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kernel linux-4.9.40 also needs CONFIG_MEDIA_RC_SUPPORT=y, CONFIG_MEDIA_SUPPORT=y and CONFIG_RC_DECODERS=y in .config file to have lirc_sam enabled and compiled.
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Last kernels (I tested kernels linux-4.9.40 and linux-4.9.38) also need CONFIG_MEDIA_RC_SUPPORT=y, CONFIG_MEDIA_SUPPORT=y and CONFIG_RC_DECODERS=y in .config file to have lirc_sam enabled and compiled.