I'm afraid at this point I'm stuck - you'll have to wait for one of the 
official developers to help I think!

cheers,
Richard

On 23 Nov 2009, at 19:00, [email protected] wrote:

> Hi Richard,
> it still doesn't work! any other suggestion?
> Dong
>> That will depend on your Linux distribution. I'm guessing you're using
>> Fedora Core 11, from your uname output. If so, then this page explains
>> all:
>> 
>>  
>> http://www.cahilig.org/how-install-sun-java-runtime-environment-jre-fedora-11
>> 
>> You'll have to Google the equivalent commands if you're using other OSes.
>> 
>> cheers,
>> Richard
>> 
>> On 23 Nov 2009, at 18:07, [email protected] wrote:
>> 
>>> I downloaded dk-6u17-linux-i586-rpm.bin from sun.com, and installed it.
>>> when I check jave version, it is still OpenJDK. how can I install this
>>> correctly?
>>> 
>>> #java -version
>>> java version "1.6.0_0"
>>> OpenJDK Runtime Environment (IcedTea6 1.6) (fedora-30.b16.fc11-i386)
>>> OpenJDK Server VM (build 14.0-b16, mixed mode)
>>> 
>>> 
>>>> Ah, you're running OpenJDK IcedTea.
>>>> 
>>>> Sometimes having versions of Java other than the official Sun one can
>>>> cause problems with GUI-intensive applications such as MartEditor.
>>>> 
>>>> Try installing the official Sun Java and see if that fixes it.
>>>> 
>>>> cheers,
>>>> Richard
>>>> 
>>>> On 21 Nov 2009, at 23:23, [email protected] wrote:
>>>> 
>>>>> I removed .biomart/ folder as you suggested, it still doesn't work.
>>>>> 
>>>>> ~]# uname -a && java -version
>>>>> Linux      2.6.30.9-90.fc11.i686.PAE #1 SMP Sat Oct 17 11:24:32 EDT
>>>>> 2009
>>>>> i686 i686 i386 GNU/Linux
>>>>> java version "1.6.0_0"
>>>>> OpenJDK Runtime Environment (IcedTea6 1.6) (fedora-30.b16.fc11-i386)
>>>>> OpenJDK Server VM (build 14.0-b16, mixed mode)
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> Did you try the thing about removing the config folder?
>>>>>> 
>>>>>> It would be really useful to know the output of this command:
>>>>>> 
>>>>>> uname -a && java -version
>>>>>> 
>>>>>> cheers,
>>>>>> Richard
>>>>>> 
>>>>>> On 21 Nov 2009, at 00:56, [email protected] wrote:
>>>>>> 
>>>>>>> it still doesn't work after I reinstalled martj-0.7 binary. i use
>>>>>>> fedora
>>>>>>> 11.
>>>>>>> 
>>>>>>> Thanks
>>>>>>> 
>>>>>>> Dong
>>>>>>> 
>>>>>>>> There is one quick thing you can do which will remove one possible
>>>>>>>> cause
>>>>>>>> (corrupt config files) - find your home directory, then find within
>>>>>>>> it
>>>>>>>> the
>>>>>>>> .biomart or .martj folders (can't remember which one it is now) and
>>>>>>>> delete/rename it. This will make MartEditor start up as if it were
>>>>>>>> a
>>>>>>>> clean
>>>>>>>> install. If that does fix it, then the problem is most likely due
>>>>>>>> to
>>>>>>>> something that was broken in the config, e.g. pointing to a
>>>>>>>> database
>>>>>>>> which
>>>>>>>> no longer exists.
>>>>>>>> 
>>>>>>>> If that doesn't do it, then it sounds like something has changed
>>>>>>>> locally
>>>>>>>> then. It would still be useful to have the uname -a and java
>>>>>>>> -version
>>>>>>>> outputs to hand, as they would help work out what system you're
>>>>>>>> using
>>>>>>>> (for
>>>>>>>> future reference if others have the same problem).
>>>>>>>> 
>>>>>>>> Seeing as it used to work but has recently stopped - and I assume
>>>>>>>> it
