[all variants] Install new version of software that is in repositories

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http://ubuntuforums.org – Hello. I'm often compiling and installing software either to get the latest version or simply because the software doesn't exist in a repository. To keep track on installed software I use checkinstall to generate .deb package files and install using package management tools ( e.g. dpkg -i <generatedDebFile>) My question: I believe that some trouble I have had in the past were caused by having installed software in a newer version that the one in repositories. This might be because my approach of installing home build versions is wrong. So what is the proper way of installing software th (Hardware)