Here is the error I begin to get with yum on some servers running CentOS 5.
root@server:~# yum update -y
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: yum.keepitsecure.net
* update: yum.keepitsecure.net
base 100% |=========================| 951 B 00:00
update 100% |=========================| 951 B 00:00
Excluding Packages in global exclude list
Finished
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package pam.i386 0:0.99.6.2-3.27.el5 set to be updated
---> Package net-snmp.x86_64 1:5.3.1-24.el5_2.1 set to be updated
---> Package krb5-devel.i386 0:1.6.1-25.el5 set to be updated
---> Package bash.x86_64 0:3.2-21.el5 set to be updated
---> Package device-mapper.i386 0:1.02.24-1.el5 set to be updated
---> Package e2fsprogs.x86_64 0:1.39-15.el5 set to be updated
---> Package glibc-headers.x86_64 0:2.5-24 set to be updated
---> Package krb5-devel.x86_64 0:1.6.1-25.el5 set to be updated
---> Package openssh.x86_64 0:4.3p2-26.el5 set to be updated
---> Package audit-libs.i386 0:1.6.5-9.el5 set to be updated
---> Package ghostscript.i386 0:8.15.2-9.3.el5 set to be updated
---> Package libselinux.x86_64 0:1.33.4-5.el5 set to be updated
---> Package glibc-devel.i386 0:2.5-24 set to be updated
---> Package dhclient.x86_64 12:3.0.5-13.el5 set to be updated
---> Package libX11.i386 0:1.0.3-9.el5 set to be updated
---> Package sudo.x86_64 0:1.6.8p12-12.el5 set to be updated
---> Package ghostscript.x86_64 0:8.15.2-9.3.el5 set to be updated
---> Package apr-util.x86_64 0:1.2.7-7.el5 set to be updated
---> Package glibc.x86_64 0:2.5-24 set to be updated
---> Package krb5-libs.i386 0:1.6.1-25.el5 set to be updated
---> Package e2fsprogs-devel.x86_64 0:1.39-15.el5 set to be updated
---> Package ntsysv.x86_64 0:1.3.30.1-2 set to be updated
---> Package net-tools.x86_64 0:1.60-78.el5 set to be updated
---> Package newt.x86_64 0:0.52.2-10.el5 set to be updated
---> Package pam-devel.i386 0:0.99.6.2-3.27.el5 set to be updated
---> Package glibc-common.x86_64 0:2.5-24 set to be updated
---> Package openssh-clients.x86_64 0:4.3p2-26.el5 set to be updated
---> Package libX11-devel.x86_64 0:1.0.3-9.el5 set to be updated
---> Package libselinux.i386 0:1.33.4-5.el5 set to be updated
---> Package tcpdump.x86_64 14:3.9.4-12.el5 set to be updated
---> Package libselinux-python.x86_64 0:1.33.4-5.el5 set to be updated
---> Package iptables.x86_64 0:1.3.5-4.el5 set to be updated
---> Package cups-libs.i386 1:1.2.4-11.18.el5_2.1 set to be updated
---> Package glibc.i686 0:2.5-24 set to be updated
---> Package krb5-libs.x86_64 0:1.6.1-25.el5 set to be updated
---> Package authconfig.x86_64 0:5.3.21-3.el5 set to be updated
---> Package audit-libs.x86_64 0:1.6.5-9.el5 set to be updated
---> Package cups-libs.x86_64 1:1.2.4-11.18.el5_2.1 set to be updated
---> Package psmisc.x86_64 0:22.2-6 set to be updated
---> Package usermode.x86_64 0:1.88-3.el5.1 set to be updated
---> Package openssh-server.x86_64 0:4.3p2-26.el5 set to be updated
---> Package popt.x86_64 0:1.10.2-48.el5 set to be updated
---> Package udev.x86_64 0:095-14.16.el5 set to be updated
---> Package popt.i386 0:1.10.2-48.el5 set to be updated
---> Package diffutils.x86_64 0:2.8.1-15.2.3.el5 set to be updated
---> Package pam.x86_64 0:0.99.6.2-3.27.el5 set to be updated
---> Package chkconfig.x86_64 0:1.3.30.1-2 set to be updated
---> Package audit-libs-python.x86_64 0:1.6.5-9.el5 set to be updated
---> Package perl.x86_64 4:5.8.8-10.el5_2.3 set to be updated
---> Package libuser.x86_64 0:0.54.7-2.el5.5 set to be updated
---> Package libX11.x86_64 0:1.0.3-9.el5 set to be updated
---> Package procps.x86_64 0:3.2.7-9.el5 set to be updated
---> Package policycoreutils.x86_64 0:1.33.12-14.el5 set to be updated
---> Package iproute.x86_64 0:2.6.18-7.el5 set to be updated
---> Package traceroute.x86_64 3:2.0.1-3.el5 set to be updated
---> Package libselinux-devel.x86_64 0:1.33.4-5.el5 set to be updated
---> Package device-mapper.x86_64 0:1.02.24-1.el5 set to be updated
---> Package file.x86_64 0:4.17-13 set to be updated
---> Package net-snmp-libs.x86_64 1:5.3.1-24.el5_2.1 set to be updated
---> Package pam-devel.x86_64 0:0.99.6.2-3.27.el5 set to be updated
---> Package glibc-devel.x86_64 0:2.5-24 set to be updated
---> Package net-snmp-utils.x86_64 1:5.3.1-24.el5_2.1 set to be updated
---> Package e2fsprogs-libs.i386 0:1.39-15.el5 set to be updated
---> Package shadow-utils.x86_64 2:4.0.17-13.el5 set to be updated
---> Package e2fsprogs-libs.x86_64 0:1.39-15.el5 set to be updated
---> Package dbus.x86_64 0:1.0.0-7.el5 set to be updated
---> Package gzip.x86_64 0:1.3.5-10.el5.centos set to be updated
--> Finished Dependency Resolution
Dependencies Resolved
