Hi Oliver
The best thing to do is get the CVS version as described on the Artemis
home page (under the Development section). This contains a Makefile and a
build.xml file.
So you can compile using make:
e.g.
make clean
make
Or use the build.xml there to compile with ant.
Regards
Tim
On Tue, 1 May 2007, Oliver Krieg wrote:
> Hello,
>
> I'm trying to compile Artemis V9 via ant. This is my buildfile.xml:
>
> <project name="Artemis" default="build" basedir=".">
> <description>Artemis V9</description>
>
> <property name="srcdir" location="${basedir}" />
> <property name="jardir" location="${basedir}/lib" />
> <property name="apidir" location="${basedir}/api" />
>
> <property name="package" value="uk.ac.sanger" />
> <property name="main" value="$
> {package}.artemis.components.ArtemisMain" />
>
> <path id="buildClassPath">
> <pathelement location="${jardir}/biojava.jar" />
> <pathelement location="${jardir}/chado-14-interface.jar" />
> <pathelement location="${jardir}/jakarta-regexp-1.2.jar" />
> <pathelement location="${jardir}/jemAlign.jar" />
> <pathelement location="${jardir}/jobcontrol.jar" />
> <pathelement location="${jardir}/macos.jar" />
> <pathelement location="${jardir}/
> postgresql-8.1-407.jdbc2ee.jar" />
> <pathelement location="${jardir}/retrotranslator-
> runtime-1.1.0.jar" />
> <pathelement location="${jardir}/j2ssh/commons-logging.jar" />
> <pathelement location="${jardir}/j2ssh/j2ssh-artemis-
> plugin.jar" />
> <pathelement location="${jardir}/j2ssh/j2ssh-core.jar" />
> <pathelement location="${jardir}/ibatis/cglib-
> nodep-2.2_beta1.jar" />
> <pathelement location="${jardir}/ibatis/ibatis-2.3.0.677.jar" />
> <pathelement location="${jardir}/ibatis/log4j-1.2.14.jar" />
> </path>
>
> <target name="build" description="Compiles the code">
> <javac srcdir="${srcdir}"
> classpathref="buildClassPath" />
> </target>
> </project>
>
>
> But it won't compile. I always get the following errors:
>
>
> build:
> [javac] Compiling 290 source files
> [javac] /Users/oliver/Documents/workspaceUVIC/ArtemisSource/
> artemis/uk/ac/sanger/artemis/ExternalProgramUtils.java:69: cannot
> access uk.ac.sanger.util.AbstractPropertyChangeable
> [javac] file uk/ac/sanger/util/AbstractPropertyChangeable.class
> not found
> [javac] new
> uk.ac.sanger.jcon.job.JobBatchImpl (administrator.getExecutableById
> (1));
> [javac] ^
> [javac] /Users/oliver/Documents/workspaceUVIC/ArtemisSource/
> artemis/uk/ac/sanger/artemis/ExternalProgramUtils.java:83: cannot
> access uk.ac.sanger.sql.MutableNestedSetTreeNode
> [javac] file uk/ac/sanger/sql/MutableNestedSetTreeNode.class not
> found
> [javac] new
> uk.ac.sanger.jcon.job.JobBatchImpl (executable);
> [javac] ^
> [javac] /Users/oliver/Documents/workspaceUVIC/ArtemisSource/
> artemis/uk/ac/sanger/artemis/ExternalProgramUtils.java:85: cannot
> access uk.ac.sanger.util.PropertyChangeable
> [javac] file uk/ac/sanger/util/PropertyChangeable.class not found
> [javac] job.setStatus
> (status_dao.readStatusById ( uk.ac.sanger.jcon.job.Status.WAITING));
> [javac] ^
> [javac] /Users/oliver/Documents/workspaceUVIC/ArtemisSource/
> artemis/uk/ac/sanger/artemis/ExternalProgramUtils.java:88:
> incompatible types
> [javac] found : java.lang.Object
> [javac] required: java.lang.String
> [javac] final String input_file_name =
> sequence_file_names.elementAt (i);
>
> [javac]
> ^
> [javac] Note: Some input files use or override a deprecated API.
> [javac] Note: Recompile with -Xlint:deprecation for details.
> [javac] Note: Some input files use unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [javac] 4 errors
>
> BUILD FAILED
>
> I already searched for the class
> uk.ac.sanger.util.AbstractPropertyChangeable, but I didn't find it in
> the source or in one of the jar-files ...
>
> What I'm doing wrong? Can anyone help me?
>
> Cheers
> Oliver
>
>
>
The Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
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