Been having trouble updating a centos 7 system.
Here is the output.
Loaded plugins: fastestmirror, priorities
Loading mirror speeds from cached hostfile
* base: centos.den.host-engine.com
* epel: mirror.oss.ou.edu
* extras: mirror.steadfast.net
* kernel-xen: us5.mirror.crc.id.au
* updates: denver.gaminghost.co
Resolving Dependencies
--> Running transaction check
---> Package drush.noarch 0:8.1.7-1.el7 will be updated
---> Package drush.noarch 0:8.1.8-2.el7 will be an update
---> Package libuv.x86_64 1:0.10.34-2.el7 will be updated
--> Processing Dependency: libuv.so.0.10()(64bit) for package: cassandra-cpp-driver-2.2.1-1.el7.remi.x86_64
--> Processing Dependency: libuv.so.0.10()(64bit) for package: php55-php-pecl-cassandra-1.0.1-1.el7.remi.x86_64
---> Package libuv.x86_64 1:1.9.1-1.el7 will be an update
---> Package libvirt.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-client.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-client.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon.x86_64 0:1.3.0-1.el7 will be updated
--> Processing Dependency: libvirt-daemon = 1.3.0-1.el7 for package: libvirt-daemon-driver-libxl-1.3.0-1.el7.x86_64
--> Processing Dependency: libvirt-daemon = 1.3.0-1.el7 for package: libvirt-daemon-driver-xen-1.3.0-1.el7.x86_64
---> Package libvirt-daemon.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-config-network.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-config-network.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-config-nwfilter.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-config-nwfilter.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-driver-interface.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-driver-interface.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-driver-lxc.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-driver-lxc.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-driver-network.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-driver-network.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-driver-nodedev.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-driver-nodedev.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-driver-nwfilter.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-driver-nwfilter.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-driver-qemu.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-driver-qemu.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-driver-secret.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-driver-secret.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-driver-storage.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-driver-storage.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package libvirt-daemon-kvm.x86_64 0:1.3.0-1.el7 will be updated
---> Package libvirt-daemon-kvm.x86_64 0:2.0.0-10.el7_3.2 will be an update
---> Package msgpack.x86_64 0:0.5.8-1.el7 will be updated
--> Processing Dependency: libmsgpack.so.3()(64bit) for package: php55-php-pecl-graphdat-1.0.4-1.el7.remi.x86_64
---> Package msgpack.x86_64 0:1.4.1-1.el7 will be an update
---> Package netcf-libs.x86_64 0:0.2.8-1.el7 will be updated
---> Package netcf-libs.x86_64 0:0.2.8-2.el7 will be an update
---> Package nfs-utils.x86_64 1:1.3.0-0.21.el7_2.1 will be updated
---> Package nfs-utils.x86_64 1:1.3.0-0.33.el7 will be an update
---> Package nodejs.x86_64 0:0.10.46-1.el7 will be updated
---> Package nodejs.x86_64 1:6.9.1-4.el7 will be an update
--> Processing Dependency: npm = 1:3.10.8-1.6.9.1.4.el7 for package: 1:nodejs-6.9.1-4.el7.x86_64
---> Package numad.x86_64 0:0.5-14.20140620git.el7 will be updated
---> Package numad.x86_64 0:0.5-17.20150602git.el7 will be an update
---> Package openscap.x86_64 0:1.2.9-5.el7_2 will be updated
---> Package openscap.x86_64 0:1.2.10-2.el7 will be an update
---> Package parted.x86_64 0:3.1-23.el7 will be updated
---> Package parted.x86_64 0:3.1-28.el7 will be an update
