On 23/11/09 2:03 PM, "Richard Holland" <[email protected]> wrote:

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

Hi Dong,
Are you trying to run it with java 1.6 or am I misreading this thread?
Nothing has been officially tested on 1.6. Only 1.5 so far I am afraid. The
new biomart release will come with java 1.6


A.


> 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-1>>>
1
>>> 
>>> 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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