LVDS_E_3R pin assingment Error (21164): Unable to create complement pin.

I don't know what logic you have in the module, but I have done a simple design just to show you how to assign the LVDS pins for the same device. When assigning pins , you need to keep in mind the IO Standard, voltage as well as the IO Type (Single-function, clock output, dual-purpose, etc).

This is the code I used for the sample build:

module c10_lvds(
	input wire  [2:0] In,
	output wire [2:0] Test_pin
	);
	
	wire [2:0]  core_input;
	wire            lvds_clock;
 
	ALT_INBUF inbuf0 (
	                  .i( In[0]         ), 
	                  .o( core_input[0] )
					); 
							
	ALT_INBUF inbuf1 (
	                  .i( In[1]         ), 
	                  .o( core_input[1] )
					); 
							
	ALT_INBUF inbuf2 (
	                  .i( In[2]         ), 
	                  .o( core_input[2] )
			); 
	
   
   // Have to include PLL since PIN_43/44 are Differential Clock outputs
   // Need to be driven by output clocks from PLL. 
	
	lvds_pll_out	lvds_pll_inst (
	                              .inclk0 ( core_input[0] ),
	                              .c0 ( lvds_clock )
	                             );
	
	ALT_OUTBUF outbuff0_lvds (
	                         .i( lvds_clock ), 
				 .o( Test_pin[0]   )
				 ); 
 
	// Since these IO are normal IO, these can be driven by any signal
	// PLL outputs need not be used for these IO
	ALT_OUTBUF outbuff1_lvds (
	                         .i( core_input[1] ), 
				 .o( Test_pin[1]   )
				 ); 
 
 
	ALT_OUTBUF outbuff2_lvds (
	                         .i( core_input[2] ), 
				 .o( Test_pin[2]   )
				 ); 
 
endmodule

I assigned the pins using Assignment Editor after compiling the design. The direction gets assigned automatically based on the design. You can see the assignments made in the Assignment Editor as well as Pin Planner: