This might not be relevant anymore, shame on me for keeping it draft for few months. However, there are still people running an older versions of Exadata storage software and it might still help someone out there.
With the release of Exadata storage software 126.96.36.199.0, Oracle announced that some 32bit (i686) packages will be removed from the OS as part of the upgrade.
This happened to me in the summer last year (blog post) and I thought back then that someone messed up the dependencies. After seeing it again for another customer a month later I thought it might be something else. So after checking the release notes for all the recent patches, I found this for the 188.8.131.52.0 release:
Note that several i686 packages may be removed from the database note when being updated. Run dbnodeupdate.sh with -N flag at prereq check time to see exactly what rpms will be removed from your system.
Now, this will be all ok if you haven't installed any additional packages. If you, however, like many other customers has packages like LDAP or Kerberos then your dbnodeupdate pre-check will fail with “Minimum' dependency check failed." and broken dependencies since all i686 package will be removed as part of dbnodeupdate pre-check.
The way around that is to run dbnodeupdate with -N flag and check the logs of what packages will be removed and what will be impacted. Then manually remove any packages you installed manually. After the Exadata storage software update, you'd need to install the relevant version of the packages again.
Having said that I need to mention the below note on what software is allowed to install on Exadata:
Is it acceptable / supported to install additional or 3rd party software on Exadata machines and how to check for conflicts? (Doc ID 1541428.1)