[Biojava-l] Biojava Dependency on Forester

[Andreas Prlic]

"exclusion" means only that the (old) forester.jar that biojava
depends on, will not be included. Instead you could configure your
newer forester dependency in its own <dependency> section. That one
will get used instead.

A

On Thu, Oct 11, 2012 at 11:43 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
> Hi Andreas,
>
> Thank you for the quick response!
>
> When you say "exclusion", sounds like the
> parts of biojava that uses forester would be excluded?
> I'm not sure, but I think our code uses some of
> the code that would be excluded.
>
> As you probably already know, the latest
> release of Forester is not backwardly
> compatible with Forester version 0.955.
>
> Thank you,
>
> Terry
>
>
> On Thu, Oct 11, 2012 at 2:32 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
>> Hi Terry,
>>
>> Biojava depends on forester version 0.955. There are no plans to get
>> rid of this dependency, as far as I know. However we can try to
>> upgrade to a newer version if that helps.
>>
>> If you are working in a Maven environment and you pull in BioJava that
>> way, you can add an exclusion to your config. Something like the XML
>> below. This forces your project to ignore the older forester library
>> configured in biojava. Is this a suitable workaround for your problem?
>>
>> Andreas
>>
>>
>>         <dependency>
>>                         <groupId>org.biojava</groupId>
>>                         <artifactId>biojava3-phylo</artifactId>
>>                         <version>3.0.4</version>
>>                         <exclusions>
>>                                 <exclusion>
>>                                         <groupId>org</groupId>
>>                                         <artifactId>forester</artifactId>
>>                                 </exclusion>
>>                         </exclusions>
>>                 </dependency>
>>
>>
>>
>>
>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:
>>> Dear Andreas,
>>>
>>> I am the lead developer of the software Tassel.
>>> http://www.maizegenetics.net/tassel
>>>
>>> We currently use Biojava 3.0.  And we are
>>> wanting to use the latest release of Forester.
>>> Since Biojava has a dependency on an older
>>> release of Forester, we are running into conflicts.
>>> Can you help explain Biojava's dependency on
>>> Forester?
>>>
>>> What version of Forester does Biojava 3.0 require?
>>> It looks like version 0.955
>>>
>>> What version of Forester does Biojava 3.0.4 require?
>>>
>>> Does any Biojava jar files include Forester classes?
>>> Or just references?
>>>
>>> Are there plans to remove Biojava's dependency
>>> on Forester?
>>>
>>>
>>> Thank you,
>>>
>>> Terry Casstevens