Might not be my actual longest (and certainly isn't anywhere near the stories that I'm sure others here have to tell), but my favorite debugging problem was one

Might not be my actual longest (and certainly isn't anywhere near the stories that I'm sure others here have to tell), but my favorite debugging problem was one I worked on a couple years ago. I had a Python service that was doing a bunch of number crunching, so I used Cython to speed up the math-intensive portions of the code. Added type definitions, referenced several C math functions from math.h, and it was working great on Windows. Set it up using the side-by-side file approach, which lets you leave your original Python files alone, and add all the type info in a ".pxd" file that has to match the exact name of the original ".py" file. So, if I had "FileA.py", I'd also have "FileA.pxd". Unfortunately, when I went to run this on Linux, it compiled fine, but started throwing some weird exceptions buried deep down in the code. I hadn't actually written the math portion of this myself, but traced it pretty far down. Finally concluded it wasn't finding "cos" somehow, which didn't make any sense, because I was explicitly importing the C function from math.h if using Cython, and importing the normal Python function from the "math" module otherwise. Took me about 6 hours of tracing, investigating, and steadily growing confusion before I finally figured out what was going on: there was a single letter casing mismatch between a .py file and its corresponding .pxd file. One had a capital 'O', the other had a lower-case 'o'. Worked fine on case-insensitive Windows, but under case-sensitive Linux, it never actually found the proper .pxd file, didn't get the right imports, and thus stuff eventually exploded. Definitely a pretty high hours-of-work to number-of-characters-changed ratio :)