Version: 2.0.1-1 This seems fixed because I have a successful build for this version.
I guess it was commit 507024ba6b9914265b5424c295363f72be9736db which fixed this.
mlpack (2.0.0-1) unstable; urgency=medium
* debian/rules
- remove code to prefix binaries with mlpack_, as this is now done upstream
Because there was not a Close statement there, I'm closing this report
by hand with this message.
Thanks.

