Transaction check error mysql



Upgrading MySQL causes errors

I am running Centos 5.8 (Linux 2.6.18-308.13.1.el5 on x86_64), and wish to upgrade MySQL version 5.0.95. I am using a tutorial found at http://www.if-not-true-then-false.com/2010/install-mysql-on-fedora-centos-red-hat-rhel/. When I get to the following, I get the host of errors. Seems to have something to do with going from 386 to 86×64. Can anyone help? Thanks

2 Answers 2

It looks like you’ve used MySQL packages from the IUS community repo. Unfortunately these packages don’t appear to be 100% compatible with the original packages, and so you get broken dependencies such as this one. Remove all of the existing MySQL packages first (your databases won’t be touched) and then install the packages from the remi repository (which ARE compatible and have no dependency issues).

You also need to be sure you have disabled or removed the conflicting repo (IUS).

It appears from that output that it’s trying to install the new version of mysql alongside the old version, rather than actually upgrading. This is likely explained by the fact that you are trying to install the x86_64 version, but previously you had the i386 version (I think that should be considered either a bug in yum or a bug in the repository you are using, and in fact here is the bug report).

Try explicitly specifying the i386 version of mysql, or using mysqldump to dump the entire instance, uninstalling, and then installing the x86_64 version and importing the dump (you can import dumps taken by mysqldump by piping them into mysql -p , as they are SQL scripts).

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Getting Transaction Check Error with Yum

I needed to install the MSSQL libraries for PHP on a CentOS 5 server and ran into a few issues when installing some of the required dependencies, getting «Transaction Check Error» error messages which indicated conflicts between files in packages.

I had been following through the instructions for installing the MS SQL libraries for PHP at my post and the HowtoForge post, and had the same issue as I’d had the last time: when running «rpmbuild -bb ./php.spec» I had some dependency issues, so went to yum-install them:

However, this time the packages didn’t install nicely, and I got this error message instead:

I had come across an error like this another time, but there were too many packages to have to try that particular solution out on (which is to erase the conflicting packages), and some of them look fairly vital to the system’s health so I didn’t want to start erasing important packages.

Instead I wondered if perhaps doing an update would help to solve the probelm:

After some time, downloading files etc, I got the following error message. This was a little more promising than the original error message as it was only one package causing the issue this time, and not such a vital one:

I tried erasing the file using rpm, but got this error message:

So I used «yum erase» to get rid of it instead:

After that, runnning «yum-update» worked fine. I then repeated the «yum install» command at the top of this post and it worked without any errors this time as well.

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Solving RPM installation conflicts in CentOS 5 and CentOS 6

Lately we’ve had many reports of the RPM packages for CentOS 5 (mostly) and CentOS 6 having issues when installing different combinations of our products, particularly with Percona Toolkit for MySQL. Examples of bugs related to these issues are lp:1031427 and lp:1051874.

These problems arise when trying to install a package from the distribution that is linked against the version of libmysqlclient.so shipped by the distribution (libmysqlclient.so.15 for CentOS 5/libmysqlclient.so.16 for CentOS 6) and a version of Percona Server that depends on another version of libmysqlclient.so, usually more recent. Bug lp:1031427 is an example of this, and shows how the packages would conflict when trying to install libmysqlclient.so.

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For example, when installing php-mysql alongside PS 5.5 in CentOS 6:

# yum -q install Percona-Server-server-55 php-mysql

Installing:
Percona-Server-server-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 15 M
php-mysql x86_64 5.3.3-14.el6_3 updates 79 k
Installing for dependencies:
Percona-Server-client-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 7.0 M
Percona-Server-shared-51 x86_64 5.1.67-rel14.3.506.rhel6 percona 2.8 M
Percona-Server-shared-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 787 k

Is this ok [y/N]: y

Transaction Check Error:
file /usr/lib64/libmysqlclient.so conflicts between attempted installs of Percona-Server-shared-51-5.1.67-rel14.3.506.rhel6.x86_64 and Percona-Server-shared-55-5.5.29-rel29.4.401.rhel6.x86_64
file /usr/lib64/libmysqlclient_r.so conflicts between attempted installs of Percona-Server-shared-51-5.1.67-rel14.3.506.rhel6.x86_64 and Percona-Server-shared-55-5.5.29-rel29.4.401.rhel6.x86_64

The traditional solution for this situation was to provide a special package, Percona-Server-shared-compat (modeled after upstream’s MySQL-shared-compat) which would contain ALL versions of libmysqlclient.so.* together and wouldn’t conflict. Probably some of you are familiar with this approach.

# yum -q install Percona-Server-server-55 Percona-Server-shared-compat php-mysql

Installing:
Percona-Server-server-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 15 M
Percona-Server-shared-compat x86_64 5.5.29-rel29.4.401.rhel6 percona 3.4 M
php-mysql x86_64 5.3.3-14.el6_3 updates 79 k
Installing for dependencies:
Percona-Server-client-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 7.0 M
Percona-Server-shared-55 x86_64 5.5.29-rel29.4.401.rhel6 percona 787 k

Notice how PS-shared-compat installs along the -shared package, providing the older libmysqlclient.so.16 required by php-mysql.

However, this has proved non-intuitive and problematic, since the shared-compat package wouldn’t get selected unless explicitely installed — and many of our users would rather have it “just work” without requiring additional knowledge of what the particular workaround was, etc..

We’re now trying a solution in which our -shared packages won’t conflict anymore at libmysqlclient.so, so we are able to install them side-by-side, modelled after the mysql-libs packages provided by CentOS/Redhat. So even if the user wants to install PS 5.5 alongside packages that depend on 5.1/5.0, the -shared packages will work together. For example installing 5.5 and postfix in CentOS:

# yum -q install Percona-Server-server-55 postfix

Installing:
Percona-Server-server-55 x86_64 5.5.29-rel29.4.402.rhel5 percona-testing 19 M
postfix x86_64 2:2.3.3-6.el5 base 3.8 M
Installing for dependencies:
Percona-SQL-shared-50 x86_64 5.0.92-b23.89.rhel5 percona-testing 1.8 M
Percona-Server-client-55 x86_64 5.5.29-rel29.4.402.rhel5 percona-testing 9.1 M
Percona-Server-shared-55 x86_64 5.5.29-rel29.4.402.rhel5 percona-testing 993 k

… and this will install without problems.

Additionally, this has the advantage of allowing an upgrade from 5.1 to 5.5 without uninstalling any software that depended on the old version.

# rpm -qa | grep ^Percona
Percona-Server-client-51-5.1.67-rel14.3.507.rhel6.x86_64
Percona-Server-shared-51-5.1.67-rel14.3.507.rhel6.x86_64
Percona-Server-server-51-5.1.67-rel14.3.507.rhel6.x86_64

In this case only Percona-Server-client-51 and Percona-Server-server-51 need be removed, allowing any package that depends on Percona-Server-shared-51 (providing libmysqlclient.so.16) to remain installed. After the server and client packages are uninstalled, you can install PS 5.5 without conflict.

The current package candidates for versions 5.0.92 (which required an update), 5.1.67-14.3 and 5.5.29-29.4 can be tested from the percona-testing repository. We encourage you to try these out and send us your feedback and/or file any bugs you find.

We’re aiming to include these fixes in our next releases of Percona Toolkit 5.1 and Percona Toolkit 5.5. Percona Toolkit users in particular will enjoy this update since it’ll mean no more trouble when installing it from repository!

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Author

Ignacio is a former Percona employee.

You rock my repos Ignacio! Thanks so much! 🙂

this is not limited to centos, i had some issues also on debian/ubuntu (don’t know if latest packages works better for dependencies, sorry). while you’re fixing rpm spec file, could you please have a look also to deb ? thanks 🙂

Our debian packages already use these approach — based in the original distribution files for 5.1 in which we based our percona packages.

Of course, this doesn’t mean they’re free of issues 🙂 Have you experienced any when installing our software? If so, please let me know of the particular problem and I’ll take a look into it.

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hello,
nice to meet you!
now,i meet a trouble and need your help!
i setup percona cluster in vm, if in file /etc/my.cnf,i add wsrep_cluster_address=gcomm:// to fill it ,the mysql server will not running

]# vi /etc/my.cnf
[mysqld]
wsrep_provider=/usr/lib/libgalera_smm.so
user=mysql
wsrep_cluster_address=gcomm://
binlog_format=ROW
wsrep_slave_threads=2
wsrep_cluster_name=trimethylxanthine
wsrep_sst_method=rsync
wsrep_node_name=mysql1
innodb_locks_unsafe_for_binlog=1
innodb_autoinc_lock_mode=2

the wrong infomaton :

