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I found this command very useful:

make localmodconfig

However, having some closed source drivers/modules ends up being a problem because this command can't find an appropriate way of including the config parameters, which do not exist, related to my closed-source software.

My question is: for example, if I have the fglrx module installed, how can I configure my kernel build?

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I don't understand your problem. Do you want to automatically rebuild the binary drivers if you are building a new kernel? If so have a look at dkms –  Ulrich Dangel Jul 15 '12 at 0:28
    
@UlrichDangel let's put this way: what options do I have with this kind of software? –  user827992 Jul 15 '12 at 0:33
    
I really don't understand your problem, if you want to automatically rebuild your binary driver when you install a new kernel use en.wikipedia.org/wiki/Dynamic_Kernel_Module_Support - i don't understand what you mean with because this command can't find an appropriate way of including the config parameters, which do not exist, related to my closed-source software –  Ulrich Dangel Jul 15 '12 at 0:37
    
"Closed source software" is unknown to the kernel source, so there is nothing to configure kernel side. Many such drivers come with some shim that has to be configured to match the kernel, which most probably has to be installed for this. –  vonbrand Jan 18 '13 at 0:59
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