[Biojava-l] Compiling with Jikes

[Bradley A. Smith]

Here is a sample of some of the errors:

compile:
    [javac] Compiling 384 source files to
/home/basmith/tmp/biojava-1.10/ant-build/classes
    [javac]
    [javac] Found 1 semantic error compiling
"/home/basmith/tmp/biojava-1.10/ant-build/src/org/biojava/bio/symbol/FiniteA
lphabet.java":
    [javac]
    [javac]     46. public interface FiniteAlphabet extends Alphabet {
    [javac]                          <----------------------------->
    [javac] *** Error: The interface "org/biojava/bio/symbol/FiniteAlphabet"
is circularly defined with its super type(s).
    [javac]
    [javac] Found 2 semantic errors compiling
"/home/basmith/tmp/biojava-1.10/ant-build/src/org/biojava/bio/symbol/Alphabe
t.java":
    [javac]
    [javac]     42. public interface Alphabet extends Annotatable {
    [javac]                          <-------------------------->
    [javac] *** Error: The interface "org/biojava/bio/symbol/Alphabet" is
circularly defined with its super type(s).
    [javac]
    [javac]
    [javac]    163.   static final Alphabet EMPTY_ALPHABET = new
EmptyAlphabet();
    [javac]
<---------------------------------->
    [javac] *** Error: The type of the left-hand side in this assignment,
"org/biojava/bio/symbol/Alphabet", is not compatible with the type of the
right-hand side expression, "org/biojava/bio/symbol/Alphabet$EmptyAlphabet".
    [javac]
    [javac] Found 1 semantic error compiling
"/home/basmith/tmp/biojava-1.10/ant-build/src/org/biojava/bio/symbol/Fundame
ntalAtomicSymbol.java":
    [javac]
    [javac]     62.     return new SingletonAlphabet(this);
    [javac]                        <------------------------->
    [javac] *** Error: The type of this return expression,
"org/biojava/bio/symbol/SingletonAlphabet", does not match the return type
of the method, "org/biojava/bio/symbol/Alphabet".

Thanks,
  Bradley

----- Original Message -----
From: "Ann Loraine" <loraine@loraine.net>
To: "Bradley A. Smith" <bradley.smith@Agouron.COM>
Cc: <biojava-l@biojava.org>
Sent: Sunday, March 04, 2001 12:19 AM
Subject: Re: [Biojava-l] Compiling with Jikes


> What sort of errors did you get?
>
> Were they complaints about accessing static (final?) class data fields
> using instance variables?
>
> e.g.,
>
> Foo foo = new foo();
> int x = foo.x;
>
> (where x is a class variable)
>
> The Sun compiler (last time I used it .. which was ages ago :-) lets this
> pass, but other compilers are stricter and report an error.
>
> -Ann
> ---
>
> Ann E. Loraine
> http://www.loraine.net
>
> On Sun, 4 Mar 2001, Bradley A. Smith wrote:
>
> > Has anyone successfully compiled BioJava 1.10 with the IBM Jikes
compiler? I receive many errors. I believe some of the errors are allowed by
the Sun compiler although they are valid errors. Is anyone interested in
fixing the errors so that the BioJava can be compiled with Jikes?
> >
> > Thanks,
> >   Bradley
> >
> >
> >
> >
>