---> Package perl-Sys-Virt.x86_64 0:1.2.17-2.el7 will be updated
---> Package perl-Sys-Virt.x86_64 0:2.0.0-1.el7 will be an update
---> Package php-punic.noarch 0:1.6.3-1.el7 will be updated
---> Package php-punic.noarch 0:1.6.4-1.el7 will be an update
---> Package php-zendframework-zend-diactoros.noarch 0:1.3.3-1.el7 will be updated
---> Package php-zendframework-zend-diactoros.noarch 0:1.3.7-1.el7 will be an update
---> Package qemu-img.x86_64 10:1.5.3-105.el7_2.7 will be updated
---> Package qemu-img.x86_64 10:1.5.3-126.el7 will be an update
---> Package qemu-kvm.x86_64 10:1.5.3-105.el7_2.7 will be updated
---> Package qemu-kvm.x86_64 10:1.5.3-126.el7 will be an update
---> Package qemu-kvm-common.x86_64 10:1.5.3-105.el7_2.7 will be updated
---> Package qemu-kvm-common.x86_64 10:1.5.3-126.el7 will be an update
---> Package quota.x86_64 1:4.01-11.el7_2.1 will be updated
---> Package quota.x86_64 1:4.01-14.el7 will be an update
---> Package quota-nls.noarch 1:4.01-11.el7_2.1 will be updated
---> Package quota-nls.noarch 1:4.01-14.el7 will be an update
---> Package rdma.noarch 0:7.2_4.1_rc6-2.el7 will be updated
---> Package rdma.noarch 0:7.3_4.7_rc2-5.el7 will be an update
---> Package redhat-rpm-config.noarch 0:9.1.0-68.el7.centos will be updated
---> Package redhat-rpm-config.noarch 0:9.1.0-72.el7.centos will be an update
---> Package rpcbind.x86_64 0:0.2.0-33.el7_2.1 will be updated
---> Package rpcbind.x86_64 0:0.2.0-38.el7 will be an update
---> Package rpm.x86_64 0:4.11.3-17.el7 will be updated
---> Package rpm.x86_64 0:4.11.3-21.el7 will be an update
---> Package rpm-build.x86_64 0:4.11.3-17.el7 will be updated
---> Package rpm-build.x86_64 0:4.11.3-21.el7 will be an update
---> Package rpm-build-libs.x86_64 0:4.11.3-17.el7 will be updated
---> Package rpm-build-libs.x86_64 0:4.11.3-21.el7 will be an update
---> Package rpm-devel.x86_64 0:4.11.3-17.el7 will be updated
---> Package rpm-devel.x86_64 0:4.11.3-21.el7 will be an update
---> Package rpm-libs.x86_64 0:4.11.3-17.el7 will be updated
---> Package rpm-libs.x86_64 0:4.11.3-21.el7 will be an update
---> Package rpm-python.x86_64 0:4.11.3-17.el7 will be updated
---> Package rpm-python.x86_64 0:4.11.3-21.el7 will be an update
---> Package rpm-sign.x86_64 0:4.11.3-17.el7 will be updated
---> Package rpm-sign.x86_64 0:4.11.3-21.el7 will be an update
---> Package xz.x86_64 0:5.1.2-12alpha.el7 will be updated
---> Package xz.x86_64 0:5.2.2-1.el7 will be an update
---> Package xz-devel.x86_64 0:5.1.2-12alpha.el7 will be updated
---> Package xz-devel.x86_64 0:5.2.2-1.el7 will be an update
---> Package xz-libs.x86_64 0:5.1.2-12alpha.el7 will be updated
--> Processing Dependency: xz-libs(x86-64) = 5.1.2 for package: perl-Compress-Raw-Lzma-2.061-1.el7.x86_64
---> Package xz-libs.x86_64 0:5.2.2-1.el7 will be an update
--> Running transaction check
---> Package libuv.x86_64 1:0.10.34-2.el7 will be updated
--> Processing Dependency: libuv.so.0.10()(64bit) for package: cassandra-cpp-driver-2.2.1-1.el7.remi.x86_64
--> Processing Dependency: libuv.so.0.10()(64bit) for package: php55-php-pecl-cassandra-1.0.1-1.el7.remi.x86_64
---> Package libvirt-daemon.x86_64 0:1.3.0-1.el7 will be updated
--> Processing Dependency: libvirt-daemon = 1.3.0-1.el7 for package: libvirt-daemon-driver-libxl-1.3.0-1.el7.x86_64
--> Processing Dependency: libvirt-daemon = 1.3.0-1.el7 for package: libvirt-daemon-driver-xen-1.3.0-1.el7.x86_64
---> Package msgpack.x86_64 0:0.5.8-1.el7 will be updated
--> Processing Dependency: libmsgpack.so.3()(64bit) for package: php55-php-pecl-graphdat-1.0.4-1.el7.remi.x86_64
---> Package npm.x86_64 1:3.10.8-1.6.9.1.4.el7 will be installed
---> Package xz-libs.x86_64 0:5.1.2-12alpha.el7 will be updated
--> Processing Dependency: xz-libs(x86-64) = 5.1.2 for package: perl-Compress-Raw-Lzma-2.061-1.el7.x86_64
--> Finished Dependency Resolution
Error: Package: libvirt-daemon-driver-xen-1.3.0-1.el7.x86_64 (@centos-virt-xen)
