[Biojava-dev] Docbook error

[sanjay]

Hi,

I had no problems with docbook (perhaps you've already fixed that), but got
a different failure in the ant build (see below).

Sanjay

-------------
Sanjay Kumar, PhD
New England Biolabs
kumar@neb.com

=======================================================================

Buildfile: build.xml

init:
     [echo] JUnit present:                   ${junit.present}
     [echo] JUnit supported by Ant:          true
     [echo] Trax API present:                true
     [echo] DocBook DTD present:             ${docbook.dtd.present}
     [echo] DocBook XSL stylesheets present: ${docbook.xsl.present}

prepare:

prepare-core:

prepare-14:

prepare-src:

compile:
    [javac] Compiling 40 source files to
E:\cvs\biojava\biojava-live\ant-build\c
lasses\main
    [javac]
E:\cvs\biojava\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\GAMEFormat.java:37: package org.biojava.bio.seq.io.game12 does not exist
    [javac] import org.biojava.bio.seq.io.game12.*;
    [javac] ^
    [javac]
E:\cvs\biojava\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\GAMEFormat.java:73: cannot resolve symbol
    [javac] symbol  : class GAMEHandler
    [javac] location: class org.biojava.bio.seq.io.GAMEFormat
    [javac]             GAMEHandler handler = new GAMEHandler(listener);
    [javac]             ^
    [javac]
E:\cvs\biojava\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
o\GAMEFormat.java:73: cannot resolve symbol
    [javac] symbol  : class GAMEHandler
    [javac] location: class org.biojava.bio.seq.io.GAMEFormat
    [javac]             GAMEHandler handler = new GAMEHandler(listener);
    [javac]                                       ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -deprecation for details.
    [javac] 3 errors

BUILD FAILED
file:E:/cvs/biojava/biojava-live/build.xml:270: Compile failed; see the
compiler
 error output for details.

Total time: 24 seconds


======================================================================
----- Original Message -----
From: "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>
To: "BioJava Dev List" <biojava-dev@biojava.org>
Sent: Wednesday, November 06, 2002 3:25 PM
Subject: [Biojava-dev] Docbook error


> Hi -
>
> I just did a cvs update and tried the docbook target in the ant build
> and got:
>
> C:\src\cvs\biojava-live>ant docbook
> Buildfile: build.xml
>
> init:
>      [echo] JUnit present:                   ${junit.present}
>      [echo] JUnit supported by Ant:          true
>
> prepare:
>
> prepare-core:
>
> prepare-docs:
>      [echo] Trax API present:                true
>     [unjar] Expanding: C:\src\cvs\biojava-live\docbook.jar into
> C:\src\cvs\biojava-live\ant-build\lib
>
> BUILD FAILED
> java.lang.IllegalArgumentException
>         at
> java.util.zip.ZipInputStream.getUTF8String(ZipInputStream.java:291)
>         at java.util.zip.ZipInputStream.readLOC(ZipInputStream.java:230)
>         at
> java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:75)
>         at
> org.apache.tools.ant.taskdefs.Expand.expandFile(Expand.java:156)
>         at org.apache.tools.ant.taskdefs.Expand.execute(Expand.java:127)
>         at org.apache.tools.ant.Task.perform(Task.java:319)
>         at org.apache.tools.ant.Target.execute(Target.java:309)
>         at org.apache.tools.ant.Target.performTasks(Target.java:336)
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1250)
>         at org.apache.tools.ant.Main.runBuild(Main.java:610)
>         at org.apache.tools.ant.Main.start(Main.java:196)
>         at org.apache.tools.ant.Main.main(Main.java:235)
>
> Total time: 6 seconds
> java.lang.IllegalArgumentException
>         at
> java.util.zip.ZipInputStream.getUTF8String(ZipInputStream.java:291)
>         at java.util.zip.ZipInputStream.readLOC(ZipInputStream.java:230)
>         at
> java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:75)
>         at
> org.apache.tools.ant.taskdefs.Expand.expandFile(Expand.java:156)
>         at org.apache.tools.ant.taskdefs.Expand.execute(Expand.java:127)
>         at org.apache.tools.ant.Task.perform(Task.java:319)
>         at org.apache.tools.ant.Target.execute(Target.java:309)
>         at org.apache.tools.ant.Target.performTasks(Target.java:336)
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
>         at
> org.apache.tools.ant.Project.executeTargets(Project.java:1250)
>         at org.apache.tools.ant.Main.runBuild(Main.java:610)
>         at org.apache.tools.ant.Main.start(Main.java:196)
>         at org.apache.tools.ant.Main.main(Main.java:235)
>
>
> Is this working on other peoples machines or am I needing to install
> some other files?
>
> Mark Schreiber PhD
> Bioinformatics
> AgResearch Invermay
> PO Box 50034
> Mosgiel
> New Zealand
>
> PH:   +64 3 489 9175
> FAX:  +64 3 489 3739
>
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