/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" <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] 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" <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] 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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