130221 17:59:00 mysqld_safe WSREP: Running position recovery with –log_error=/tmp/tmp.cuCEbd7883
130221 17:59:05 mysqld_safe WSREP: Recovered position 00000000-0000-0000-0000-000000000000:-1
130221 17:59:05 [Note] WSREP: wsrep_start_position var submitted: ‘00000000-0000-0000-0000-000000000000:-1’
130221 17:59:05 [Note] WSREP: Read nil XID from storage engines, skipping position init
130221 17:59:05 [Note] WSREP: wsrep_load(): loading provider library ‘/usr/lib/libgalera_smm.so’
130221 17:59:05 [Note] WSREP: wsrep_load(): Galera 2.3(r143) by Codership Oy loaded succesfully.
130221 17:59:05 [Note] WSREP: Found saved state: 00000000-0000-0000-0000-000000000000:-1
130221 17:59:05 [Note] WSREP: Reusing existing ‘/var/lib/mysql//galera.cache’.
130221 17:59:05 [Note] WSREP: Passing config to GCS: base_host = 192.168.14.150; base_port = 4567; cert.log_conflicts = no; gcache.dir = /var/lib/mysql/; gcache.keep_pages_size = 0; gcache.mem_size = 0; gcache.name = /var/lib/mysql//galera.cache; gcache.page_size = 128M; gcache.size = 128M; gcs.fc_debug = 0; gcs.fc_factor = 1; gcs.fc_limit = 16; gcs.fc_master_slave = NO; gcs.max_packet_size = 64500; gcs.max_throttle = 0.25; gcs.recv_q_hard_limit = 2147483647; gcs.recv_q_soft_limit = 0.25; gcs.sync_donor = NO; replicator.causal_read_timeout = PT30S; replicator.commit_order = 3
130221 17:59:06 [Note] WSREP: Assign initial position for certification: -1, protocol version: -1
130221 17:59:06 [Note] WSREP: wsrep_sst_grab()
130221 17:59:06 [Note] WSREP: Start replication
130221 17:59:06 [Note] WSREP: Setting initial position to 00000000-0000-0000-0000-000000000000:-1
130221 17:59:06 [Note] WSREP: protonet asio version 0
130221 17:59:06 [Note] WSREP: backend: asio
terminate called after throwing an instance of ‘gu::NotFound’
01:59:06 UTC – mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed,
something is definitely wrong and this may fail.
Please help us make Percona Server better by reporting any
bugs at http://bugs.percona.com/

key_buffer_size=0
read_buffer_size=131072
max_used_connections=0
max_threads=151
thread_count=0
connection_count=0
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 329809 K bytes of memory
Hope that’s ok; if not, decrease some variables in the equation.

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CentOS

The Community ENTerprise Operating System

[SOLVED] Yum Transaction Check Error

[SOLVED] Yum Transaction Check Error

Post by JohnMontes » 2015/02/03 15:06:03

I’m having a tough time trying to get passed a yum transaction check error and cannot update packages on my CentOS 6.6 64bit system.

Below is the error message, a list of commands tried thus far, and the yum repos that I have.

Any tips or suggestions that might help?

Error Message:
Transaction Check Error:
file /usr/lib64/libpostproc.so.51.2.0 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-libpostproc-0.6.5-1.el6.rf.x86_64

Commands I’ve tried thus far
yum-complete-transaction
package-cleanup —dupes
package-cleanup —cleandupes
yum reinstall ffmpeg-compat-0.6.7-1.el6.x86_64
rpm -e —justdb ffmpeg-compat-0.6.7-1.el6.x86_64
yum update ffmpeg-compat-0.6.7-1.el6.x86_64
sudo yum update —skip-broken
sudo rpm -Va —nofiles —nodigest

List of Repos:
* base: centos.expedientevirtual.com
* elrepo: repos.dfw.lax-noc.com
* epel: mirror.cogentco.com
* extras: centos.expedientevirtual.com
* rpmforge: mirror.teklinks.com
* rpmfusion-free-updates: mirror.nexcess.net
* rpmfusion-nonfree-updates: mirror.nexcess.net
* updates: centos.arvixe.com

Re: Yum Transaction Check Error

Post by JohnMontes » 2015/02/03 15:18:17

I was able to get rid of the initial ffmpeg-compat-0.6.7-1.el6.x86_64 conflict by removing the rpmforge repo
$ sudo yum remove rpmforge-release

However, now I get the following after running $ sudo yum update -y —skip-broken

Transaction Check Error:
file /usr/lib64/libpostproc.so.51.2.0 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-libpostproc-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavcodec.so.52.72.2 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavdevice.so.52.2.0 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavfilter.so.1.19.0 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavformat.so.52.64.2 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavutil.so.50.15.1 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libswscale.so.0.11.0 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64

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Re: Yum Transaction Check Error

Post by TrevorH » 2015/02/03 16:23:34

Don’t use —skip-broken, it’s broken and I have no idea why the yum developers put out such a stupid suggestion as part of the error message. It really means «your system is broken, if you want to break it some more then do this»!

