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