problem with running Jalview on Mountain Lion

Hi there,

After several unsuccessful tries I installed "successfully", according to the message on the program, Jalview 2.8.0b1 in my Mac Os 10.8.5. However, when I open the program it just does not run at all. First the examples are not showed, and then it does not allow to do the analysis after copying the FASTA sequences on the text box. I run this program without problems in my lab computer which is a bit older, Mac Os 10.6 or so, without problems.

Any help there? Many, many thanks!

Natalia

Hi Natalia
Requena Sanchez, Natalia (BOTANIK) wrote:

After several unsuccessful tries I installed "successfully", according to the message on the program, Jalview 2.8.0b1 in my Mac Os 10.8.5. However, when I open the program it just does not run at all. First the examples are not showed, and then it does not allow to do the analysis after copying the FASTA sequences on the text box. I run this program without problems in my lab computer which is a bit older, Mac Os 10.6 or so, without problems.

It doesn't sound like you are having much fun. Please take a look in the directory where you installed Jalview - you should see a file called 'Output.txt' - if you send this to me, I'll take a look and see what's going on.

Jim.
ps. if you can't find Output.txt - then there are some instructions on the FAQ about opening the Jalview Java console so you can send me the console output from launching Jalview:
http://www.jalview.org/node/44

Hi. Thanks for sending the output.txt...

I copy here below the output.text file I found. It is somehow odd because it says Jalview version 2.4 which was the old version I had in my old laptop 10.5.8 and that did not run in this computer….. can it be that the old version is still there? ummm, I thought I had deleted it when installing the new one.

Yes - you're right - that's definitely an old output file.

I assumed you installed Jalview via the InstallAnywhere installer.. Jalview launched in that way should log every error to output.txt. Have a look at the timestamp - that should show whether it is the right 'output.txt' file ! If nothing else, try a search in spotlight.

I suggest you follow the instructions at http://www.jalview.org/node/44 to launch Jalview, open the Jalview Java console, shut down Jalview (this bit is important) .. and then launch it again to get the console log for Jalview. This should give me enough information to diagnose the problem.

There's one other thing that might help. If you've migrated your home from an old computer, your .jalview_properties file might have old/invalid settings. Shut down any jalviews that are running, then open a terminal window and type

mv ~/.jalview_properties ~/.jalview_properties_old

Then try launching Jalview again.

Jim.

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On 13/02/2014 06:15, Requena Sanchez, Natalia (BOTANIK) wrote: