[Biojava-l] Installation woes
Peter Robinson
peter.robinson at t-online.de
Sun Jul 27 07:23:13 UTC 2008
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
peter at peter:~/bin/biojava/biojava-live_1.6/demos$ echo $CLASSPATH
/home/peter/bin/biojava/biojava-live_1.6/biojava.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-dbcp-1.1.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-cli.jar:/home/peter/bin/biojava/biojava-live_1.6/bytecode.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-collections-2.1.jar:/home/peter/bin/biojava/biojava-live_1.6/commons-pool-1.1.jar:.
************ The paths appear to be correct:
peter at peter:~/bin/biojava/biojava-live_1.6/demos$ 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
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$
Richard Holland wrote:
> Hello.
>
> Before typing the javac instruction, type the following to check what
> your classpath actually contains:
>
> echo $CLASSPATH
>
> If this doesn't immediately 'look right' (i.e. it has curly braces or
> variable names embedded in it, or doesn't match where you think the
> files are), then this'll be where the problem is.
>
> If you can't see any obvious problems with it, then post it as a reply
> to this message and we can take a closer look.
>
> cheers,
> Richard
>
>
> 2008/7/26 James Carman <james at carmanconsulting.com>:
>
>> Try export CLASSPATH=$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$
>>>
>>> _______________________________________________
>>> Biojava-l mailing list - Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>> _______________________________________________
>> Biojava-l mailing list - Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>
>
>
>
More information about the Biojava-l
mailing list