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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