Hi Ximin,
On Thu, Dec 08, 2016 at 04:08:00PM +0000, Ximin Luo wrote:
> Andreas Tille:
> > [javac] first method: notifyEnabled(CBK) in JmolCallbackListener
> > [javac] second method: notifyEnabled(EnumCallback) in
> > MyJmolStatusListener
> > [javac] Note:
> > /build/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/JmolPanel.java
> > uses or overrides a deprecated API.
> > [javac] Note: Recompile with -Xlint:deprecation for details.
> > [javac] Note: Some input files use unchecked or unsafe operations.
> > [javac] Note: Recompile with -Xlint:unchecked for details.
> > [javac] 9 errors
> >
> > BUILD FAILED
> > /build/biojava3-live-3.1.0+dfsg/biojava3-structure-gui/build.xml:73:
> > Compile failed; see the compiler error output for details.
> >
>
> This basically means that Jmol changed its API between version 12 and 14. I
> don't think I messed up the packaging, the missing things like
> org.jmol.constant.EnumCallback are not even in the current source code.
While I have no idea about BioJava itself I can confirm that BioJava3 is
in (very) low maintenance and has not seen any release for years - so
your explanation sounds quite probable.
> Someone will have to go through the changes and make biojava3-live work with
> Jmol 14 again, this involves Java coding. What I normally do is grep the
> source code to see if there's anything "similar" in the current source. Or
> perhaps upstream has a patch, commit, or ticket lying around somewhere where
> this is already done or half-done.
>
> To avoid problems like this in the future, it's recommended to only use
> things that are clearly labeled as public API. The current version of Jmol
> has a src/org/jmol/api/ directory, perhaps you can edit the currently-failing
> code to use this instead.
>
> Or, if it is already an old/abandoned project (I notice that biojava4-live
> exists too) I suggest to consider just removing it from Debian.
Yes, BioJava 4 exists and is packaged. Olivier is working on the latest
upstream version - thus I did not tested Jmol with this since the
packaging is currently in flux. I fully trust Olivier to decide whether
to remove BioJava3 from Debian or whether it is worth to find a solution
for the issue above. I'd be personally in favour of getting a recent
Jmol and drop BioJava3.
> > BTW, if it helps I could migrate biojava3-live from SVN to Git if this
> > might be more convenient for interested people to directly change things
> > in VCS.
> >
>
> That would help me if I had time to work on it, but probably not directly on
> the code, for another few weeks.
Olivier, if you confirm that it is worth keeping BioJava3 I'd volunteer to
do this.
Kind regards
Andreas.
--
http://fam-tille.de
