If you want to recompile the code, use java 1.4 or 1.5. Biomart0.7 is not tested in java1.6.
On 11-02-11 10:21 AM, "Syed Haider" <[email protected]> wrote: > Hi Sergio, > > no need to recompile the code, the OS specific binaries are already > available on the link: > > http://www.biomart.org/install-overview.html > > the binaries are under bin/ > > Do they not work for you ? > > Best, > Syed > > On 11/02/2011 18:29, Sergio Martinez Cuesta wrote: >> 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? >> >> ----------------------------------------------------------------------------- >> ------------ >> >> $ ant jar >> Buildfile: build.xml >> >> prepare: >> [mkdir] Created dir: >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/docs/api >> [mkdir] Created dir: >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/build >> [mkdir] Created dir: >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/build/classes >> [mkdir] Created dir: >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/dist >> [mkdir] Created dir: >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/dist/martj-0.7 >> [mkdir] Created dir: >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/reports >> [mkdir] Created dir: >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/reports/tests >> >> compile: >> [javac] Compiling 310 source files to >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/build/classes >> [javac] >> /home/sergio/Documents/EMBL-EBI_U.CAMBRIDGE/Research/Missing_Boys_Review/mart >> j/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/mart >> j/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/mart >> j/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/mart >> j/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/mart >> j/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/mart >> j/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/mart >> j/build.xml:203: >> Compile failed; see the compiler error output for details. >> >> Total time: 8 seconds >> >> ---------------------------------------------- >> >> Thanks >> >> > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
