[Debichem-devel] Problems regarding the jmol package sitting in NEW

[Michael Banck]

Hi,

On Sat, Feb 12, 2011 at 09:44:11PM +0100, Vincent Fourmond wrote:
>   I saw only very recently that your team had taken on the burden of
> packaging jmol, and I was glad since that meant that I could provide a
> non-crippled version of jalview (see ITP at
> http://bugs.debian.org/507436). Then I had a look at the binary
> packages, and in particular the dependencies, and I was surprised to
> find that it depends on nothing, while in my memory jmol relied
> heavily on not-yet-packaged software. Then, I took a look at the
> source package, and found out that the following files are present in
> your .orig tarball (I got it using uscan, I guess it must not be very
> different from the one in the NEW queue):
> 
> -rw-r--r-- 0/0            9506 2010-07-24 21:14 jmol-12.0.RC27/jars/Acme.jar
> -rw-r--r-- 0/0          194050 2010-07-24 21:14
> jmol-12.0.RC27/jars/ant-contrib.jar
> -rw-r--r-- 0/0           30117 2010-07-24 21:14
> jmol-12.0.RC27/jars/commons-cli-1.0.jar
> -rw-r--r-- 0/0           69620 2010-07-24 21:14
> jmol-12.0.RC27/jars/gnujaxp-onlysax.jar
> -rw-r--r-- 0/0          231523 2010-07-24 21:14 jmol-12.0.RC27/jars/gnujaxp.jar
> -rw-r--r-- 0/0         1841952 2010-07-24 21:14
> jmol-12.0.RC27/jars/itext-1.4.5.jar
> -rw-r--r-- 0/0          121070 2010-07-24 21:14 jmol-12.0.RC27/jars/junit.jar
> -rw-r--r-- 0/0           43195 2010-07-24 21:14 jmol-12.0.RC27/jars/netscape.jar
> -rw-r--r-- 0/0          625687 2010-07-24 21:14 jmol-12.0.RC27/jars/saxon.jar
> -rw-r--r-- 0/0          110658 2010-07-24 21:14
> jmol-12.0.RC27/jars/vecmath1.2-1.14.jar
> -rw-r--r-- 0/0           75291 2010-07-24 21:14
> jmol-12.0.RC27/jars/vecmath1.2-1.14.tar.gz
> 
>   These are sourceless binary-ony libraries. If they are still in the
> tarball, your package will be rejected.

Those jars got stripped off the orig tarball prior to source package
bundling.
 
>   Moreover, the source also contains already built .jar files, which
> embed these sourceless .jar files.

Likewise.

>   What is worse is the discussion about the netscape.jar dependency,
> see my original ITP

Well, the jar gets removed, and the relevent classes are
implemented/imported.  Not sure, maybe it is provided by standard
OpenJDK runtime.

Currently, the applet doesn't work, and it was suspected that the
netscape classes might be the issue.  However, I added a 

import netscape.javascript.JSObject;

to the main JMol.java file, rebuilt and ran the application without
import errors.

If anybody has some insight on how to get the applet working, that'd be
great.  I uplodaded the debs from the NEW queue to

deb http://people.debian.org/~mbanck/debichem-jmol/ ./


Regards,

Michael