=============================================================================
Package Arch Version Repository Size
=============================================================================
Updating:
apr-util x86_64 1.2.7-7.el5 base 74 k
audit-libs i386 1.6.5-9.el5 base 67 k
audit-libs x86_64 1.6.5-9.el5 base 67 k
audit-libs-python x86_64 1.6.5-9.el5 base 75 k
authconfig x86_64 5.3.21-3.el5 base 452 k
bash x86_64 3.2-21.el5 base 1.9 M
chkconfig x86_64 1.3.30.1-2 base 160 k
cups-libs i386 1:1.2.4-11.18.el5_2.1 update 181 k
cups-libs x86_64 1:1.2.4-11.18.el5_2.1 update 177 k
dbus x86_64 1.0.0-7.el5 base 465 k
device-mapper i386 1.02.24-1.el5 base 656 k
device-mapper x86_64 1.02.24-1.el5 base 685 k
dhclient x86_64 12:3.0.5-13.el5 base 280 k
diffutils x86_64 2.8.1-15.2.3.el5 base 211 k
e2fsprogs x86_64 1.39-15.el5 base 986 k
e2fsprogs-devel x86_64 1.39-15.el5 base 626 k
e2fsprogs-libs i386 1.39-15.el5 base 116 k
e2fsprogs-libs x86_64 1.39-15.el5 base 116 k
file x86_64 4.17-13 base 322 k
ghostscript i386 8.15.2-9.3.el5 update 5.9 M
ghostscript x86_64 8.15.2-9.3.el5 update 5.9 M
glibc x86_64 2.5-24 base 4.7 M
glibc i686 2.5-24 base 5.2 M
glibc-common x86_64 2.5-24 base 16 M
glibc-devel i386 2.5-24 base 2.0 M
glibc-devel x86_64 2.5-24 base 2.4 M
glibc-headers x86_64 2.5-24 base 602 k
gzip x86_64 1.3.5-10.el5.centos base 103 k
iproute x86_64 2.6.18-7.el5 base 813 k
iptables x86_64 1.3.5-4.el5 base 245 k
krb5-devel i386 1.6.1-25.el5 base 1.9 M
krb5-devel x86_64 1.6.1-25.el5 base 1.9 M
krb5-libs i386 1.6.1-25.el5 base 656 k
krb5-libs x86_64 1.6.1-25.el5 base 664 k
libX11 i386 1.0.3-9.el5 base 795 k
libX11 x86_64 1.0.3-9.el5 base 795 k
libX11-devel x86_64 1.0.3-9.el5 base 665 k
libselinux x86_64 1.33.4-5.el5 base 96 k
libselinux i386 1.33.4-5.el5 base 94 k
libselinux-devel x86_64 1.33.4-5.el5 base 137 k
libselinux-python x86_64 1.33.4-5.el5 base 59 k
libuser x86_64 0.54.7-2.el5.5 base 448 k
net-snmp x86_64 1:5.3.1-24.el5_2.1 update 703 k
net-snmp-libs x86_64 1:5.3.1-24.el5_2.1 update 1.2 M
net-snmp-utils x86_64 1:5.3.1-24.el5_2.1 update 182 k
net-tools x86_64 1.60-78.el5 base 367 k
newt x86_64 0.52.2-10.el5 base 109 k
ntsysv x86_64 1.3.30.1-2 base 24 k
openssh x86_64 4.3p2-26.el5 base 283 k
openssh-clients x86_64 4.3p2-26.el5 base 446 k
openssh-server x86_64 4.3p2-26.el5 base 258 k
pam i386 0.99.6.2-3.27.el5 base 973 k
pam x86_64 0.99.6.2-3.27.el5 base 970 k
pam-devel i386 0.99.6.2-3.27.el5 base 188 k
pam-devel x86_64 0.99.6.2-3.27.el5 base 189 k
perl x86_64 4:5.8.8-10.el5_2.3 update 12 M
policycoreutils x86_64 1.33.12-14.el5 base 631 k
popt x86_64 1.10.2-48.el5 base 71 k
popt i386 1.10.2-48.el5 base 69 k
procps x86_64 3.2.7-9.el5 base 211 k
psmisc x86_64 22.2-6 base 62 k
shadow-utils x86_64 2:4.0.17-13.el5 base 1.1 M
sudo x86_64 1.6.8p12-12.el5 base 223 k
tcpdump x86_64 14:3.9.4-12.el5 base 458 k
traceroute x86_64 3:2.0.1-3.el5 base 40 k
udev x86_64 095-14.16.el5 base 2.4 M
usermode x86_64 1.88-3.el5.1 base 157 k
Transaction Summary
=============================================================================
Install 0 Package(s)
Update 67 Package(s)
Remove 0 Package(s)
Total download size: 83 M
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test
Transaction Check Error:
file /usr/lib/perl5/5.8.8/pod/perldiag.pod from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/c2ph.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/cpan.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/dprofpp.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/enc2xs.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/find2perl.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/h2ph.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/h2xs.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/instmodsh.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/libnetcfg.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/perlbug.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/perlcc.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/perldiag.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/perlivp.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/piconv.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/pl2pm.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/pod2html.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/pod2latex.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/pod2man.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/pod2text.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/pod2usage.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/podchecker.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/podselect.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/prove.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/psed.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/pstruct.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/s2p.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/splain.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
