[Debichem-devel] Will we manage to upgrade jmol

[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.

X

-- 
GPG: ed25519/56034877E1F87C35
GPG: rsa4096/1318EFAC5FBBDBCE
https://github.com/infinity0/pubkeys.git