I do not have a joypad, but I saw you made a deb so I cared to try anyway, since I couldn't compile the GTK GUI before. The package installs with some work, but if you don't have all dependencies it fails, so you have to install them manually. Could you fix it? Here's the output I got:
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ruti@ruti-desktop:~$ sudo dpkg -i /home/ruti/Desktop/vbam_0.svn696-1_i386.deb
Selecting previously deselected package vbam.
(Reading database ... 143125 files and directories currently installed.)
Unpacking vbam (from .../vbam_0.svn696-1_i386.deb) ...
dpkg: dependency problems prevent configuration of vbam:
vbam depends on libglademm-2.4-1c2a (>= 2.6.0); however:
Package libglademm-2.4-1c2a is not installed.
vbam depends on libgtkglextmm-x11-1.2; however:
Package libgtkglextmm-x11-1.2 is not installed.
dpkg: error processing vbam (--install):
dependency problems - leaving unconfigured
Errors were encountered while processing:
vbam
The dependencies are available in Ubuntu's repos (and the package worked when I had them installed), it just seems like something is set up wrong in the package.
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I also think I found a bug in the GUI, related to input. It seems the B button is constantly pressed. This doesn't happen in the SDL version.