Your problem is that you have conflicting packages installed from different third party repos. Your current installation contains a package from rpmforge (hence the .rf. in its name). You’re trying to replace that with a newer package set from a different repo but the packages are structured in a different way. You can either remove the current set of packages first — but that’s likely to want to take out a bunch of other packages which depend on them, or you can try using yum shell to remove one set of packages and install the replacements in one transaction.

Re: Yum Transaction Check Error

Post by JohnMontes » 2015/02/03 17:34:18

Thanks so much for the tip Trevor.
I tried it out, it appeared it was going to work, but then other Transaction errors appeared, below is the sample output.

$ sudo yum shell
Loaded plugins: fastestmirror, refresh-packagekit, security
Setting up Yum Shell
> remove ffmpeg-libpostproc
Setting up Remove Process
> install ffmpeg-compat
Loading mirror speeds from cached hostfile
* base: centos.expedientevirtual.com
* elrepo: repos.dfw.lax-noc.com
* epel: mirror.cogentco.com
* extras: centos.expedientevirtual.com
* rpmfusion-free-updates: mirror.nexcess.net
* rpmfusion-nonfree-updates: mirror.nexcess.net
* updates: centos.arvixe.com
Setting up Install Process
> run
—> Running transaction check
—> Package ffmpeg-compat.x86_64 0:0.6.7-1.el6 will be installed
—> Processing Dependency: libx264.so.120()(64bit) for package: ffmpeg-compat-0.6.7-1.el6.x86_64
—> Package ffmpeg-libpostproc.x86_64 0:0.6.5-1.el6.rf will be erased
—> Running transaction check
—> Package x264-libs.x86_64 0:0.120-5.20120303.el6 will be installed
—> Finished Dependency Resolution

Total size: 2.9 M
Is this ok [y/N]: y
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Error: Transaction Check Error:
file /usr/lib64/libavcodec.so.52.72.2 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavdevice.so.52.2.0 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavfilter.so.1.19.0 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavformat.so.52.64.2 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libavutil.so.50.15.1 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64
file /usr/lib64/libswscale.so.0.11.0 from install of ffmpeg-compat-0.6.7-1.el6.x86_64 conflicts with file from package ffmpeg-0.6.5-1.el6.rf.x86_64

Re: Yum Transaction Check Error

Post by JohnMontes » 2015/02/04 00:27:16

Yeah, the issue is fixed after making a minor adjustment, will mark this post as SOLVED
Thanks for leading in the right direction Trevor

I had to add an additional statement to remove ffmpeg, and then perform the install ffmpeg-compat

yum shell
remove ffmpeg-libpostproc
remove ffmpeg
install ffmpeg-compat
run

> install ffmpeg-compat
Setting up Install Process
Loading mirror speeds from cached hostfile
* base: reflector.westga.edu
* elrepo: ftp.utexas.edu
* epel: mirror.oss.ou.edu
* extras: mirror.cisp.com
* rpmfusion-free-updates: mirror.web-ster.com
* rpmfusion-nonfree-updates: mirror.web-ster.com
* updates: ftpmirror.your.org
> run
—> Running transaction check
—> Package ffmpeg-compat.x86_64 0:0.6.7-1.el6 will be installed
—> Processing Dependency: libx264.so.120()(64bit) for package: ffmpeg-compat-0.6.7-1.el6.x86_64
—> Running transaction check
—> Package x264-libs.x86_64 0:0.120-5.20120303.el6 will be installed
—> Finished Dependency Resolution

Total size: 2.9 M
Installed size: 7.6 M
Is this ok [y/N]: y
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
Installing : x264-libs-0.120-5.20120303.el6.x86_64 1/2
Installing : ffmpeg-compat-0.6.7-1.el6.x86_64 2/2
Verifying : ffmpeg-compat-0.6.7-1.el6.x86_64 1/2
Verifying : x264-libs-0.120-5.20120303.el6.x86_64 2/2

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