[Biojava-l] Installation woes

[James Carman]

Try export CLASSPATH=$CLASSPATH:...

Basically, remove the "squiggly braces"


On Sat, Jul 26, 2008 at 6:41 AM, Peter Robinson
<peter.robinson at t-online.de> wrote:
> 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$
>
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