Certainly, it allows you to compile with the compiler options you want, you are able to optimize the binaries for your CPU, but: does it really matter? Are the speed improvements really visible?
Tweaking the compiler flags and targetting your specific CPU architecture generally doesn't make a visible difference. More precisely, if you aren't benchmarking the changes, they are likely to not be significant enough that you can tell.
However, for some categories of software, such as multimedia players and the like which want to take advantage of MMX/SSE/3Dnow!/etc, doing so can make quite a difference.
Dependencies was another argument: you compile with the correct headers of dependant files, well... is that really so? If you upgraded the dependant binaries, wouldn't you get the same effect?
If the dependencies are done correctly, you'll get the same effect.
However, as soon as you start considering options like which version of BerkeleyDB to use, or which version of SASL, etc, the number of combinations becomes large enough that the generic precompiled packages may not correspond to your specific environment.
One certain drawback of compiling from source is the compilation time. Large packages like KDE or OpenOffice take ages, so you can't just "quickly" upgrade a whole system, or a large part of it. I might add that I am more the typical desktop user, not using my machines for real and specific server apps.
Well, yes. KDE and OpenOffice are vast, bloated, suffer from creeping featurism, and thus resemble the Windows products they attempt to emulate in more ways then their authors probably want them to.
One could pick on Mozilla or many other large, cross-platform software packages for this sort of thing as well. Mozilla seems to internally re-implement most of the BSD sockets APIs internally, as well as bits and pieces of many other Unix/POSIX APIs.
So, my question is basically: did you, in your experience, find that compiling from source *really* has any serious advantages that make up for the time it takes?
Oh, yes. The first time you run into a problem and fix it yourself, or make a change to the programs to add some feature that you want, you will discover the serious advantages.
However, if you never try to fix bugs or write code for yourself, then you aren't going to gain nearly as much from using source compared with using precompiled binaries.
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