[Biojava-dev] Problems building biojava v2 (trunk or alpha1)

[Michael Heuer]

Hello Bruno,

I've committed the patch I sent to the list yesterday (that hasn't yet
made it through moderation), so if you've worked around the Override
problem you should be ok with a svn update to revision 40 or above on the
trunk.

   michael


On Thu, 6 May 2004, Bruno Aranda - BioDev wrote:

> Hello everybody!
>
> I wanted to try the alpha1 of biojava v2, but I could'nt build it
> completely. I am using a jdk1.5beta, svn, ant 1.6.1 in a windows os. The
> two fixes Michael provided work perfectly. Then I found an error with the
> "@override" as the j2sdk1.5 beta distribution hasn't been updated yet. A
> workaround for this one is easy: I've created a Override.java identical to
> Overrides.java (any smarter alternatives? is there any current dist with
> Override?)... Well, but then I got some errors more that I couldn't fix:
>
> ---------------------------- extract of the ant output
>
> compile:
>     [javac] Compiling 73 source files to
> C:\dev\java\biojava2\bjv2\trunk\data\ant-build\classes
>     [javac]
> C:\dev\java\biojava2\bjv2\trunk\data\src\org\bjv2\gql\Evaluator.java:430:
> cannot find symbol
>     [javac] symbol  : constructor Or(java.util.ArrayList)
>     [javac] location: class org.bjv2.gql.Or<T>
>     [javac]     return new Or<T>(new ArrayList(items));
>     [javac]            ^
>     [javac]
> C:\dev\java\biojava2\bjv2\trunk\data\src\org\bjv2\gql\impl\MergingQueryable.java:15:
> org.bjv2.gql.impl.MergingQueryable is not abstract and does not
> override abstract method isSingleton() in org.bjv2.gql.Queryable
>     [javac] public class MergingQueryable<T>
>     [javac]        ^
>     [javac]
> C:\dev\java\biojava2\bjv2\trunk\data\src\org\bjv2\integrator\Integrators.java:18:
> cannot find symbol
>     [javac] symbol  : constructor
> NoKeyIntegrator(org.bjv2.integrator.UserIntrospector)
>     [javac] location: class
> org.bjv2.integrator.impl.NoKeyIntegrator<UserType>
>     [javac]         return new NoKeyIntegrator<UserType>(userIntrospector);
>     [javac]                ^
>     [javac]
> C:\dev\java\biojava2\bjv2\trunk\data\src\org\bjv2\integrator\Integrators.java:20:
> cannot find symbol
>     [javac] symbol  : constructor
> SingleKeyIntegrator(org.bjv2.integrator.UserIntrospector)
>     [javac] location: class
> org.bjv2.integrator.impl.SingleKeyIntegrator<UserType>
>     [javac]         return new
> SingleKeyIntegrator<UserType>(userIntrospector);
>     [javac]                ^
>     [javac]
> C:\dev\java\biojava2\bjv2\trunk\data\src\org\bjv2\integrator\PropertyMappings.java:58:
> cannot find symbol
>     [javac] symbol  : constructor
> PropertyMappingImpl(org.bjv2.integrator.UserIntrospector,org.bjv2.integrator.DataIntrospector)
>     [javac] location: class
> org.bjv2.integrator.impl.PropertyMappingImpl<UserType,DataType>
>     [javac]       mapping = new PropertyMappingImpl<UserType,DataType>(ui,
> di);
>     [javac]                 ^
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] 5 errors
>
>
> -----------------------
>
> Does it have to compile? Am I missing something?
>
> I want to contribute as much as possible to Biojava 2 because it is a very
> interesting project indeed, and I want to follow it from the very
> begining... As for the license stuff, I have to say that I work in a small
> bioinformatics company in Spain and I want to use as much as possible open
> source tools (so costs are cheaper and this allows to give for free our
> products to the research community)...
>
> Thanks in anticipation!!!
>
> Bruno
>
>
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