[BioMart Users] Installation problem

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[BioMart Users] Installation problem

Sergio Martinez Cuesta
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

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Re: [BioMart Users] Installation problem

Syed Haider
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
>
>
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Re: [BioMart Users] Installation problem

Yong Liang
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


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