[Debian-med-packaging] [rt.broad #134497] IGV license

[Shaun Jackman]

On 22 July 2010 10:49, James Robinson via RT
<igv-help at broadinstitute.org> wrote:
...
>> Due to these dependencies, IGV may not be used by the military:
>> src/org/broad/igv/tdf/LEDataInputStream.java
>> lib/ledatastream.jar and
>> lib/colt.jar
>> which expressly forbid use by military organizations. I feel this
>> limitation should be be mentioned explicitly on the IGV web page.
>
> Thanks for pointing that out.   I've recoded to eliminate these
> dependencies (release 1.5.10).   I still include the colt packages,
> but no longer  the hep.aida.* packages which contain this
> restriction.   The LED streams have been replaced, largely by the nio
> ByteBuffer class included with the JDK.

The following colt classes depend on hep.aida:
./src/cern/colt/matrix/bench/BenchmarkMatrix.java
./src/cern/colt/matrix/doublealgo/Formatter.java
./src/cern/colt/matrix/doublealgo/Sorting.java
./src/cern/colt/matrix/doublealgo/Statistic.java
./src/cern/colt/matrix/impl/TestMatrix2D.java
./src/cern/jet/random/Benchmark.java
./src/cern/jet/stat/quantile/DoubleQuantileFinder.java
./src/cern/jet/stat/quantile/Quantile1Test.java
./src/cern/jet/stat/quantile/QuantileFinderFactory.java

Does IGV use any of these classes?

I think that I'll remove the above classes from the Debian package as
well as remove all the hep.aida classes. Potentially, these non-free
classes could potentially go into a colt-contrib package that depends
on the free colt package and a non-free hep-aida package. There's the
free JAIDA package, but it seems to implement a newer version of AIDA
than HEP AIDA does, and so wouldn't be compatible out-of-the-box with
colt.

Cheers,
Shaun