my upgrade prompts me to say No or Yes to ignoring packages?

[kazuya]

Upon doing my installation and then accepting upgrades as displayed by my software installer, it decided to ignore certain packages or things. It asked whether I could ignore the packages or not?
my upgrade prompts me to say No or Yes to ignoring packages?

What does this mean? Any ideas? Is this harmful to my overall system?

[ubuntumaneh]

It means lots of things. It will depend on the program. Sometime you have changed the default configuration of a program, then by the time of upgrade, you are asked if you want to keep your configuration, or if you want the default. Anyway, usually there will be no harm whatsoever to your system. In doubt, just press <enter>, for the default choice of the installer. One advice is to read and take notes on the question, then ask on some foruns or look at google.