables-1.4.21-18.2.el7_4.x86_64
libgcc-4.8.5-16.el7_4.2.x86_64 is a duplicate with libgcc-4.8.5-16.el7_4.1.x86_64
libgomp-4.8.5-16.el7_4.2.x86_64 is a duplicate with libgomp-4.8.5-16.el7_4.1.x86_64
libgudev1-219-42.el7_4.10.x86_64 is a duplicate with libgudev1-219-42.el7_4.7.x86_64
libstdc++-4.8.5-16.el7_4.2.x86_64 is a duplicate with libstdc++-4.8.5-16.el7_4.1.x86_64
libteam-1.25-6.el7_4.3.x86_64 is a duplicate with libteam-1.25-5.el7.x86_64
php-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-5.4.16-43.el7_4.x86_64
php-cli-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-cli-5.4.16-43.el7_4.x86_64
php-common-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-common-5.4.16-43.el7_4.x86_64
php-fpm-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-fpm-5.4.16-43.el7_4.x86_64
php-gd-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-gd-5.4.16-43.el7_4.x86_64
php-mbstring-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-mbstring-5.4.16-43.el7_4.x86_64
php-mysql-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-mysql-5.4.16-43.el7_4.x86_64
php-pdo-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-pdo-5.4.16-43.el7_4.x86_64
php-xml-5.4.16-43.el7_4.1.x86_64 is a duplicate with php-xml-5.4.16-43.el7_4.x86_64
python-perf-3.10.0-693.21.1.el7.x86_64 is a duplicate with python-perf-3.10.0-693.17.1.el7.x86_64
selinux-policy-3.13.1-166.el7_4.9.noarch is a duplicate with selinux-policy-3.13.1-166.el7_4.7.noarch
selinux-policy-targeted-3.13.1-166.el7_4.9.noarch is a duplicate with selinux-policy-targeted-3.13.1-166.el7_4.7.noarch
systemd-219-42.el7_4.10.x86_64 is a duplicate with systemd-219-42.el7_4.7.x86_64
systemd-libs-219-42.el7_4.10.x86_64 is a duplicate with systemd-libs-219-42.el7_4.7.x86_64
systemd-sysv-219-42.el7_4.10.x86_64 is a duplicate with systemd-sysv-219-42.el7_4.7.x86_64
teamd-1.25-6.el7_4.3.x86_64 is a duplicate with teamd-1.25-5.el7.x86_64
Error: check all

do you have any idea how I can fix this mess?

 

[themew]

Used this a long time ago when something similar happened..

    yum-complete-transaction
    package-cleanup --problems
    package-cleanup --dupes
    package-cleanup --cleandupes
    rpm -Va --nofiles --nodigest

    yum clean all
    rpm --rebuilddb
    yum update