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Dependency tracking is performed as a side-effect of compilation. Each time the build system compiles a source file, it computes its list of dependencies (in C these are the header files included by the source being compiled). Later, any time make is run and a dependency appears to have changed, the dependent files will be rebuilt.
When configure is executed, you can see it probing each compiler for the dependency mechanism it supports (several mechanisms can be used):
~/amhello-1.0 % ./configure --prefix /usr ... checking dependency style of gcc... gcc3 ...
Because dependencies are only computed as a side-effect of the
compilation, no dependency information exists the first time a package
is built. This is OK because all the files need to be built anyway:
make
does not have to decide which files need to be rebuilt.
In fact, dependency tracking is completely useless for one-time builds
and there is a configure option to disable this:
Some compilers do not offer any practical way to derive the list of dependencies as a side-effect of the compilation, requiring a separate run (maybe of another tool) to compute these dependencies. The performance penalty implied by these methods is important enough to disable them by default. The option --enable-dependency-tracking must be passed to configure to activate them.
See Dependency Tracking Evolution, for some discussion about the different dependency tracking schemes used by Automake over the years.