I've somehow missed much of this discussion, which has got a little confused.
I'll repeat some key facts here:-

- MTJ depends on netlib-java
- I'm the maintainer of netlib-java
- netlib-java depends on PURE JAVA code, generated by F2J from netlib.org
BLAS/LAPACK (and ARPACK). Keith Seymour (author of f2j) deserves all the
praise for that magnificent task! The necessary jar is distributed with
netlib-java.
- BLAS/LAPACK are industry standard APIs.
- netlib-java is technically a "translation" of netlib.org's
BLAS/LAPACK/ARPACK API, so is therefore BSD licensed
- netlib-java can be *optionally* configured at runtime to use a native
library instead of the Java implementation.
- the java implementation is pretty damn fast and will be more than adequate
for most users. However, it will *never* be as fast as native code running
on specialist hardware (no matter how much the JVM improves).

Being the maintainer of netlib-java, I'd be more than happy to re-license
all the bits that aren't technically "translations" of netlib.org, for
inclusion in commons-math (in fact, it makes sense to do so). But you'd
still need to depend on the f2j translated implementation. They are BSD
license.

Hell, it makes a *lot* of sense for commons-math to provide the BLAS/LAPACK
API... they are industry standards after all, and all reference
implementations for linear algebra algorithms make use of them.


Luc Maisonobe wrote:
> 
> I have an additional reason for avoiding native libraries. Pure Java can
> be processed by external tools for either inspection (think findbugs,
> cobertura, traceability, auditing) or modification (think Nabla!). The
> Nabla case is especially important to me, but I am aware this is a
> corner-case.
> 

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