Requires: libvirt-daemon = 1.3.0-1.el7
Removing: libvirt-daemon-1.3.0-1.el7.x86_64 (@centos-virt-xen)
libvirt-daemon = 1.3.0-1.el7
Updated By: libvirt-daemon-2.0.0-10.el7_3.2.x86_64 (updates)
libvirt-daemon = 2.0.0-10.el7_3.2
Available: libvirt-daemon-1.2.15-104.el7.x86_64 (centos-virt-xen)
libvirt-daemon = 1.2.15-104.el7
Available: libvirt-daemon-2.0.0-10.el7.x86_64 (base)
libvirt-daemon = 2.0.0-10.el7
Error: Package: cassandra-cpp-driver-2.2.1-1.el7.remi.x86_64 (@remi)
Requires: libuv.so.0.10()(64bit)
Removing: 1:libuv-0.10.34-2.el7.x86_64 (@epel)
libuv.so.0.10()(64bit)
Updated By: 1:libuv-1.9.1-1.el7.x86_64 (epel)
Not found
Error: Package: php55-php-pecl-graphdat-1.0.4-1.el7.remi.x86_64 (@remi)
Requires: libmsgpack.so.3()(64bit)
Removing: msgpack-0.5.8-1.el7.x86_64 (@epel)
libmsgpack.so.3()(64bit)
Updated By: msgpack-1.4.1-1.el7.x86_64 (epel)
Not found
Error: Package: php55-php-pecl-cassandra-1.0.1-1.el7.remi.x86_64 (@remi)
Requires: libuv.so.0.10()(64bit)
Removing: 1:libuv-0.10.34-2.el7.x86_64 (@epel)
libuv.so.0.10()(64bit)
Updated By: 1:libuv-1.9.1-1.el7.x86_64 (epel)
Not found
Error: Package: libvirt-daemon-driver-libxl-1.3.0-1.el7.x86_64 (@centos-virt-xen)
Requires: libvirt-daemon = 1.3.0-1.el7
Removing: libvirt-daemon-1.3.0-1.el7.x86_64 (@centos-virt-xen)
libvirt-daemon = 1.3.0-1.el7
Updated By: libvirt-daemon-2.0.0-10.el7_3.2.x86_64 (updates)
libvirt-daemon = 2.0.0-10.el7_3.2
Available: libvirt-daemon-1.2.15-104.el7.x86_64 (centos-virt-xen)
libvirt-daemon = 1.2.15-104.el7
Available: libvirt-daemon-2.0.0-10.el7.x86_64 (base)
libvirt-daemon = 2.0.0-10.el7
Error: Package: perl-Compress-Raw-Lzma-2.061-1.el7.x86_64 (@epel)
Requires: xz-libs(x86-64) = 5.1.2
Removing: xz-libs-5.1.2-12alpha.el7.x86_64 (@base)
xz-libs(x86-64) = 5.1.2-12alpha.el7
Updated By: xz-libs-5.2.2-1.el7.x86_64 (base)
xz-libs(x86-64) = 5.2.2-1.el7
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
appreciate help.
Status:
Active
Comments
Submitted by andreychek on Tue, 12/20/2016 - 19:05 Comment #2
Howdy -- it looks like you have a third party repository enabled there, and it appears that packages from it are conflicting with the CentOS base packages.
My suggestion would be to disable any third party repositories, and then attempt your updates again.
Not sure which ones to disable
yum repolist enabledLoaded plugins: fastestmirror, priorities
Loading mirror speeds from cached hostfile
* base: centos.unixheads.org
* epel: mirror.oss.ou.edu
* extras: mirror.vcu.edu
* kernel-xen: us5.mirror.crc.id.au
* updates: mirror.hmc.edu
repo id repo name status
base/7/x86_64 CentOS-7 - Base 9,363
centos-virt-xen/7/x86_64 CentOS-7 - xen 232
cloudmin-universal Cloudmin Distribution Neutral 96
epel/x86_64 Extra Packages for Enterprise Linux 7 - x86_64 10,936
extras/7/x86_64 CentOS-7 - Extras 435
kernel-xen kernel-xen 106
rhscl-php54-epel-6-x86_64 PHP 5.4 - epel-6-x86_64 56
rhscl-php55-epel-7-x86_64 PHP 5.5 - epel-7-x86_64 45
updates/7/x86_64 CentOS-7 - Updates 393
virtualmin/7/x86_64 RHEL/CentOS/Scientific 7 - x86_64 - Virtualmin 196
virtualmin-universal Virtualmin Distribution Neutral Packages 75
repolist: 21,933
[root@a ~]#
Submitted by andreychek on Tue, 12/20/2016 - 20:29 Comment #4
Hmm, upon closer inspection, it may be related to the Xen packages.
Though it's a bit tough to say, there's quite a few errors there!
Is this particular server running Cloudmin? And if so, is it also acting as a Xen host?
I do see 'create xen instance' under cloudmin: I assume it is acting as Xen host.
When I do recheck config, I get the following error:
The status of your system is being checked to ensure that all enabled features are available, that the mail server is properly configured, and that quotas are active ..
Your system has 3.86 GB of memory, which is at or above the Virtualmin recommended minimum of 256 MB.
BIND DNS server is installed, and the system is configured to use it.
Mail server Postfix is installed and configured.
