If your solidity source code references libraries, then the generated byte code will contain placeholders for the real addresses of the referenced libraries. These have to be updated via a process called linking before deploying the contract.

solcjs provides the linkByteCode method to link library addresses to the generated byte code.

Here is an example to demonstrate this:

var solc = require("solc"); 

var input = { 
    "lib.sol": "library L { function f() returns (uint) { return 7; } }", 
    "cont.sol": "import 'lib.sol'; contract x { function g() { L.f(); } }" 
}; 

var output = solc.compile({sources: input}, 1); 

var finalByteCode = solc.linkBytecode(output.contracts["x"].bytecode, { 'L': '0x123456...' });