That's a big part of the problem, actually. If it was clear which patents they were then they could be specifically avoided. The problem is that there are so many overly broad patents that you can't even know which ones you're infringing until the troll jumps out from under the bridge.
But to answer the question in broad terms, the compiler you're using and the operating system you're running it on will probably infringe something or other in its rather comprehensive standard library or system call implementation, which you've incorporated when you type the equivalent of "#include <stdio.h>" in your Hello World program.
But to answer the question in broad terms, the compiler you're using and the operating system you're running it on will probably infringe something or other in its rather comprehensive standard library or system call implementation, which you've incorporated when you type the equivalent of "#include <stdio.h>" in your Hello World program.