[Biojava-dev] biojava3 and forester question

[olivier.sallou at codeless.fr]

Le 5/25/12 5:16 PM, Andreas Prlic a écrit :
> Hi,
>
> We are having an external dependency on the forester package for the
> phylo module and do not include it together with our source. Since
> there is no maven repository for it (that we are aware of) we uploaded
> a version of (0.955) to our maven repository. Sources and binaries are
> at
>
> http://www.biojava.org/download/maven/org/forester/0.955/
Thanks,
I will try to build with this source jar.
However, for the Debian packaging, this means that either:

- I create a package biojava3-forester from those sources, that will not
evolve

- I use forester project sources and try to build with those, using
different package references (evoinference). But this would not match
the same version and could have side effects.


Olivier
>
> Andreas
>
>
>
> On Fri, May 25, 2012 at 7:31 AM, Chris Friedline <cfriedline at vcu.edu> wrote:
>> I replied earlier to Olivier, but forgot to copy the list.  Here's the reply:
>>
>> -----
>> Strange, I just looked at the biojava3-phylo source jar and saw an included forester package, with the phylogenyinference under it.  However, this refers to the evoinference package (and subpackages) in the actual forester source.  Given that forester is actively developed, should it really be inluded with the biojava3-phylo source in the first place?
>>
>> The references in biojava3 are below:
>> CheckTreeAccuracy.java:import org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix;
>> CheckTreeAccuracy.java:import org.forester.phylogenyinference.DistanceMatrix;
>> TreeConstructor.java:import org.forester.phylogenyinference.BasicSymmetricalDistanceMatrix;
>> TreeConstructor.java:import org.forester.phylogenyinference.DistanceMatrix;
>> TreeConstructor.java:import org.forester.phylogenyinference.NeighborJoining;
>>
>> However, these classes are missing from the phylogenyinference package distributed with biojava3-phylo.  In forester itself, they are here:
>>
>> ./forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java
>> ./forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java
>> ./forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
>>
>> Seems like some clean-up/separation might be needed.
>>
>> Chris
>>
>> On May 25, 2012, at 8:43 AM, Olivier Sallou wrote:
>>
>>> Hi,
>>> biojava3-phylo refers to package classes: org.forester.phylogenyinference.*
>>>
>>> from maven dependency "forester"
>>>
>>> Could you tell me where those sources comes from ?
>>>
>>> I cannot find those in forester sources
>>> (http://code.google.com/p/forester/source/browse/#svn%2Fforester%2Fjava%2Fsrc%2Forg%2Fforester)
>>>
>>> (not jar on their web site).
>>>
>>> This prevent complete rebuild from source (still related to Debian
>>> packaging).
>>>
>>> Thanks
>>>
>>> Olivier
>>>
>>> --
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>>
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