[Biojava-l] problem running demos from the biojava-live dir ...
sarathchandra
sarathjanga@yahoo.com
Tue, 21 Aug 2001 20:58:02 -0700 (PDT)
hi
I was trying to install the package in red hat linux
7.1 though my pc has both windows millinium edition
and linux installed on the same system with
windows/linux connectivity enabled.
here is what my environment looks like from linux
when i run some commands from bash
[sarath@localhost symbol]$ pwd
/home/sarath/packages/biojava-live/resources/org/biojava/bio/symbol
[sarath@localhost symbol]$ ls
AlphabetManager.xml ResidueProperties.xml
[sarath@localhost symbol]$ echo $CLASSPATH
/home/sarath/jars/biojava-20010813.jar:/home/sarath/jars/jakarta-regexp.jar:/home/sarath/jars/xml.jar:/home/sarath/jars/bytecode-0.90.jar:/home/sarath/jars/xerces.jar:/home/sarath/packages/biojava-live/demos:/home/sarath/packages/biojava-live/resources:.
[sarath@localhost symbol]$ java -version
Kaffe virtual Machine
copyright (c) 1996-2000
Transvirtual Technologies,Inc.All rights reserved
Engine: Just-in-time V3 version:1.0.6 Java
version:1.1
As I said there is a file in manifest ( i think
this file is named default*.*) which shows a path to
resources/org/biojava/bio/seq/tools/AlphabetManager.xml
but when i try to find such file no such file
exists.Is it some thing of our concern for the
failure.
Now coming to my windows environment i tried running
the same way as you have setup . Here is how my
environment looks like but still the problem is a
single exception in main appears irrespective of the
program i run
C:\biojava\biojava-live\demos\>java -version
java version "1.3.0"
Java(TM) 2 Runtime Environment, standard Edition
(build 1.3.0-c)
Java Hotspot(TM) client VM(build 1.3.0.c,mixed mode)
C:\biojava\biojava-live\demos>javac
seq\GCContent.java
C:\biojava\biojava-live\demos>java seq.GCContent
Exception in thread "main"
java.lang.NoclassDefFounderError : seq\GCContent
C:\biojava\biojava-live\demos>java seq.GCContent
AL121903.genbank
Exception in thread "main"
java.lang.NoclassDefFounderError : seq\GCContent
I am not able to get a clue of what is going
wrong.would you advise me to build the whole tree and
make a copy of my own.But i checked the size of the
biojava-jar it is perfectly fine as compared to that
available online.Hope the above output of my command
line will help you to solve my problem.
from sarath
--- Matthew Pocock <mrp@sanger.ac.uk> wrote:
> Hi. My development biojava copy is in
> C:\stuff\biojava\biojava-live on
> my PC. I can find Alphabetmanager.xml here:
>
>
C:\stuff\biojava\biojava-live\resources\org\biojava\bio\symbol>ls
> AlphabetManager.xml AlphabetManager.xml~ CVS
>
> To check if the resource is in the jar I type
> something like this:
>
> C:\stuff\biojava\biojava-live\ant-build>jar -tf
> biojava.jar > out
>
> C:\stuff\biojava\biojava-live\ant-build>grep
> AlphabetManager.xml out
> org/biojava/bio/symbol/AlphabetManager.xml
>
> To check the version of Java, I typed:
>
> C:\>java -version
> java version "1.4.0-beta"
> Java(TM) 2 Runtime Environment, Standard Edition
> (build 1.4.0-beta-b65)
> Java HotSpot(TM) Client VM (build 1.4.0-beta-b65,
> mixed mode)
>
> What kind of output do you get when you do similar
> things?
