Emerge I think should continue running even if a specific app isn't available for download for some reason (in tonights example it was lyx 1.2.2). Just because lyx can't be downloaded for some reason or another shouldn't stop a huge upgrade. For example is lyx really a dependancy to the new gcc version? Just because it's listed as being gotten before gcc in this specific update and fails shouldn't stop the rest of the system from getting updated right? It should only effect those apps that depend on it. This really should be "fixed" before 1.4's release in my opinion.
*** This bug has been marked as a duplicate of 12768 ***