[Biojava-l] Intsall Problems Update

[Orion Hunter]

So, I added

/home/user/biojava/main to my classpath, since org.biojava.* sits in this 
directory (maybe this should be mentioned in the getting started page).  I 
got rid of all my compile errors, but am encountering runtime errors now:

/home/user/biojava/demos>$ java seq.TestEmbl seq/AL121903.embl
java.lang.NoClassDefFoundError: 
org/biojava/bio/symbol/SimpleCrossProductAlphabet
        at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:54)
rethrown as org.biojava.bio.BioError: Unable to initialize DNATools
        at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:85)
        at seq.TestEmbl.main(TestEmbl.java:22)

If I go into the directory of this package, there is no .class file for this 
file (which is of course why I got this error).  HOwever, I cannot figure 
out why there is no .class file.  I didn't get any compile errors, but I 
would have thought this class file would have been compiled then. ANy 
suggestions?


>From: "Orion Hunter" <orion2480 at hotmail.com>
>To: biojava-l at biojava.org
>Subject: RE: [Biojava-l] Intsall Problems
>Date: Fri, 27 Feb 2004 21:11:47 +0000
>
>In case it makes a difference, I forgot to mention that I am using 
>j2sdk1.5.0beta on an Intel based RedHat  9.1 machine.
>
>Matt
>
>p.s. Sorry for the "intsall" mispell
>
>
>>From: "Orion Hunter" <orion2480 at hotmail.com>
>>To: biojava-l at biojava.org
>>Subject: [Biojava-l] Intsall Problems
>>Date: Fri, 27 Feb 2004 20:39:21 +0000
>>
>>I am trying to install biojava.  I d/l biojava1.3.1, unziped and untarred 
>>it.  I installed ANT, but I am confused.  It specifies to execute ANT from 
>>the "biojava-live" directory, but I cannot find this directory, nor any 
>>build.xml files anywhere.
>>
>>So, then I try to download the jar file.  I download all three required 
>>files (biojava.jar, bytecode.jar, and xerces.jar).  I add them to my 
>>classpath (and have confirmed that the classpath is correct and is 
>>remembered by the machine in my env).
>>
>>So, with a set of jars, I decided to try out the demo.  Following the 
>>instructions on the website (in the "getting started" section), I cd to 
>>the demos/, and type the following:
>>
>>/home/user/biojava/>javac seq/TestEmbl.java
>>
>>I get a whole slew of errors, of which all look like they have to do with 
>>the fact that it can't find the packages in org.biojava.bio, etc.  Now, I 
>>can see this package structure in
>>
>>/home/user/biojava/main/org/biojava/bio, etc.
>>
>>And I was trying to execute from /home/user/biojava/demos
>>
>>So, why can't it find the packages?  I'm not new to java, but it's been a 
>>long time since I've had to deal with packages, and I can't recall how to 
>>make biojava see where the packages are located.  Any suggestions?
>>
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