If you’re a power user or have special software needs, then there are several package managers like Fink, MacPorts, and HomeBrew that can be used for accessing open-source software programs and services. If you have installed these a while ago on Yosemite, then you might find after upgrading to El Capitan that they no longer work, and give error outputs instead of updating or installing new programs you specify.
If this is the case, then for the most part the fix should be relatively easy. When you upgrade OS X, Apple will remove incompatible software, including versions of XCode’s included command line tools that are specific for older versions of OS X. This in turn means programs that rely on these tools may not work; however, simply re-installing the tools should be a quick fix, so open the Terminal and run the following command:
If this command results in a message stating the command-line tools are already installed, then try running the following command to reset the default command-line tools path:
If there is still a problem then, try reinstalling your package manager, using the latest version from the developers’ site. Often package managers are built to work with a specific version of OS X, so if you have upgraded without updating your package manager first, then you might run into these problems.
Note that if you install XCode 7 then you don’t need to install the Command Line Tools as they are already included in XCode itself. Reseting xcode-select would be the only thing you might need to do.