Dear Biomart:
I was following http://www.biomart.org/install-overview.html
instructions and I got the installation problem below, when I tried to
install then source dist'n of BioMart.
Could you please help me?
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$ ant jar
Buildfile: build.xml
prepare:
[mkdir] Created dir:
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/docs/api
[mkdir] Created dir:
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/build
[mkdir] Created dir:
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/build/classes
[mkdir] Created dir:
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/dist
[mkdir] Created dir:
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/dist/martj-0.7
[mkdir] Created dir:
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/reports
[mkdir] Created dir:
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/reports/tests
compile:
[javac] Compiling 310 source files to
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/build/classes
[javac]
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/src/java/org/biomart/common/view/gui/BioMartGUI.java:114:
warning: non-varargs call of varargs method with inexact argument type
for last parameter;
[javac] cast to java.lang.Class<?> for a varargs call
[javac] cast to java.lang.Class<?>[] for a non-varargs call and to
suppress this warning
[javac]
app.getClass().getMethod("addAboutMenuItem", null).invoke(app,
[javac] ^
[javac]
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/src/java/org/biomart/common/view/gui/BioMartGUI.java:115:
warning: non-varargs call of varargs method with inexact argument type
for last parameter;
[javac] cast to java.lang.Object for a varargs call
[javac] cast to java.lang.Object[] for a non-varargs call and to
suppress this warning
[javac] null);
[javac] ^
[javac]
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/src/java/org/biomart/common/view/gui/BioMartGUI.java:116:
warning: non-varargs call of varargs method with inexact argument type
for last parameter;
[javac] cast to java.lang.Class<?> for a varargs call
[javac] cast to java.lang.Class<?>[] for a non-varargs call and to
suppress this warning
[javac]
app.getClass().getMethod("addPreferencesMenuItem", null)
[javac]
^
[javac]
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/src/java/org/biomart/common/view/gui/BioMartGUI.java:117:
warning: non-varargs call of varargs method with inexact argument type
for last parameter;
[javac] cast to java.lang.Object for a varargs call
[javac] cast to java.lang.Object[] for a non-varargs call and to
suppress this warning
[javac] .invoke(app, null);
[javac] ^
[javac]
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/src/java/org/biomart/common/resources/Resources.java:142:
warning: non-varargs call of varargs method with inexact argument type
for last parameter;
[javac] cast to java.lang.Object for a varargs call
[javac] cast to java.lang.Object[] for a non-varargs call and to
suppress this warning
[javac] return
MessageFormat.format(Resources.getValue(key), values);
[javac] ^
[javac]
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/src/java/org/ensembl/mart/lib/DetailedDataSource.java:58:
org.ensembl.mart.lib.DetailedDataSource is not abstract and does not
override abstract method isWrapperFor(java.lang.Class<?>) in
java.sql.Wrapper
[javac] public class DetailedDataSource implements DataSource {
[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] 1 error
[javac] 5 warnings
BUILD FAILED
/home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/martj/build.xml:203:
Compile failed; see the compiler error output for details.
Total time: 8 seconds
----------------------------------------------
Thanks
--
Sergio Martinez Cuesta
PhD student @ EMBL-European Bioinformatics Institute
Thornton Group - http://www.ebi.ac.uk/Thornton/
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
UK
Phone: +44(0)1223494607
Mobile: +44(0)7884312566
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