[Biojava-dev] compilation of 1.8.2

[Olivier Sallou]

Hi,
I am trying to compile biojava 1.8.2 from source but I have an issue.

I do not use Maven, and created an ant build file, for Debian packaging
reasons.

I failed at compile time in DAS library, not finding
org.biojava.bio.structure.Atom

Indeed, nor core or das define this interface:
osallou at debiansid:$ ls core/src/main/resources/org/biojava/bio/structure
blosum62.mat  standardaminos.pdb
osallou at debiansid:$ ls das/src/main/java/org/biojava/bio/structure
io


    [mkdir] Created dir:
/home/osallou/DEBIAN-MED/biojava/biojava-live-1.8.2.orig/build/biojava-das/classes
    [javac]
/home/osallou/DEBIAN-MED/biojava/biojava-live-1.8.2.orig/das/build.xml:56:
warning: 'includeantruntime' was not set, defaulting to
build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 100 source files to
/home/osallou/DEBIAN-MED/biojava/biojava-live-1.8.2.orig/build/biojava-das/classes
    [javac] Alignment.java:33: cannot find symbol
    [javac] symbol  : class Atom
    [javac] location: package org.biojava.bio.structure
    [javac] import org.biojava.bio.structure.Atom;

Has anyone an idea of why it is missing or what I should get to find it?

-- 


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