Consider the following output:
> ./configure --prefix=/usr/local/bashdb | tail
./configure: line 9188: : supported targets:.* elf: command not found
/bin/rm: cannot remove 'libtoolT': No such file or directory
=========================================================
Bash version: GNU bash, version 4.4.12(1)-release (x86_64-pc-linux-gnu)
Copyright (C) 2016 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Location : /bin/bash
Prefix : /usr/share
prefix checks out
Note that the --prefix argument has been ignored and replaced with /usr/share.
bashdb is showing its age, autoconf-wise. Should be fixed in e7d58e1
Also, I've changed the bug-reporting link to go here (as you've correclty done) nstead of the bashdb-devel mailing list.