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

[Bruno Aranda - BioDev]

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