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/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 _______________________________________________ Users mailing list [hidden email] https://lists.biomart.org/mailman/listinfo/users |
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/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 > > Users mailing list [hidden email] https://lists.biomart.org/mailman/listinfo/users |
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" <[hidden email]> 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 > [hidden email] > https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [hidden email] https://lists.biomart.org/mailman/listinfo/users |
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