> When I try to run the second compiled binary, I get:
> httrack: htscore.c:967: httpmirror: Assertion `szf + 1 <
> sizeof(r.req.user_agent)' failed.
> Aborted

Humm, this migh tbe related to a too small structure 
somewhere.
Can you change, in the file src/htslib.c, at line 65, the 
line:
  char user_agent[64];
into:
  char user_agent[128];

And then recompile as you did on the #2 try?The error message should
disappear.