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.
Matt
From: David Huen <[EMAIL PROTECTED]> Reply-To: [EMAIL PROTECTED] To: "Orion Hunter" <[EMAIL PROTECTED]>, [EMAIL PROTECTED] 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 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?
> >>
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> ant
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 directory.
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.
Regards, David Huen
_________________________________________________________________
Watch high-quality video with fast playback at MSN Video. Free! http://click.atdmt.com/AVE/go/onm00200365ave/direct/01/
_______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
