Hi Donghe,
just to extend Arek's point, it wont work on JDK > 1.5. The reason for
it to fail would be JDK 1.6 or above in the first place and then OpenJDK.
Cheers
Syed
Arek Kasprzyk wrote:
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/