[Biojava-l] build error w/ JBuilder

Thomas Down td2@sanger.ac.uk
Fri, 18 Aug 2000 10:58:30 +0100

On Thu, Aug 17, 2000 at 01:19:54PM -0700, Ann Loraine wrote:
> I just updated my copy of biojava and picked up your change.
> Sorry to be a pain, but now I have another problem -- again w/
> building on Windows.  Has anyone else run into this, as well?
> I'm not sure about this, but it seems that the xerces and Sun xml
> jars are perhaps incompatible.  (the ones from biojava Web site)
> When I try to build biojava I get this error:
> "cannot access class com.sun.xml.tree.ElementNode; no source found; must
> be compiled, because org.w3c.dom.Element.normalize referenced by
> class com.sun.xml.tree.ElementNode has changed."

Hmmm, are you trying to compile BioJava with both xml.jar (crimson)
and xerces.jar on your classpath.  I wouldn't expect these to be
compatible, since xml.jar includes the w3c DOM level 1 API, while
Xerces-J provides level 2.  Since the big switch a few days back,
the BioJava HEAD should now be compiled with xerces.jar -- there
should be no need for xml.jar as well, and I'll remove it from the
CVS repository soon.

If you use the latest version of the BioJava build tool, it will
compile with xerces.jar rather than xml.jar.

Is there some particular reason why you need Sun's xml.jar instead
of Xerces?  If this has created a clash, I'll have to look into ways
of sorting things out.  But generally, Xerces offers pretty much
everything that Crimson did, plus proper handling of XML namespaces
(this is the main change in the SAX2 and DOM level 2 APIs).

Let me know if there's any more trouble,

PS. For people using the release-1_0-branch, this still uses the
   old xml.jar.
One of the advantages of being disorderly is that one is
constantly making exciting discoveries.
                                       -- A. A. Milne