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/
