SOGo does not start - segfault error 6 in libgnustep-base

pagaille · May 20, 2020, 8:08pm

Does that help ?

rpm -qi gnustep-base
Name        : gnustep-base
Version     : 1.24.6
Release     : 6.el7.centos
Architecture: x86_64
Install Date: Wed 20 May 2020 08:43:54 PM CEST
Group       : Development/Libraries
Size        : 2586189
License     : LGPLv2+ and GPLv2+ and GPLv3+
Signature   : RSA/SHA1, Mon 18 Jul 2016 02:26:56 PM CEST, Key ID 9cb28ea039baf5c1
Source RPM  : gnustep-base-1.24.6-6.el7.centos.src.rpm
Build Date  : Wed 15 Oct 2014 09:03:30 PM CEST
Build Host  : shiva.inverse
Relocations : (not relocatable)
URL         : http://www.gnustep.org/
Summary     : GNUstep Base library package

and

# yum repoinfo 
Loaded plugins: changelog, fastestmirror, nethserver_events, remove-with-leaves
Loading mirror speeds from cached hostfile
 * ce-base: mirrors.coreix.net
 * ce-extras: mirrors.coreix.net
 * ce-sclo-rh: mirrors.coreix.net
 * ce-sclo-sclo: mirrors.coreix.net
 * ce-updates: mirrors.coreix.net
 * epel: mirrors.n-ix.net
 * nethforge: mirror.alpix.eu
 * nethserver-base: mirror.alpix.eu
 * nethserver-updates: mirror.alpix.eu
Repo-id      : ce-base/7/x86_64
Repo-name    : CE-Base-7.8.2003
Repo-revision: 1587512243
Repo-updated : Wed Apr 22 01:37:50 2020
Repo-pkgs    : 10,070
Repo-size    : 8.9 G
Repo-mirrors : http://mirrorlist.nethserver.org/?release=7&repo=ce-base&arch=x86_64&nsrelease=7.8.2003
Repo-baseurl : http://mirrors.coreix.net/centos/7.8.2003/os/x86_64/ (9 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:20 2020)
  Filter     : read-only:present
Repo-filename: /etc/yum.repos.d/NethServer.repo

Repo-id      : ce-extras/7/x86_64
Repo-name    : CE-Extras-7.8.2003
Repo-revision: 1588115200
Repo-updated : Wed Apr 29 01:06:41 2020
Repo-pkgs    : 392
Repo-size    : 571 M
8.2003
Repo-baseurl : http://mirrors.coreix.net/centos/7.8.2003/extras/x86_64/ (9 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:20 2020)
  Filter     : read-only:present
Repo-filename: /etc/yum.repos.d/NethServer.repo

Repo-id      : ce-sclo-rh/7/x86_64
Repo-name    : CE-SCLo-rh-7.8.2003
Repo-revision: 1587378242
Repo-updated : Mon Apr 20 12:24:02 2020
Repo-pkgs    : 6,509
Repo-size    : 6.0 G
Repo-mirrors : http://mirrorlist.nethserver.org/?release=7&repo=ce-sclo-rh&arch=x86_64&nsrelease=7.8.2003
Repo-baseurl : http://mirrors.coreix.net/centos/7.8.2003/sclo/x86_64/rh/ (9 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:20 2020)
  Filter     : read-only:present
Repo-filename: /etc/yum.repos.d/NethServer.repo

Repo-id      : ce-sclo-sclo/7/x86_64
Repo-name    : CE-SCLo-sclo-7.8.2003
Repo-revision: 1589804896
Repo-updated : Mon May 18 14:28:16 2020
Repo-pkgs    : 796
Repo-size    : 271 M
Repo-mirrors : http://mirrorlist.nethserver.org/?release=7&repo=ce-sclo-sclo&arch=x86_64&nsrelease=7.8.2003
Repo-baseurl : http://mirrors.coreix.net/centos/7.8.2003/sclo/x86_64/sclo/ (9 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:20 2020)
  Filter     : read-only:present
Repo-filename: /etc/yum.repos.d/NethServer.repo

Repo-id      : ce-updates/7/x86_64
Repo-name    : CE-Updates-7.8.2003
Repo-revision: 1589552075
Repo-updated : Fri May 15 16:14:40 2020
Repo-pkgs    : 671
Repo-size    : 2.7 G
Repo-mirrors : http://mirrorlist.nethserver.org/?release=7&repo=ce-updates&arch=x86_64&nsrelease=7.8.2003
Repo-baseurl : http://mirrors.coreix.net/centos/7.8.2003/updates/x86_64/ (9 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:20 2020)
  Filter     : read-only:present
Repo-filename: /etc/yum.repos.d/NethServer.repo

Repo-id      : epel/x86_64
Repo-name    : Extra Packages for Enterprise Linux 7 - x86_64
Repo-revision: 1589935208
Repo-updated : Wed May 20 02:41:44 2020
Repo-pkgs    : 13,269
Repo-size    : 15 G
Repo-metalink: https://mirrors.fedoraproject.org/metalink?repo=epel-7&arch=x86_64&infra=stock&content=centos
  Updated    : Wed May 20 02:41:44 2020
Repo-baseurl : https://mirrors.n-ix.net/fedora-epel/7/x86_64/ (100 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 20:42:52 2020)
  Filter     : read-only:present
Repo-exclude : gnustep*
Repo-excluded: 7
Repo-filename: /etc/yum.repos.d/epel.repo

Repo-id      : nethforge/7/x86_64
Repo-name    : NethForge 7
Repo-revision: 1589655575
Repo-updated : Sat May 16 20:59:36 2020
Repo-pkgs    : 171
Repo-size    : 729 M
Repo-mirrors : http://mirrorlist.nethserver.org/?release=7&repo=nethforge&arch=x86_64&nsrelease=7.8.2003
Repo-baseurl : https://mirror.alpix.eu/nethserver/7.8.2003/nethforge/x86_64/ (17 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:21 2020)
  Filter     : read-only:present
Repo-filename: /etc/yum.repos.d/NethForge.repo

Repo-id      : nethserver-base/7/x86_64
Repo-name    : NethServer-7.8.2003 - Base
Repo-revision: 1588949715
Repo-updated : Fri May  8 16:55:20 2020
Repo-pkgs    : 363
Repo-size    : 1.3 G
Repo-mirrors : http://mirrorlist.nethserver.org/?release=7&repo=base&arch=x86_64&nsrelease=7.8.2003
Repo-baseurl : https://mirror.alpix.eu/nethserver/7.8.2003/base/x86_64/ (17 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:21 2020)
  Filter     : read-only:present
Repo-filename: /etc/yum.repos.d/NethServer.repo

Repo-id      : nethserver-updates/7/x86_64
Repo-name    : NethServer-7.8.2003 - Updates
Repo-revision: 1589880763
Repo-updated : Tue May 19 11:32:44 2020
Repo-pkgs    : 35
Repo-size    : 378 M
Repo-mirrors : http://mirrorlist.nethserver.org/?release=7&repo=updates&arch=x86_64&nsrelease=7.8.2003
Repo-baseurl : https://mirror.alpix.eu/nethserver/7.8.2003/updates/x86_64/ (17 more)
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:21 2020)
  Filter     : read-only:present
Repo-filename: /etc/yum.repos.d/NethServer.repo

Repo-id      : stephdl/7
Repo-name    : Stephdl (Stephane de Labrusse) repository for nethserver 7 - x86_64
Repo-revision: 1589994001
Repo-updated : Wed May 20 19:00:19 2020
Repo-pkgs    : 198
Repo-size    : 266 M
Repo-baseurl : http://mirror.de-labrusse.fr/NethServer/7/
Repo-expire  : 21,600 second(s) (last: Wed May 20 19:13:21 2020)
  Filter     : read-only:present
Repo-excluded: 189
Repo-filename: /etc/yum.repos.d/stephdl.repo

repolist: 32,474

pagaille · May 20, 2020, 8:11pm

Yep I remember having read that Sogo provides that library. And it seems to me that I saw that my (working) version is coming from nethforge.

mark_nl · May 20, 2020, 8:14pm

Will try to hunt it down later, however are you settled now?

mark_nl · May 21, 2020, 5:53am

Probably one of the AutoReqProv: off in the SPEC files sheds light on this mystery.

To be frank just learned about the Automatic Dependencies option;
This while I am responsible for porting the Spec files from upstream Sogo to NethForge.

Do not want to change it. It worked pretty good last years, @stephdl what do you think?

BTW next time we build SOGo we should update libwbxml. This may improve / introduce ActiveSync (EAS) 16 support.

pagaille · May 21, 2020, 8:59am

I don’t know exactly what’s going on but this dependency problem should be fixed I guess, or at least fully understood.

