[Biojava-l] Installation woes

[Peter Robinson]

Hi Biojava,

I am entirely new to Biojava and have limited Java experience (C is more 
my thing), and so this is almost certainly a dumb question, but I cannot 
seem to find an answer in the online docs. I am running debian 4 linux 
and have:

java version "1.6.0_06"
Java(TM) SE Runtime Environment (build 1.6.0_06-b02)
Java HotSpot(TM) Server VM (build 10.0-b22, mixed mode)



I have downloaded the biojava code, unpacked it, and set the CLASSPATH 
in bashrc :

BIOJAVA_BASE=/home/peter/bin/biojava/biojava-live_1.6
export CLASSPATH=${BIOJAVA_BASE}/biojava.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-cli.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-collections-2.1.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/bytecode.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-dbcp-1.1.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-pool-1.1.jar
export CLASSPATH=${CLASSPATH}:.


This also goes through without error from the command line. However, 
when I try to compile one of the test programs as instructed on the page:
http://biojava.org/wiki/BioJava:GetStarted

peter at peter:~/bin/biojava/biojava-live_1.6/demos$ javac seq/TestEmbl.java


I get a bunch of errors, apparently javac cannot find the imports it needs. (see bottom of this mail).

I would greatly appreciate any tips how to get started here!
Thanks, Peter




peter at peter:~/bin/biojava/biojava-live_1.6/demos$ javac seq/TestEmbl.java
seq/TestEmbl.java:25: package org.biojavax does not exist
import org.biojavax.Namespace;
                   ^
seq/TestEmbl.java:26: package org.biojavax does not exist
import org.biojavax.RichObjectFactory;
                   ^
seq/TestEmbl.java:27: package org.biojavax.bio.seq does not exist
import org.biojavax.bio.seq.RichSequence;
                           ^
seq/TestEmbl.java:28: package org.biojavax.bio.seq does not exist
import org.biojavax.bio.seq.RichSequenceIterator;
                           ^
seq/TestEmbl.java:48: cannot find symbol
symbol  : class Namespace
location: class seq.TestEmbl
      Namespace ns = RichObjectFactory.getDefaultNamespace();
      ^
seq/TestEmbl.java:48: cannot find symbol
symbol  : variable RichObjectFactory
location: class seq.TestEmbl
      Namespace ns = RichObjectFactory.getDefaultNamespace();
                     ^
seq/TestEmbl.java:50: cannot find symbol
symbol  : class RichSequenceIterator
location: class seq.TestEmbl
      RichSequenceIterator seqI =
      ^
seq/TestEmbl.java:51: package RichSequence does not exist
        RichSequence.IOTools.readEMBLDNA(br, ns);
                    ^
seq/TestEmbl.java:54: cannot find symbol
symbol  : class RichSequence
location: class seq.TestEmbl
        RichSequence seq = seqI.nextRichSequence();
        ^
seq/TestEmbl.java:57: package RichSequence does not exist
        RichSequence.IOTools.writeEMBL(System.out, seq, ns);
                    ^
10 errors
peter at peter:~/bin/biojava/biojava-live_1.6/demos$ java -version
java version "1.6.0_06"
Java(TM) SE Runtime Environment (build 1.6.0_06-b02)
Java HotSpot(TM) Server VM (build 10.0-b22, mixed mode)
peter at peter:~/bin/biojava/biojava-live_1.6/demos$ javac seq/TestEmbl.java
seq/TestEmbl.java:25: package org.biojavax does not exist
import org.biojavax.Namespace;
                   ^
seq/TestEmbl.java:26: package org.biojavax does not exist
import org.biojavax.RichObjectFactory;
                   ^
seq/TestEmbl.java:27: package org.biojavax.bio.seq does not exist
import org.biojavax.bio.seq.RichSequence;
                           ^
seq/TestEmbl.java:28: package org.biojavax.bio.seq does not exist
import org.biojavax.bio.seq.RichSequenceIterator;
                           ^
seq/TestEmbl.java:48: cannot find symbol
symbol  : class Namespace
location: class seq.TestEmbl
      Namespace ns = RichObjectFactory.getDefaultNamespace();
      ^
seq/TestEmbl.java:48: cannot find symbol
symbol  : variable RichObjectFactory
location: class seq.TestEmbl
      Namespace ns = RichObjectFactory.getDefaultNamespace();
                     ^
seq/TestEmbl.java:50: cannot find symbol
symbol  : class RichSequenceIterator
location: class seq.TestEmbl
      RichSequenceIterator seqI =
      ^
seq/TestEmbl.java:51: package RichSequence does not exist
        RichSequence.IOTools.readEMBLDNA(br, ns);
                    ^
seq/TestEmbl.java:54: cannot find symbol
symbol  : class RichSequence
location: class seq.TestEmbl
        RichSequence seq = seqI.nextRichSequence();
        ^
seq/TestEmbl.java:57: package RichSequence does not exist
        RichSequence.IOTools.writeEMBL(System.out, seq, ns);
                    ^
10 errors
peter at peter:~/bin/biojava/biojava-live_1.6/demos$