>
> Matthew
>
> sarathchandra wrote:
>
> > hi pocock
> > I have tried to check the existence of the file
> > alphabetmanager.xml in the directory tools nested
> > inside resources i think this file should be
> > somewhere like this
> > resources/../../tools/alphabetmanager.xml but the
> file
> > alphabetmanager.xml isnt present in the tools
> > directory.. is this some where the problem is
> arising
> > ... if this is so adding resources deliberately to
> my
> > classpath wouldnt help i guess, but still i will
> check
> > it.however do u feel it is the problem with the
> > biojava.jar file? may be? or may be not? have you
> ever
> > faced such problems like the program getting
> compiled
> > well but still the unhealthy exceptions like the
> one i
> > get.
> > awaiting your help
> > from sarath
> > --- Matthew Pocock <mrp@sanger.ac.uk> wrote:
> >
> >>Hi Sarath,
> >>
> >>Weird. It sounds like alphabetmanager.xml can't be
> >>found within the
> >>biojava.jar repository. To test this out, can you
> >>add the 'resources'
> >>directory to the beginning of your classpath
> >>explicitly? If the program
> >>works then Java is having trouble finding the file
> >>within the jar file.
> >>Could you check that alphabetmanager.xml is in the
> >>same directory as
> >>AlphabetManager.class in the jar?
> >>
> >>I've occasionaly come up against strange resource
> >>resolution problems
> >>(do you or don't you add a leading slash to the
> >>path-name?). Mabey it is
> >>one of these.
> >>
> >>Matthew
> >>
> >>ps I've never seen a stack-trace quite like this.
> >>What Java are you running?
> >>
> >>
> >>sarathchandra wrote:
> >>
> >>
> >>>hi thomas and pocock
> >>> I have been using biojava for quite some time
> >>>now,But recently i installed red hat linux 7.1
> and
> >>>added biojava.jar , xerces.jar,
> >>>
> >>xml.jar,bytecode.jar
> >>
> >>>and the jakarta-regexp.jar but inspite of this
> >>>
> >>when i
> >>
> >>>try to run the demos from the biojava-live
> >>>
> >>directory i
> >>
> >>>am getting the followingstack trace for the
> >>>
> >>programs
> >>
> >>>[sarath@localhost demos]javac seq/GCCgbk.java
> >>>[sarath@localhost demos]java seq.GCCgbk
> >>>
> >>seq/utrs.fa
> >>
> >>> java.lang.ExceptionInIntializerError: [exception
> >>>
> >>was
> >>
> >>>org.biojava.bio.bioerror: unable to initialize
> >>>AlphabetManager]
> >>>java.lang.NullpointerException
> >>> rethrown as org.biojava.bio.BioError:unable to
> >>>initialize AlphabetManager
> >>> at
> >>>
> >>>
> >
>
java.lang.Throwable.FillInstanceTrace(Throwable.java:native)
> >
> >>>at java.lang.Throwable.<init>(Throwable.java:38)
> >>>at java.lang.Error.<init>(Error.java:21)
> >>>at org.biojava.utils.NestedError.<init>(Nested
> >>>Error.java:60)
> >>>at
> >>>
> >>org.biojava.bio.bioError,<init>(BioError.java:48)
> >>
> >>> Hope this stack trace will help you to tell
> >>>
> >>me
> >>
> >>>whats wrong with the running of programs is it
> >>>
> >>because
> >>
> >>>the file alphabetmanager.xml in manifest
> directory
> >>>
> >>is
> >>
> >>>missing as i found that such file exists in this
> >>>directory.. Anyway hope to hear an early reply
> >>>
> >>from
> >>
> >>>you
> >>>from sarath
> >>>
> >>>
> >>>
> >>>=====
> >>>
> >
> >
> > =====
> > TIME AND TIDE WAIT FOR NO MAN
> > KNOWLEDGE IS POWER
> >
> > sarath chandra J
> > B.tech 3rd yr
> > IIT Delhi
> >
> > __________________________________________________
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> > http://biojava.org/mailman/listinfo/biojava-l
> >
> >
>
>
>
=====
TIME AND TIDE WAIT FOR NO MAN
KNOWLEDGE IS POWER
sarath chandra J
B.tech 3rd yr
IIT Delhi
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