Compiling the 50-line app again; this time the results were a little different:
Compiling code. 0.17
Generating R file. 0.67
Compiling generated Java code. 1.37
Convert byte code - optimized dex. 0.51
Packaging files. 0.33
Copying libraries resources 0.08
Signing package file (debug key).
At this point, the progress bar was about half way across and quit moving, then after a couple of more minutes, the "Process is running longer than expected." window came up and the progress bar jumped to about 3/4.
I said No, not to cancel. It sat for another couple of minutes then added "Error" to the "Signing package file" line and said "Process timed out."
I had changed the timeout to 300 seconds, but I just checked and it's back to 120 seconds.