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I have a cyclone EP3C10F256C8 and configuration flash EPCS4SI8N.
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Does the EP3C10F256C8 have an N postfix? i.e. is it a lead free part? The Flash you mention is a lead fre part
Mixing Lead Free and Leaded parts needs careful control at assembly.
I only say that because I have worked on a mixed board and seen signal integrity problems on some PCBs due to incorrect solder temperatures.
From the Altera website:
Q: Can I use both leaded and RoHS-compliant parts on the same board?
A: Yes, both leaded and RoHS-compliant parts can be used on the same board. There are high-volume consumer products that are currently using both types of packages. However, using both lead and RoHS-compliant parts together will add to the complexity of the manufacturing process. Altera does not recommend this design for volume production.
Might be worth checking with the PCB assembler.