Re: Biojava Dependency on Forester
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CALthepzyPJDJ-jsmn_in5c=1rPho6pTy+oWrBCkou4oBVH0a3Q@mail.gmail.com> |
"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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l