[Biojava-l] Installation woes

James Carman james at carmanconsulting.com
Sun Jul 27 11:43:49 UTC 2008 

This is exactly why BioJava needs to be Mavenized!

On Sun, Jul 27, 2008 at 3:23 AM, Peter Robinson
<peter.robinson at t-online.de> wrote:
> 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
>>>>
>>>>
>>>
>>> _______________________________________________
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>>>
>>>
>>
>>
>>
>>
>
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