Issue yum fails duplicated packages

[ludm]

Hello,
I have Plesk 12.0.x on an CentOS and I have a problem with duplicated packages when I try to update with yum.

I have seen some solutions to solve this, but I would like to know if it safe to do this. And if not safe, how could I do a backup of the system (not only website) before running these commands.

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

yum clean all
rpm --rebuilddb
yum update

 

[IgorG]

I would not recommend using this radical method with rebuilding rpm base, etc.
What do you mean "problem with duplicated packages"? Packages with different architecture (x86 and 64bit)?
And there are many third-party software for backup whole servers. Acronis True Image, for instance, etc.

 

[ludm]

By problem, I mean this situation:
I have tried to update libcurl (for Paypal communication) and I have the following:

[root@nsXXXXXXX ~]# rpm -Uvh http://www.city-fan.org/ftp/contrib/yum-repo/rhel6/x86_64/city-fan.org-release-1-13.rhel6.noarch.rpm
R▒cup▒ration de http://www.city-fan.org/ftp/contrib/yum-repo/rhel6/x86_64/city-fan.org-release-1-13.rhel6.noarch.rpm
attention: /var/tmp/rpm-tmp.S63a1C: Ent▒te V3 DSA/SHA1 Signature, key ID b56a8bac: NOKEY
Pr▒paration... ########################################### [100%]
paquetage city-fan.org-release-1-13.rhel6.noarch d▒j▒ install▒
[root@nsXXXXXXX ~]# yum install libcurl
Modules compl▒mentaires charg▒s▒: fastestmirror, priorities
Configuration du processus d'installation
Loading mirror speeds from cached hostfile
* atomic: www4.atomicorp.com
* base: centos.trisect.eu
* city-fan.org: www.city-fan.org
* extras: centos.trisect.eu
* updates: centos.trisect.eu
195 packages excluded due to repository priority protections
R▒solution des d▒pendances
--> Lancement de la transaction de test
---> Package libcurl.x86_64 0:7.19.7-37.el6_5.3 will be mis ▒ jour
--> Traitement de la d▒pendance▒: libcurl = 7.19.7-37.el6_5.3 pour le paquet▒: libcurl-devel-7.19.7-37.el6_5.3.x86_64
--> Traitement de la d▒pendance▒: libcurl = 7.19.7-37.el6_5.3 pour le paquet▒: curl-7.19.7-37.el6_5.3.x86_64
---> Package libcurl.x86_64 0:7.50.3-1.0.cf.rhel6 will be an update
--> Traitement de la d▒pendance▒: libssh2(x86-64) >= 1.7.0 pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
--> Traitement de la d▒pendance▒: c-ares(x86-64) >= 1.11.0 pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
--> Traitement de la d▒pendance▒: libnghttp2.so.14()(64bit) pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
--> Traitement de la d▒pendance▒: libcares.so.2()(64bit) pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
--> Lancement de la transaction de test
---> Package c-ares.x86_64 0:1.11.0-1.0.cf.rhel6 will be install▒
---> Package curl.x86_64 0:7.19.7-37.el6_5.3 will be mis ▒ jour
---> Package curl.x86_64 0:7.50.3-1.0.cf.rhel6 will be an update
--> Traitement de la d▒pendance▒: libmetalink.so.3()(64bit) pour le paquet▒: curl-7.50.3-1.0.cf.rhel6.x86_64
---> Package libcurl.x86_64 0:7.50.3-1.0.cf.rhel6 will be an update
--> Traitement de la d▒pendance▒: libssh2(x86-64) >= 1.7.0 pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
--> Traitement de la d▒pendance▒: libnghttp2.so.14()(64bit) pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
---> Package libcurl-devel.x86_64 0:7.19.7-37.el6_5.3 will be mis ▒ jour
---> Package libcurl-devel.x86_64 0:7.50.3-1.0.cf.rhel6 will be an update
