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/