Postfix can support per-domain outgoing IP addresses, but is not currently configured to do so. This can be setup in the Postfix Mailserver module.
Apache is installed.
The following PHP versions are available : 5.4.16 (/bin/php-cgi), 5.5.30 (/bin/php55-cgi)
PHP versions have changed to 5, 5.5 since last check. Regenerating any missing php.ini files.
Failed to copy /etc/php.ini to /home/a1z/domains/a.a1z.us/etc/php5/php.ini : cp: cannot create regular file '/home/a1z/domains/a.a1z.us/etc/php5/php.ini': No such file or directory
Submitted by andreychek on Tue, 12/20/2016 - 23:46 Comment #7
It's safe to ignore those Config Check warnings -- those should be fixed up in the next Virtualmin version.
Could you try temporarily disabling the centos-virt-xen repo, and the epel repo, run "yum clean all", and then try doing the update again?
After doing all you said in #7, I get the following error:
Loaded plugins: fastestmirror, prioritiesLoading mirror speeds from cached hostfile
* base: mirrors.usinternet.com
* extras: mirror.steadfast.net
* updates: mirror.steadfast.net
Resolving Dependencies
--> Running transaction check
---> Package xz.x86_64 0:5.1.2-12alpha.el7 will be updated
---> Package xz.x86_64 0:5.2.2-1.el7 will be an update
---> Package xz-devel.x86_64 0:5.1.2-12alpha.el7 will be updated
---> Package xz-devel.x86_64 0:5.2.2-1.el7 will be an update
---> Package xz-libs.x86_64 0:5.1.2-12alpha.el7 will be updated
--> Processing Dependency: xz-libs(x86-64) = 5.1.2 for package: perl-Compress-Raw-Lzma-2.061-1.el7.x86_64
---> Package xz-libs.x86_64 0:5.2.2-1.el7 will be an update
--> Finished Dependency Resolution
Error: Package: perl-Compress-Raw-Lzma-2.061-1.el7.x86_64 (@epel)
Requires: xz-libs(x86-64) = 5.1.2
Removing: xz-libs-5.1.2-12alpha.el7.x86_64 (@base)
xz-libs(x86-64) = 5.1.2-12alpha.el7
Updated By: xz-libs-5.2.2-1.el7.x86_64 (base)
xz-libs(x86-64) = 5.2.2-1.el7
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
even after manually installing perl-Compress-Raw-Lzma using
cpan Compress::Raw::Lzmaas rootSubmitted by andreychek on Wed, 12/21/2016 - 09:03 Comment #9
Okay, that's a step in the right direction!
Do you know what is using the perl-Compress-Raw-Lzma package, which is from EPEL?
That package isn't installed by default on a typical CentOS system, and it looks like there are dependency issues it's causing.
I'm wondering if maybe we can remove it, but I'm reluctant to do that without knowing what it's being used for.
Don't know how to find which program/package is using it. But this is what I get when I run
yum remove perl-Compress-Raw-Lzma-2.061-1.el7Loaded plugins: fastestmirror, priorities
Resolving Dependencies
--> Running transaction check
---> Package perl-Compress-Raw-Lzma.x86_64 0:2.061-1.el7 will be erased
--> Processing Dependency: perl(Compress::Raw::Lzma) >= 2.061 for package: perl-IO-Compress-Lzma-2.061-1.el7.noarch
--> Running transaction check
---> Package perl-IO-Compress-Lzma.noarch 0:2.061-1.el7 will be erased
--> Processing Dependency: perl(IO::Compress::Xz) for package: perl-Fsdb-2.61-1.el7.noarch
--> Running transaction check
---> Package perl-Fsdb.noarch 0:2.61-1.el7 will be erased
--> Finished Dependency Resolution
Dependencies Resolved
===============================================================================================================================================
Package Arch Version Repository Size
===============================================================================================================================================
Removing:
perl-Compress-Raw-Lzma x86_64 2.061-1.el7 @epel 107 k
Removing for dependencies:
perl-Fsdb noarch 2.61-1.el7 @epel 1.3 M
perl-IO-Compress-Lzma noarch 2.061-1.el7 @epel 138 k
Transaction Summary
===============================================================================================================================================
Remove 1 Package (+2 Dependent packages)
Installed size: 1.6 M
Is this ok [y/N]:
I did not remove it yet!
Submitted by andreychek on Wed, 12/21/2016 - 11:44 Comment #11
Okay, that looks like 3 Perl modules.
If you run into problems, you can certainly reinstall those 3 modules from EPEL... or you could even install those outside of EPEL, just using: cpan -i PERL_MODULE_NAME
So you should be okay removing those, and then trying to perform your system updates again.
Thanks Andrew. After removing the lzma package, installation succeeded.
The only remaining/other problem is that of php, which you said will be taken care of in next vm version
Thanks again.