[Debichem-devel] Will we manage to upgrade jmol

[Ximin Luo]

Ximin Luo:
> Andreas Tille:
>> compile:
>>     [mkdir] Created dir: /build/biojava3-live-3.1.0+dfsg/build/biojava3-structure/classes
>>     [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/build.xml:72: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
>>     [javac] Compiling 342 source files to /build/biojava3-live-3.1.0+dfsg/build/biojava3-structure/classes
>>     [javac] /build/biojava3-live-3.1.0+dfsg/biojava3-structure/src/main/java/org/biojava/bio/structure/asa/AsaCalculator.java:8: error: package javax.vecmath does not exist
>>     [javac] import javax.vecmath.Point3d;
>>     [javac]                     ^
> 
> Hey Andreas,
> 
> The error occurs because either you're missing a dependency on libvecmath-java, and/or because biojava3-live's build files can't find it on the system.
> 
> If I remember correctly, this didn't happen for Jmol 12 because it bundles all the class files of its dependencies inside Jmol.jar. This isn't what we like to do for Debian, so I did things differently for Jmol 14 - add a Class-Path attribute inside the jar manifest, to point to the other jars instead.
> 
> The solution for biojava3-live will depend on the build system; for ANT you can take a look at my patches for Jmol. Its online documentation is quite good, and is how I learnt to work with it many years ago.
> 

To clarify, this is also an upstream bug. If org/biojava/bio/structure/asa/AsaCalculator.java (and the other files) directly use classes from vecmath, then their build process should be searching for and using vecmath.jar, rather than relying on Jmol to include it transitively.

There seems to be some more documentation in debian/{README.Debian,build.xml} about this. Probably you just need to add an extra entry for vecmath.

X

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