Hi,
Thanks. I think that squiggly braces are OK for the shell, but in any
case, I removed them from .bashrc, which now goes as follows:
export CLASSPATH=/home/peter/bin/biojava/biojava-live_1.6/biojava.jar
export
CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/commons-dbcp-1.1.jar
export
CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/commons-cli.jar
export
CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/bytecode.jar
export
CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/commons-collections-2.1.jar
export
CLASSPATH=$CLASSPATH:/home/peter/bin/biojava/biojava-live_1.6/commons-pool-1.1.jar
export CLASSPATH=$CLASSPATH:.
**************The class path variable seems to be set OK
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ echo $CLASSPATH
/home/peter/bin/biojava/biojava-live_1.6/biojava.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-dbcp-1.1.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-cli.jar:/home/peter/bin/biojava/biojava-live_1.6/bytecode.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-collections-2.1.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-pool-1.1.jar:.
************ The paths appear to be correct:
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ ls
/home/peter/bin/biojava/biojava-live_1.6/*.jar
/home/peter/bin/biojava/biojava-live_1.6/apps-live.jar
/home/peter/bin/biojava/biojava-live_1.6/commons-dbcp-1.1.jar
/home/peter/bin/biojava/biojava-live_1.6/biojava-live.jar
/home/peter/bin/biojava/biojava-live_1.6/commons-pool-1.1.jar
/home/peter/bin/biojava/biojava-live_1.6/bytecode.jar
/home/peter/bin/biojava/biojava-live_1.6/demos-live.jar
/home/peter/bin/biojava/biojava-live_1.6/commons-cli.jar
/home/peter/bin/biojava/biojava-live_1.6/jgrapht-jdk1.5.jar
/home/peter/bin/biojava/biojava-live_1.6/commons-collections-2.1.jar
/home/peter/bin/biojava/biojava-live_1.6/junit-4.4.jar
***********But again, I cannot compile any of the demo programs
[EMAIL PROTECTED]:~/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
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$
Richard Holland wrote:
Hello.
Before typing the javac instruction, type the following to check what
your classpath actually contains:
echo $CLASSPATH
If this doesn't immediately 'look right' (i.e. it has curly braces or
variable names embedded in it, or doesn't match where you think the
files are), then this'll be where the problem is.
If you can't see any obvious problems with it, then post it as a reply
to this message and we can take a closer look.
cheers,
Richard
2008/7/26 James Carman <[EMAIL PROTECTED]>:
Try export CLASSPATH=$CLASSPATH:...
Basically, remove the "squiggly braces"
On Sat, Jul 26, 2008 at 6:41 AM, Peter Robinson
<[EMAIL PROTECTED]> 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
[EMAIL PROTECTED]:~/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
[EMAIL PROTECTED]:~/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
[EMAIL PROTECTED]:~/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)
[EMAIL PROTECTED]:~/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
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$
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