>>>>>>>> used
>>>>>>>> to work on this machine and not somewhere else - have you done a
>>>>>>>> recent
>>>>>>>> upgrade on any OS component, or recently installed or removed any
>>>>>>>> other
>>>>>>>> software? Have you recently upgraded to a newer version of BioMart,
>>>>>>>> or
>>>>>>>> updated the source if you're building from source?
>>>>>>>> 
>>>>>>>> cheers,
>>>>>>>> Richard
>>>>>>>> 
>>>>>>>> On 20 Nov 2009, at 21:46, [email protected] wrote:
>>>>>>>> 
>>>>>>>>> it used to work, and martbuilder still works
>>>>>>>>> 
>>>>>>>>>> Hello,
>>>>>>>>>> 
>>>>>>>>>> A bit more information will help diagnose your problem. Can you
>>>>>>>>>> cut-and-paste the output from the following command line please:
>>>>>>>>>> 
>>>>>>>>>> uname -a && java -version
>>>>>>>>>> 
>>>>>>>>>> Also, what version of BioMart are you using, and did you download
>>>>>>>>>> the
>>>>>>>>>> binaries or did you build it from source? If source, which branch
>>>>>>>>>> or
>>>>>>>>>> tag
>>>>>>>>>> in CVS did you check out? Did it used to work but has now
>>>>>>>>>> stopped,
>>>>>>>>>> or
>>>>>>>>>> has
>>>>>>>>>> it never worked?
>>>>>>>>>> 
>>>>>>>>>> Does typing 'xterm' at the same prompt work? If not, you've
>>>>>>>>>> probably
>>>>>>>>>> got a
>>>>>>>>>> general X windows misconfiguration.
>>>>>>>>>> 
>>>>>>>>>> cheers,
>>>>>>>>>> Richard
>>>>>>>>>> 
>>>>>>>>>> On 20 Nov 2009, at 20:05, [email protected] wrote:
>>>>>>>>>> 
>>>>>>>>>>> Hi, friends,
>>>>>>>>>>> 
>>>>>>>>>>> I have a problem to start marteditor on my box, marteditor
>>>>>>>>>>> window
>>>>>>>>>>> didn't
>>>>>>>>>>> pop up when I type ./marteditor.sh,  any suggestion?
>>>>>>>>>>> 
>>>>>>>>>>> Thanks!
>>>>>>>>>>> 
>>>>>>>>>>> Dong
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>>> --------------------------
>>>>>>>>>>> bin]# ./marteditor.sh
>>>>>>>>>>> Starting MartEditor please wait ....
>>>>>>>>>>> getting driver com.mysql.jdbc.Driver
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>>> ------------------------------------
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> --
>>>>>>>>>> Richard Holland, BSc MBCS
>>>>>>>>>> Operations and Delivery Director, Eagle Genomics Ltd
>>>>>>>>>> T: +44 (0)1223 654481 ext 3 | E: [email protected]
>>>>>>>>>> http://www.eaglegenomics.com/
>>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> --
>>>>>>>> Richard Holland, BSc MBCS
>>>>>>>> Operations and Delivery Director, Eagle Genomics Ltd
>>>>>>>> T: +44 (0)1223 654481 ext 3 | E: [email protected]
>>>>>>>> http://www.eaglegenomics.com/
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> Richard Holland, BSc MBCS
>>>>>> Operations and Delivery Director, Eagle Genomics Ltd
>>>>>> T: +44 (0)1223 654481 ext 3 | E: [email protected]
>>>>>> http://www.eaglegenomics.com/
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> --
>>>> Richard Holland, BSc MBCS
>>>> Operations and Delivery Director, Eagle Genomics Ltd
>>>> T: +44 (0)1223 654481 ext 3 | E: [email protected]
>>>> http://www.eaglegenomics.com/
>>>> 
>>>> 
>>> 
>>> 
>> 
>> --
>> Richard Holland, BSc MBCS
>> Operations and Delivery Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: [email protected]
>> http://www.eaglegenomics.com/
>> 
>> 
> 
> 

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/

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