'yum upgrade' fails strangely

[Necator]

I'm tryling to update on a freshley installed FC6 x86_64 system.

First, yum hanged on the kernel-update (30+ minutes without progress, yum getting 0% CPU in top).
After a restart, yum fails on libtool, which can be resolved by deinstalling libtool and reinstalling it.

After that, yum fails on gpm, mkinitrd and libgcj.
To upgrade the rest of the packages, I had to use 'yum upgrade -x gpm -x mkinitrd -x libgcj'

However there 3 packages still cannot be upgraded.

[root@localhost holger]# yum clean all
Loading "installonlyn" plugin
Cleaning up Everything
[root@localhost holger]# yum upgrade
Loading "installonlyn" plugin
Setting up Upgrade Process
Setting up repositories
core                      100% |=========================| 1.1 kB    00:00     
updates                   100% |=========================| 1.2 kB    00:00     
extras                    100% |=========================| 1.1 kB    00:00     
Reading repository metadata in from local files
primary.xml.gz            100% |=========================| 1.0 MB    00:01     
core      : ################################################## 2931/2931
primary.xml.gz            100% |=========================| 514 kB    00:00     
updates   : ################################################## 1594/1594
primary.xml.gz            100% |=========================| 1.9 MB    00:02     
extras    : ################################################## 5859/5859
Resolving Dependencies
--> Populating transaction set with selected packages. Please wait.
---> Downloading header for mkinitrd to pack into transaction set.
mkinitrd-5.1.19.0.2-1.i38 100% |=========================|  51 kB    00:00     
---> Package mkinitrd.i386 0:5.1.19.0.2-1 set to be updated
---> Downloading header for libgcj to pack into transaction set.
libgcj-4.1.1-51.fc6.i386. 100% |=========================|  56 kB    00:00     
---> Package libgcj.i386 0:4.1.1-51.fc6 set to be updated
---> Downloading header for gpm to pack into transaction set.
gpm-1.20.1-80.fc6.i386.rp 100% |=========================|  17 kB    00:00     
---> Package gpm.i386 0:1.20.1-80.fc6 set to be updated
--> Running transaction check

Dependencies Resolved

=============================================================================
 Package                 Arch       Version          Repository        Size 
=============================================================================
Updating:
 gpm                     i386       1.20.1-80.fc6    updates           185 k
 libgcj                  i386       4.1.1-51.fc6     updates            17 M
 mkinitrd                i386       5.1.19.0.2-1     updates           438 k

Transaction Summary
=============================================================================
Install      0 Package(s)         
Update       3 Package(s)         
Remove       0 Package(s)         

Total download size: 17 M
Is this ok [y/N]: y
Downloading Packages:
(1/3): mkinitrd-5.1.19.0. 100% |=========================| 438 kB    00:00     
(2/3): libgcj-4.1.1-51.fc 100% |=========================|  17 MB    00:24     
(3/3): gpm-1.20.1-80.fc6. 100% |=========================| 185 kB    00:00     
Running Transaction Test
Finished Transaction Test


Transaction Check Error:   file /sbin/mkinitrd from install of mkinitrd-5.1.19.0.2-1 conflicts with file from package mkinitrd-5.1.19-1
  file /usr/share/java/libgcj-4.1.1.jar from install of libgcj-4.1.1-51.fc6 conflicts with file from package libgcj-4.1.1-30
  file /usr/share/man/man1/fastjar.1.gz from install of libgcj-4.1.1-51.fc6 conflicts with file from package libgcj-4.1.1-30
  file /usr/share/man/man1/gcj-dbtool.1.gz from install of libgcj-4.1.1-51.fc6 conflicts with file from package libgcj-4.1.1-30
  file /usr/share/man/man1/gij.1.gz from install of libgcj-4.1.1-51.fc6 conflicts with file from package libgcj-4.1.1-30
  file /usr/share/man/man1/grepjar.1.gz from install of libgcj-4.1.1-51.fc6 conflicts with file from package libgcj-4.1.1-30
  file /usr/share/man/man1/grmic.1.gz from install of libgcj-4.1.1-51.fc6 conflicts with file from package libgcj-4.1.1-30
  file /usr/share/man/man1/grmiregistry.1.gz from install of libgcj-4.1.1-51.fc6 conflicts with file from package libgcj-4.1.1-30
  file /usr/share/man/man1/jv-convert.1.gz from install of libgcj-4.1.1-51.fc6 conflicts with file from package libgcj-4.1.1-30

E.g. the gpm-package even fails on removing it (with 'yum remove gpm')

yum remove gpm
Loading "installonlyn" plugin
Setting up Remove Process
Resolving Dependencies
--> Populating transaction set with selected packages. Please wait.
---> Package gpm.i386 0:1.20.1-74.1 set to be erased
--> Running transaction check

Dependencies Resolved

=============================================================================
 Package                 Arch       Version          Repository        Size 
=============================================================================
Removing:
 gpm                     i386       1.20.1-74.1      installed         306 k

Transaction Summary
=============================================================================
Install      0 Package(s)         
Update       0 Package(s)         
Remove       1 Package(s)         

Is this ok [y/N]: y
Downloading Packages:
Running Transaction Test
Finished Transaction Test
Transaction Test Succeeded
Running Transaction
install-info: Warnung: keine Einträge für „/usr/share/info/gpm.info.gz“ gefunden; nichts entfernt
Fehler beim Lesen der Informationen über den Dienst gpm: Datei oder Verzeichnis nicht gefunden
error: %preun(gpm-1.20.1-74.1.i386) scriptlet failed, exit status 1

Removed: gpm.i386 0:1.20.1-74.1
Complete!

It says ok, but it's still there. ... (yeah, it also says 'scriptlet failed, so no wonder on that).

I hope, someone can help me.

[bob]

You can report dependency errors through Bugzilla or wait a day or two for them to clear up. What I've found is a good way to work around the problem is to use 'yum.sh'. How this works is to first copy this code in a text editor like gedit:

 #!/bin/sh
 for i in `yum list updates |cut -f 1 -d " " |grep -A 500 -e Updated |\
 grep -v -e Updated` ; do
       echo "Updating $i"
       yum -y update $i
 done

and then save it in your /home/username as 'yum.sh'

Then, when you want to update the packages and exclude those with dependency errors, simply open a terminal, sign in as root (just 'su' will suffice as it leaves you in your /home/username) and then run:

sh yum.sh

That picks each updated and processes it independently and bypasses the problems.

[Necator]

Thanks alot. The yum-script makes it easier to use than always specifying the exclude flag.

Yet I want to stress out, that my problem is no dependency problem, at least, it doesent look like for me. (Deinstall script seems to fail?!)
It is also persiting now for ... well ... 4 Days. First I had it on my update FC5 to FC6 (Yes I'm a early-adopter ), where ist failed. Then I thougt on doing a fresh install ... where the problem persists.

[bob]

Try this; install yumex "yum -y install yumex" and see if you have duplicate packages, perhaps both the i386 and X86_64 versions. I had that problem myself where updates and removals failed because of two versions being installed.

[Necator]

Thanks.
With yumex I yust deinstalled the old versions (all problematic packages have there been in two versions ... one old and one newer). I deleted the old one, and voilà ... it's fine again.

rpm with its thousands of options and switches is a pain in the ass to use ... yum takes away to much possibilities ... yet yumex is somehow great and easy to use.
(For updating I will however stick tu yum ... "yum upgrade" is faster typed than yumex starts up ;-))

Thanks again!