that's it! it is fixed,
thank you Arek and Rechard !
Have a good day!
Dong
>
>
>
> 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/
>>
>
>
