I don't have an issue.... yet. I want to prevent one. I have been doing some maintenance on my server after a long break. The two things that I did are;1 - installed php 55 using the latest documentation for Virtualmin, "Multiple PHP Versions" and 2 added Letsencrypt to start trying out their Certs. The PHP install seems to have added a repo "rhscl-php55-epel-6-x86_64.repo" and the LetsEncrypt instructions had me add EPEL. I did not think about the package repos and need for Virtualmin to have some control over them until I noticed that EPEL wanted to update several of the packages that I knew were key to Virtualmin. I did not do the updates and pulled the epel repo out of the repos.d directory. Did yum clean all, yum update. Then, I noticed that I have "CentOS-SCLo-scl-rh.repo" added in and it is wanting to upgrade php54. I believe php54 was installed quite a while back using the old multiple php installation instructions. I did not do that upgrade either.
My goal is to NOT mess up Virtualmin and need some advice on how to proceed.
Here are the repos in repos.d:
CentOS-Base.repo CentOS-SCLo-scl-rh.repo CentOS-Base.repo.rpmnew CentOS-Vault.repo CentOS-Debuginfo.repo rhscl-php55-epel-6-x86_64.repo CentOS-fasttrack.repo virtualmin.repo CentOS-Media.repo
PHP 5.5 did not turn out to work properly with my templates so would not mind removing that if needed to get Virtualmin back to a safe repo state; it looks like I won't use it.