[Biojava-l] Re: biojava-acedb

[Francois Pepin]

Guys,

Could someone who know acedb take a look at it? I just did a clean
checkout from the cvs and ant still crashed on me.

The build.xml references the resources directory which doesn't exist
(should probably be commented in). It looks like it's missing some
biojava code as well in there. It's giving me a ton of mistakes when
trying to compile either.

Did someone manage to do a build from a fresh checkout recently?

Francois

-----Original Message-----
From: Suman Kanuganti [mailto:bioinformatics4suman at yahoo.com] 
Sent: 11 aout, 2003 12:00
To: Francois Pepin
Subject: RE: [Biojava-l] Re: biojava-acedb


Well right, I logged in root whatsoever for the
permissions.

[root at newtondell biojava-acedb]# ant
Buildfile: build.xml

init:

prepare:
    [mkdir] Created dir:
/home/newton/biojava-acedb/ant-build

prepare-src:
    [mkdir] Created dir: /home/newton/biojava-acedb/ant-build/src
    [mkdir] Created dir: /home/newton/biojava-acedb/ant-build/classes
     [copy] Copying 53 files to /home/newton/biojava-acedb/ant-build/src
     [copy] Copying 1 file to /home/newton/biojava-acedb/ant-build/src

BUILD FAILED
file:/home/newton/biojava-acedb/build.xml:89:
/home/newton/biojava-acedb/resources not found.

-- I manually created the resources directory, then I
ant again, it tries to compile AceSequence.java at
first and fails when it is looking for
org.biojava.bio.seq.genomic.* ; I looked at api, but I
havent found this package. Even I noticed it first
time. So could you tell me how to resolve this, here
is a part of the error,

[root at newtondell biojava-acedb]# ant -buildfile
build.xml
Buildfile: build.xml

init:

prepare:

prepare-src:

compile:
    [javac] Compiling 45 source files to
/home/newton/biojava-acedb/ant-build/classes
    [javac] This version of java does not support the
classic compiler; upgrading to modern
    [javac]
/home/newton/biojava-acedb/ant-build/src/org/acedb/seq/AceSequence.java:
33:
package org.biojava.bio.seq.genomic does not exist
    [javac] import org.biojava.bio.seq.genomic.*;
    [javac] ^
    [javac]
/home/newton/biojava-acedb/ant-build/src/org/acedb/seq/AceAnnotation.jav
a:34:
org.acedb.seq.AceAnnotation should be declared
abstract; it does not define
isUnchanging(org.biojava.utils.ChangeType) in
org.acedb.seq.AceAnnotation

....... and continues, as the first one itself failed.

Thanks for any suggestions,
Suman K

--- Francois Pepin <fpepin at cs.mcgill.ca> wrote:
> Hi Suman,
> 
> My guess is that you have a permission problem
> somewhere, or that your
> disk is full or something similar.
> 
> Try to see if you can create that directory by
> yourself.
> 
> The error seems to be about being able to create the directory itself.

> It happened before any of the code was touched for compilation, so the
> problem would not be with the code, but with the
> machine that you're
> building on.
> 
> Francois
> 
> -----Original Message-----
> From: biojava-l-bounces at biojava.org
> [mailto:biojava-l-bounces at biojava.org] On Behalf Of Suman Kanuganti
> Sent: 10 aout, 2003 18:40
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Re: biojava-acedb
> 
> 
> I figured out something that I need to use ant to
> build the acedb-biojava, with the build.xml provided
> by the package. Now the problem:
> 
> [newton at newtondell bin]$ ant -buildfile ~/biojava-acedb/build.xml
> Buildfile: /home/newton/biojava-acedb/build.xml
> 
> init:
> 
> prepare:
> 
> BUILD FAILED
> file:/home/newton/biojava-acedb/build.xml:61:
> Directory /home/newton/biojava-acedb/ant-build
> creation was not successful for an unknown reason
> 
> Total time: 1 second
> 
> Any suggestions,
> Suman K
> 
> 
> --- Suman Kanuganti <bioinformatics4suman at yahoo.com>
> wrote:
> > Is there any jar for acedb-biojava for running its programs. I
> > downloaded biojava-acedb.tar but
> couldnt
> > figure how to build corresponding .jar to add it
> in
> > my
> > path.
> > 
> > Could any one tell me about this?
> > 
> > Suman K
> > 
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! SiteBuilder - Free, easy-to-use web site
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> > 
> 
> 
> =====
> Suman K
> BioInformatics Associate,
> Genomics Research,
> University of Missouri - Columbia.
> 
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> 


=====
Suman K
BioInformatics Associate,
Genomics Research,
University of Missouri - Columbia.

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