Bug #3267

ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems

Added by Derik Barseghian over 14 years ago. Updated over 14 years ago.

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ENM/GARP_SingleSpecies_BestRuleSet-IV.xml crashes Ubuntu Kepler.
On mac execution completes but gives ImageJ "Unrecognized comand: ASC TextReader" messages.

Related issues

Blocked by Kepler - Bug #3245: Release 1.0 installer tracking bugResolved04/29/2008


#1 Updated by Chad Berkley over 14 years ago

I just ran this on ubuntu and had no problems. Is there a way to make the error occur?

#2 Updated by Jing Tao over 14 years ago

It crashed my kepler in ubuntu too.

#3 Updated by Dan Higgins over 14 years ago

The Mac error 'ImageJ "Unrecognized comand: ASC
TextReader" also occurs on the GARP Model ImageJ workflow. It looks like this is another problem due to rearranging the files on the Mac. ImageJ looks for plugins in the working directory. If the 'plugins" dir is moved out of the '' dir on the Mac and into the containing 'Kepler' dir the error does not occur because ImageJ can then find the ASC reader plugin code

#4 Updated by Chad Berkley over 14 years ago

Fixed the problem on the mac by creating a symlink to the plugins directory.

#5 Updated by Chad Berkley over 14 years ago

I was finally able to reproduce the crash on ubuntu by installing a fresh version of ubuntu in a VM and running kepler from there. It appears they changed the libexpat and libscew versions in the new release which is causing problems with garp. I recompiled scew and expat and it seems to be working. I don't think we can distribute expat or scew though, so I think we're just going to have to put a note in the workflow or in a readme to let people know that they might have problems on linux.

#6 Updated by Chad Berkley over 14 years ago

I added a note in the README and in the workflow itself about scew and expat for linux.

#7 Updated by Aaron Aaron over 14 years ago

GARP_SingleSpecies_BestRuleSet-IV.xml runs on windows v3 installer and Mac os X v3 installer.
garpModel_ImageJ.xml runs on win & mac v3 installers.
garpModel_ImageJ_withData.xml - the data source was taking so long to load (on win and mac) I did not finish testing...

#8 Updated by Derik Barseghian over 14 years ago

this may again be that i didn't succeed with the expat and scew instructions, but after trying those instructions this workflow didn't crash like before on ubuntu (unless i didn't wait long enough), but instead just seemed to get stuck.

#9 Updated by Redmine Admin over 9 years ago

Original Bugzilla ID was 3267

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