--> Traitement de la d▒pendance▒: openssl-devel pour le paquet▒: libcurl-devel-7.50.3-1.0.cf.rhel6.x86_64
--> Traitement de la d▒pendance▒: libssh2-devel pour le paquet▒: libcurl-devel-7.50.3-1.0.cf.rhel6.x86_64
--> Lancement de la transaction de test
---> Package libcurl.x86_64 0:7.50.3-1.0.cf.rhel6 will be an update
--> Traitement de la d▒pendance▒: libssh2(x86-64) >= 1.7.0 pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
--> Traitement de la d▒pendance▒: libnghttp2.so.14()(64bit) pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
---> Package libmetalink.x86_64 0:0.1.2-9.rhel6 will be install▒
---> Package libssh2-devel.x86_64 0:0.18-10.el6.art will be install▒
--> Traitement de la d▒pendance▒: libssh2 = 0.18-10.el6.art pour le paquet▒: libssh2-devel-0.18-10.el6.art.x86_64
---> Package openssl-devel.x86_64 0:1.0.1e-48.el6_8.3 will be install▒
--> Traitement de la d▒pendance▒: krb5-devel pour le paquet▒: openssl-devel-1.0.1e-48.el6_8.3.x86_64
--> Lancement de la transaction de test
---> Package krb5-devel.x86_64 0:1.10.3-57.el6 will be install▒
--> Traitement de la d▒pendance▒: krb5-libs = 1.10.3-57.el6 pour le paquet▒: krb5-devel-1.10.3-57.el6.x86_64
--> Traitement de la d▒pendance▒: libselinux-devel pour le paquet▒: krb5-devel-1.10.3-57.el6.x86_64
--> Traitement de la d▒pendance▒: libcom_err-devel pour le paquet▒: krb5-devel-1.10.3-57.el6.x86_64
--> Traitement de la d▒pendance▒: keyutils-libs-devel pour le paquet▒: krb5-devel-1.10.3-57.el6.x86_64
---> Package libcurl.x86_64 0:7.50.3-1.0.cf.rhel6 will be an update
--> Traitement de la d▒pendance▒: libssh2(x86-64) >= 1.7.0 pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
--> Traitement de la d▒pendance▒: libnghttp2.so.14()(64bit) pour le paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64
---> Package libssh2-devel.x86_64 0:0.18-10.el6.art will be install▒
--> Traitement de la d▒pendance▒: libssh2 = 0.18-10.el6.art pour le paquet▒: libssh2-devel-0.18-10.el6.art.x86_64
...
--> Traitement de la d▒pendance▒: libssh2 = 0.18-10.el6.art pour le paquet▒: libssh2-devel-0.18-10.el6.art.x86_64
--> R▒solution des d▒pendances termin▒e
Erreur▒: Paquet▒: e2fsprogs-1.41.12-14.el6_4.2.x86_64 (@updates)
Requiert▒: libcom_err = 1.41.12-14.el6_4.2
Suppression▒: libcom_err-1.41.12-14.el6_4.2.x86_64 (@updates)
libcom_err = 1.41.12-14.el6_4.2
Mis ▒ jour par▒: libcom_err-1.41.12-22.el6.x86_64 (base)
libcom_err = 1.41.12-22.el6
Suppression▒: libcom_err-1.41.12-21.el6.x86_64 (installed)
libcom_err = 1.41.12-21.el6
Mis ▒ jour par▒: libcom_err-1.41.12-22.el6.x86_64 (base)
libcom_err = 1.41.12-22.el6
Erreur▒: Paquet▒: libcurl-7.50.3-1.0.cf.rhel6.x86_64 (city-fan.org)
Requiert▒: libnghttp2.so.14()(64bit)
Erreur▒: Paquet▒: libselinux-utils-2.0.94-5.3.el6_4.1.x86_64 (@updates)
Requiert▒: libselinux = 2.0.94-5.3.el6_4.1
Suppression▒: libselinux-2.0.94-5.3.el6_4.1.x86_64 (@updates)
libselinux = 2.0.94-5.3.el6_4.1
Mis ▒ jour par▒: libselinux-2.0.94-7.el6.x86_64 (base)
libselinux = 2.0.94-7.el6
Suppression▒: libselinux-2.0.94-5.8.el6.x86_64 (installed)
libselinux = 2.0.94-5.8.el6
Mis ▒ jour par▒: libselinux-2.0.94-7.el6.x86_64 (base)
libselinux = 2.0.94-7.el6
....
Vous pouvez essayer d'utiliser --skip-broken pour contourner le probl▒me
** 99 probl▒mes RPMDB pr▒-existants trouv▒s, la sortie de ▒▒yum check▒▒ est la suivante▒:
atk-1.30.0-1.el6.x86_64 est un doublon de atk-1.28.0-2.el6.x86_64
audit-libs-2.3.7-5.el6.x86_64 est un doublon de audit-libs-2.2-2.el6.x86_64
...
...

 

[IgorG]

What is output of commands:

# rpm -qa --qf '%{NAME}-%{VERSION}-%{RELEASE} (%{ARCH})\n' | grep libselinux
# rpm -qa --qf '%{NAME}-%{VERSION}-%{RELEASE} (%{ARCH})\n' | grep libcom_err

?

 

[ludm]

Here is the output :

# rpm -qa --qf '%{NAME}-%{VERSION}-%{RELEASE} (%{ARCH})\n' | grep libselinux
libselinux-utils-2.0.94-5.8.el6 (x86_64)
libselinux-utils-2.0.94-5.3.el6_4.1 (x86_64)
libselinux-2.0.94-5.8.el6 (x86_64)
libselinux-2.0.94-5.3.el6_4.1 (x86_64)

# rpm -qa --qf '%{NAME}-%{VERSION}-%{RELEASE} (%{ARCH})\n' | grep libcom_err
libcom_err-1.41.12-21.el6 (x86_64)
libcom_err-1.41.12-14.el6_4.2 (x86_64)
[root@nsXXXXXX ~]#

 

[IgorG]

Well, try to remove old versions with something like

# rpm -e libcom_err-1.41.12-14.el6_4.2 libselinux-2.0.94-5.3.el6_4.1

 

[ludm]

Thanks, I'll try this.
I have few questions:
Is it "risky" ? ;-)
How do you know that libcom_err-1.41.12-14.el6_4.2 (x86_64) is older than libcom_err-1.41.12-21.el6 (x86_64) ?

The following commands don't remove the old versions ?
package-cleanup –dupes # list out duplicates
package-cleanup –cleandupes # clean up duplicates

 

[IgorG]

How do you know that libcom_err-1.41.12-14.el6_4.2 (x86_64) is older than libcom_err-1.41.12-21.el6 (x86_64) ?

Number of version.
Also you can check 'Build data' in output of

# rpm -qi libcom_err-1.41.12-14.el6_4.2
# rpm -qi libcom_err-1.41.12-21.el6

 

[ludm]

Sorry, I haven't seen the 12-14 and 12-21 difference, I thought it was between el6 and el6_4.2

 

[ludm]

I have ran the command with --test, here is the result :

# rpm -e --test libcom_err-1.41.12-14.el6_4.2
erreur: D▒pendances requises: (required dependencies)

# rpm -e --test libcom_err-1.41.12-14.el6_4.2
erreur: D▒pendances requises:(required dependencies)
        libcom_err = 1.41.12-14.el6_4.2 est n▒cessaire pour (d▒j▒ install▒) libss-1.41.12-14.el6_4.2.x86_64
        libcom_err = 1.41.12-14.el6_4.2 est n▒cessaire pour (d▒j▒ install▒) e2fsprogs-libs-1.41.12-14.el6_4.2.x86_64
        libcom_err = 1.41.12-14.el6_4.2 est n▒cessaire pour (d▒j▒ install▒) e2fsprogs-1.41.12-14.el6_4.2.x86_64
# rpm -e --test libcom_err-1.41.12-21.el6
erreur: D▒pendances requises:(required dependencies)
        libcom_err = 1.41.12-21.el6 est n▒cessaire pour (d▒j▒ install▒) e2fsprogs-libs-1.41.12-21.el6.x86_64
        libcom_err = 1.41.12-21.el6 est n▒cessaire pour (d▒j▒ install▒) libss-1.41.12-21.el6.x86_64
        libcom_err = 1.41.12-21.el6 est n▒cessaire pour (d▒j▒ install▒) e2fsprogs-1.41.12-21.el6.x86_64
# rpm -e --test libselinux-2.0.94-5.8.el6
erreur: D▒pendances requises:(required dependencies)
        libselinux = 2.0.94-5.8.el6 est n▒cessaire pour (d▒j▒ install▒) libselinux-utils-2.0.94-5.8.el6.x86_64
# rpm -e --test libselinux-2.0.94-5.3.el6_4.1
erreur: D▒pendances requises:(required dependencies)
        libselinux = 2.0.94-5.3.el6_4.1 est n▒cessaire pour (d▒j▒ install▒) libselinux-utils-2.0.94-5.3.el6_4.1.x86_64

 

[ludm]

How can I do as all versions seems to have dependencies ?

 

[IgorG]

How can I do as all versions seems to have dependencies ?

I would suggest you contact Plesk Support Team. Looks like there is a serious mix of packages on your server, and these complex dependencies issue can be resolved by experienced Plesk supporters only directly on your server.