This has been reported as Debian Bug #751603:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=751603
"Eureka fails to open a read only file, for example a WAD that is in /usr/somewhere/."
And indeed:
$ eureka /usr/share/games/doom/doom1.wad
Eureka DOOM Editor v1.00 (C) 2013 Andrew Apted, et al
Current time: 09:31 on 2014/06/16
Home dir: /home/greffrath/.eureka
Cache dir: /home/greffrath/.eureka
Install dir: /usr/share/eureka
Reading config file: /home/greffrath/.eureka/config.cfg
Reading recent list from: /home/greffrath/.eureka/misc.cfg
Looking for IWADs....
Writing recent list to: /home/greffrath/.eureka/misc.cfg
Reading key bindings from: /usr/share/eureka/bindings.cfg
Reading key bindings from: /home/greffrath/.eureka/bindings.cfg
Opening WAD file: /usr/share/games/doom/doom1.wad
open failed: Permission denied
FATAL ERROR: Cannot load pwad: /usr/share/games/doom/doom1.wad
FATAL ERROR: Cannot load pwad: /usr/share/games/doom/doom1.wad
Thanks for the report, bug confirmed and noted.
I will close this ticket when it's fixed.
Fixed now (revision 1436)