[Biojava-dev] install Biojava

[mark.schreiber at novartis.com]

I think this came up a week ago. Is this a repost of the same problem or 
is it the flakey mail server sending old messages again?

- Mark





Te-yuan Chyou <chyte374 at student.otago.ac.nz>
Sent by: biojava-dev-bounces at portal.open-bio.org
11/23/2005 12:37 PM

 
        To:     biojava-dev at biojava.org
        cc:     biojava-l at biojava.org, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] install Biojava


Hi:

I'm trying to install Biojava onto MacOS following informations in the
"Getting Started" section of the Biojava website, by putting the following
jar files:

biojava.jar
commons-cli.jar
commons-collections-2.1.jar
commons-dbcp-1.1.jar
commons-pool-1.1.jar
bytecode-0.92.jar

into the directory

Macintosh HD/System/Library/Java/Extensions

Then, while trying to compile the demo code "TestEmbl.java" I get 15
errors and looks like the computer cannot find the packages in Biojava.

At that time I didn't set the CLASSPATH because the website says "It is
also possible to "install" JAR files onto your system by copying them...".

Then I put all the jar files in the directory:
/Users/davidchyou/Desktop/david/
Then set the CLASSPATH by typing:

 export
CLASSPATH=/Users/davidchyou/Desktop/david/biojava.jar:/Users/davidchyou/Desktop/commons-cli.jar:/Users/davidchyou/Desktop/david/commons-collections-2.1.jar:/Users/davidchyou/Desktop/david/commons-dbcp-1.1.jar:/Users/davidchyou/Desktop/david/commons-pool-1.1.jar:

in a single line, and the command works. BUT after that when I compile the
demos again, the computer still produces the same set of error messages
(package not exist).

Could anyone tell me what else I missed out? A step-by-step istallation
guide may be helpful also.

Thanks

Te-yuan (David) Chyou

I attached the error messages I get below:

ou003153:~ davidchyou$ javac Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:5: package org.biojava.bio
does not exist
import org.biojava.bio.*;
^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:6: package
org.biojava.bio.symbol does not exist
import org.biojava.bio.symbol.*;
^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:7: package
org.biojava.bio.seq does not exist
import org.biojava.bio.seq.*;
^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:8: package
org.biojava.bio.seq.io does not exist
import org.biojava.bio.seq.io.*;
^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot resolve symbol
symbol  : class SequenceFormat
location: class seq.TestEmbl
      SequenceFormat eFormat = new EmblLikeFormat();
      ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:18: cannot resolve symbol
symbol  : class EmblLikeFormat
location: class seq.TestEmbl
      SequenceFormat eFormat = new EmblLikeFormat();
                                   ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot resolve symbol
symbol  : class SequenceBuilderFactory
location: class seq.TestEmbl
      SequenceBuilderFactory sFact = new
EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY);
      ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: package EmblProcessor
does not exist
      SequenceBuilderFactory sFact = new
EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY);
                                                      ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:21: cannot resolve symbol
symbol  : variable SimpleSequenceBuilder
location: class seq.TestEmbl
      SequenceBuilderFactory sFact = new
EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY);
                                                               ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot resolve symbol
symbol  : class Alphabet
location: class seq.TestEmbl
      Alphabet alpha = DNATools.getDNA();
      ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:22: cannot resolve symbol
symbol  : variable DNATools
location: class seq.TestEmbl
      Alphabet alpha = DNATools.getDNA();
                       ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:23: cannot resolve symbol
symbol  : class SymbolTokenization
location: class seq.TestEmbl
      SymbolTokenization rParser = alpha.getTokenization("token");
      ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:24: cannot resolve symbol
symbol  : class SequenceIterator
location: class seq.TestEmbl
      SequenceIterator seqI =
      ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:25: cannot resolve symbol
symbol  : class StreamReader
location: class seq.TestEmbl
        new StreamReader(eReader, eFormat, rParser, sFact);
            ^
Desktop/Biojava-1.4.1/demos/seq/TestEmbl.java:28: cannot resolve symbol
symbol  : class Sequence
location: class seq.TestEmbl
        Sequence seq = seqI.nextSequence();
        ^
15 errors
ou003153:~ davidchyou$

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