[Biojava-l] Intsall Problems Update

Orion Hunter orion2480 at hotmail.com
Sat Feb 28 13:10:49 EST 2004

Thanks for the response.  I got everything working, but it took a little 

First off, I never found the biojava-live directory.  I know I had ANT 
installed correctly, because it worked from the command line... but I never 
found the biojava-live nor the build.xml that ant looks for.

So, I d/l the jars themselves.  However, in order to get everything to work, 
I had to include in my classpath the location of the packages (basically, I 
had to include /home/user/biojava/main in my class path, because this is the 
root of where the pakcage structure is located), in addition to the normal 
classpath of the JARS.

The second thing I had to do was go in and individually compile many of the 
.java files in the packages.  Javac'ing the demo files for whatever reason 
did not do this (and I tried several times, recompiling the demofiles to see 
if that would result in the necessary class files from the packages).

Anyway, in the end I got it to work.  Just took a little extra work.


>From: David Huen <smh1008 at cus.cam.ac.uk>
>Reply-To: smh1008 at cus.cam.ac.uk
>To: "Orion Hunter" <orion2480 at hotmail.com>, biojava-l at biojava.org
>Subject: Re: [Biojava-l] Intsall Problems Update
>Date: Sat, 28 Feb 2004 12:50:25 +0000
>On Friday 27 Feb 2004 9:36 pm, Orion Hunter wrote:
> > So, I added
> >
> > /home/user/biojava/main to my classpath, since org.biojava.* sits in 
> > 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 
> > 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 
> > >>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 
> > >>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, 
> > >>  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 
> > >> 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?
> > >>
>OK, I will go thru' the steps necessary to do a compile and installing the
>jars that result from the compile.
>1) install ant
>You mentioned you have done this.  Do ensure that the ant bin/ directory is
>in PATH so typing "ant" will execute ant.
>2) compile the BJ source tree.
>cd <wherever the the biojava-live directory is>
>3) setting up the CLASSPATH
>Java relies on the CLASSPATH to find classes it needs.  You have to set the
>CLASSPATH to include the jars that biojava depends on as well as the jar in
>which biojava resides.
>running ant creates the biojava.jar in the biojava-live/ant-build 
>If you wish to use that jar, you must put it into your CLASSPATH.  I
>usually set up my CLASSPATH in .bash_profile at login.
>If you are just d/ling the precompiled biojava-1.3.jar, you still need to
>put it into your CLASSPATH or java will nto find the classes it wants and
>give you the error messages your are reading.
>At this stage, things should just work.
>David Huen

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