file /usr/share/man/man1/xsubpp.1.gz from install of perl-5.8.8-10.el5_2.3 conflicts with file from package perl-5.8.8-10.el5_0.2
Error Summary
-------------
Partial solution:
First it is obvious that perl cannot be upgraded because of conflicts. See what happens if we try to upgrade glibc:
root@server:~# yum update glibc
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: yum.keepitsecure.net
* update: yum.keepitsecure.net
base 100% |=========================| 951 B 00:00
update 100% |=========================| 951 B 00:00
Excluding Packages in global exclude list
Finished
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package glibc.i686 0:2.5-24 set to be updated
--> Processing Dependency: glibc-common = 2.5-24 for package: glibc
--> Processing Dependency: glibc = 2.5-18.el5_1.1 for package: glibc-headers
--> Processing Dependency: glibc = 2.5-18.el5_1.1 for package: glibc-devel
--> Processing Dependency: glibc = 2.5-18.el5_1.1 for package: glibc-devel
---> Package glibc.x86_64 0:2.5-24 set to be updated
--> Running transaction check
---> Package glibc-devel.x86_64 0:2.5-24 set to be updated
---> Package glibc-headers.x86_64 0:2.5-24 set to be updated
---> Package glibc-common.x86_64 0:2.5-24 set to be updated
--> Finished Dependency Resolution
Dependencies Resolved
=============================================================================
Package Arch Version Repository Size
=============================================================================
Updating:
glibc i686 2.5-24 base 5.2 M
glibc x86_64 2.5-24 base 4.7 M
glibc-common x86_64 2.5-24 base 16 M
Updating for dependencies:
glibc-devel x86_64 2.5-24 base 2.4 M
glibc-headers x86_64 2.5-24 base 602 k
Transaction Summary
=============================================================================
Install 0 Package(s)
Update 5 Package(s)
Remove 0 Package(s)
Total download size: 29 M
Is this ok [y/N]: y
Downloading Packages:
Running rpm_check_debug
ERROR with rpm_check_debug vs depsolve:
Package glibc-devel needs glibc = 2.5-18.el5_1.1, this is not available.
Package glibc-devel needs glibc-headers = 2.5-18.el5_1.1, this is not available.
Package glibc-devel needs glibc-headers = 2.5-18.el5_1.1, this is not available.
Package glibc-devel needs glibc = 2.5-18.el5_1.1, this is not available.
Complete!
This time the problem is dependencies are not resolved for glibc-devel.
However, we can still update packages which do not depend either on perl or on glibc. For example traceroute:
root@server:~# yum update traceroute
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: yum.keepitsecure.net
* update: yum.keepitsecure.net
base 100% |=========================| 951 B 00:00
update 100% |=========================| 951 B 00:00
Excluding Packages in global exclude list
Finished
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package traceroute.x86_64 3:2.0.1-3.el5 set to be updated
--> Finished Dependency Resolution
Dependencies Resolved
=============================================================================
Package Arch Version Repository Size
=============================================================================
Updating:
traceroute x86_64 3:2.0.1-3.el5 base 40 k
Transaction Summary
=============================================================================
Install 0 Package(s)
Update 1 Package(s)
Remove 0 Package(s)
Total download size: 40 k
Is this ok [y/N]: y
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test
Transaction Test Succeeded
Running Transaction
Updating : traceroute ######################### [1/2]
Cleanup : traceroute ######################### [2/2]
Updated: traceroute.x86_64 3:2.0.1-3.el5
Complete!
Complete Solution
Until now (Sat Jul 12 09:49:48 EEST 2008) I have not found a complete solution yet. There are many recommendations like uninstalling conflicting packages (perl and glibs - which does not seem a good thing to test on a production server 
) I have read also about running 'yum clean all && yum upgrade' which does not help at all either
I think this problem occurs only with CentOS 5 x64 architecture. Adding 32 bit repositories might help but again does not seem a good idea to me
As always, I will wait for a few days (nothing urgent to upgrade at my end) and see if the problem solves by itself Hopefully the repositories will be fixed to solve the dependencies. If not, I will have to think of something