@mrmarkuz seems to be able to run Sogo with gnustep-base-1.24.9-1 while I can’t… And further there are different versions floating around and we don’t know why… That’s a bit too much to be left as is IMHO

pagaille · May 21, 2020, 10:08am

Have a look a this Sogo Install Guide :

SOGo relies on the GNUstep packages provided by Inverse and must not use the packages from EPEL. Adjust the repository definition to exclude those packages:

sed -i ‘/enabled=1/a
exclude=gnustep*’ /etc/yum.repos.d/epel.repo

mark_nl · May 21, 2020, 11:13am

Through the years, me (and others) installed nethserver-sogo dozen times. And until now we have 3 known reports, two from 2 years ago with sogo version 3.2, of a issue with libgnustep-* from epel.
I remember it was a issue with sogo 2.x on centos 6 before the version-2 branch got re-based to version 3.

We have been trough multiple updates (in-place) since then…

Given: never tried to reinstall a newer version of sogo after removal. Meaning the mismatch of the library could be related to yum/rpm too.

This being said,
IMO the risk we are going to break all those other installs is bigger than trying to salvage the incidental occurrences.

pagaille · May 21, 2020, 4:13pm

I see your point. Maybe you could simply add the gnustep* epel exclusion when installing nethserver-sogo ? After all that’s the safest and recommended way.

That said, my installation still doesn’t work. It’s hard to debug because there is virtually no log.

The only thing I see is that the sogo database and user are created, but not the tables. Appart from that, the daemon tries to start and then give up.

There is a mention of that problem here and there but no fix provided. There is even a bug report that is marked as solved.

mark_nl · May 21, 2020, 4:29pm

My point is, i do not want to change all future installs because of what seems to be a rare occurrence.

Please note if we would do this all former installations will remain having the epel library’s installed - forever - until the quirky internal “provide” supersede the epel version.

I’m sorry to say, and realy want to help you out, but thinking more and more about this: It;s realy bad idea, only worth the risk if it would happen more.

The real issue is how ot remove all package’s and get in par with fresh installs. Unfortunate yum (pardon my words) S*ck& at this.

mark_nl · May 21, 2020, 5:08pm

Does the data base from your old install (which is still present) contain valuable data?,
in other words could we drop the old database?

stephdl · May 21, 2020, 7:16pm

normally we have backup of sogo database I think

pagaille · May 21, 2020, 7:22pm

Nope. I deleted it altogether.

stephdl · May 21, 2020, 7:27pm

I can see in sope.spec and sogo.spec : AutoReqProv: off
But in the doc and my other spec I can read : AutoReqProv: no

Indeed we could try to fix for the other version, but I bet my trouser that it won’t fix your issue.

For libwbxml need to check

mark_nl · May 21, 2020, 7:55pm

I presume you mean you deleted it from disk, this does nont mean mariadb (mysql) “knows” it is gone.

It’d been a while since there was a need to “drop” a db from mysql. It is not on my finger tips, something like:

EDIT: (see below)

mysql -e "drop database sogo;"

~~mysql --defaults-file=/root/.my.cnf drop database sogo; exit~~

~~not sure about the above (@ support_team help!)~~ , however you manage to drop the db

you may run:
signal-event nethserver-sogo-update

stephdl · May 21, 2020, 8:02pm

well the build failed

mark_nl · May 21, 2020, 8:05pm

Let me investigate…

stephdl · May 21, 2020, 8:05pm

Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.5VUYC4
+ umask 022
+ cd /builddir/build/BUILD
+ cd libwbxml-0.11.6
+ cd x86_64-redhat-linux-gnu
+ ctest
*********************************
No test configuration file found!
*********************************
ctest version 2.8.12.2
Usage

You have some missing docs also to remove, but this is the worst error I think

mark_nl · May 21, 2020, 8:17pm

it a long while ago (1y and 8m) sogo 4.0.1, can not remember how… It did build though…

You may put a project card in nethforge project and assign me.

do you think my recollection of dropping sogo the db adds up?

mrmarkuz · May 21, 2020, 8:23pm

That should work but defining the conf file should not be necessary and with -e you get a one liner:

mysql -e "drop database sogo;"

pagaille · May 22, 2020, 5:28am

I should have been more specific. I dropped the database. The user and the DB are created but not the tables. That’s all I can say.

Do you mean that the version provided by nethforge is not the latest ? Then it could be the bug I mentioned earlier that triggers. It is said to be fixed in 4.0.8, maybe you could provide a new version ? Can I help ?

Thank you anyway !