[Biojava-l] Source dist corrupted?

[Matthew Pocock]

Matthew Pocock wrote:

> I am just about to post today's build to the FTP site, and also update the README. I
> will post once this is done.
>
> Matthew
>

Done! You can grab biojava.jar from the FTP site at:

ftp://biojava.org/pub/biojava/

  or

ftp://bioperl.org/pub/biojava/

I can't make explorer 5 connect to the biojava ftp server, but netscape does (don't ask
me why). This distribution should work, but please tell me if you have any problems.

Matthew

>
> hilmar.lapp@pharma.Novartis.com wrote:
>
> > Dear all,
> >
> > maybe no-one of you is using the source distribution packaged as .tar.gz from
> > the download
> > area the web site points to, but that's what I did today (already the 2nd
> > attempt), and I failed to compile (build) the classes (I'm using a Java 1.2.2
> > port on Irix) because some files seem to be missing from the distribution:
> >
> > [...]
> > src/org/biojava/bio/dp/FlatModel.java:39: Superclass
> > org.biojava.bio.dp.ModelView of class org.biojava.bio.dp.FlatModel not found.
> > public class FlatModel extends ModelView {
> >                                ^
> > src/org/biojava/bio/dp/FlatModel.java:322: Superclass
> > org.biojava.bio.dp.StateView of nested class org.biojava.bio.dp.FlatModel.
> > EmissionWrapper not found.
> >   extends StateView
> >           ^
> > src/org/biojava/bio/seq/tools/SimpleCrossProductAlphabet.java:40: Interface
> > org.biojava.bio.seq.tools.CrossProductAlphabet of class
> > org.biojava.bio.seq.tools.SimpleCrossProductAlphabet not found.
> > class SimpleCrossProductAlphabet implements FiniteAlphabet, CrossProductAlphabet
> > {
> > [... lots of further errors deleted]
> >
> > The classes seem to present in the jar which is also provided for download. I'm
> > wondering
> > whether you expect people to either get the jar or fetch their own CVS tree. CVS
> > is not an
> > option for me because I can't get through our firewall.
> >
> > Second, while I skimmed through the mail archive, I noticed that apparently you
> > recently
> > renamed some of the core classes (like ResidueList), and moved others. Maybe I
> > misunderstood
> > this, but if not, would it mean, that the current API will partially become
> > invalid in the very next distribution, or already is in the current CVS
> > controlled repository. That is, how
> > stable is the API, and if it is still unstable but at least parts have already
> > settled, how can one discriminate between these.
> >
> > Cheers,
> >
> >      Hilmar
> >
> > -----------------------------------------------------------------------------
> > Hilmar Lapp                            email: Hilmar.Lapp@pharma.novartis.com
> > NFI Vienna, IFD/Bioinformatics         phone: +43 1 86634 631
> > A-1235 Vienna                          fax:   +43 1 86634 727
> > ROI: Bioinformatics (arrays, expression, seqs), Programming (OO), Databases
> > -----------------------------------------------------------------------------
> >
> > _______________________________________________
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> > http://biojava.org/mailman/listinfo/biojava-l
>
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