Issue with getting randomisation to run for CANAPE

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Andre Alexander

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Feb 18, 2020, 4:52:41 PM2/18/20
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Hi there,

Big fan of the Biodiverse package here, but I'm currently having some issues getting my randomizations to run completely. Im running Biodiverse 3.0 on a Mac, and when I try to run step 3 after running step 2 successfully (http://biodiverse-analysis-software.blogspot.com/2014/11/do-it-yourself-canape.html), an error message appears about a third of the way into the randomization runs:

"Cannot open /CANAPE_CSV_rand_structured_iter_10.bds.tmp at Biodiverse/Common.pm line 833

 at Biodiverse/GUI/Tabs/Randomise.pm line 696.
 at Biodiverse/GUI/Tabs/Randomise.pm line 696.
 at Biodiverse/GUI/Tabs/Randomise.pm line 696."

I've already made sure that my tip labels and BaseData names match using "Trim to match Tree Nodes", and have tried changing the number of iterations and checkpoints saved but to no avail.

Any clues/suggestions?

Thanks!
Andre

Shawn Laffan

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Feb 18, 2020, 5:14:30 PM2/18/20
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Hello Andre,

Good to hear you're enjoying the software. 

This issue was reported off-list by another user late last year, and users will be warned if it might happen in version 3.1.  It is logged under https://github.com/shawnlaffan/biodiverse/issues/746

The workaround in that issue is to set your working directory under the File menu.  That is where any temporary files are written, and for some reason the Mac version of Biodiverse sets it to be the system root directory.

The other alternative is to not write out any checkpoint files.  They were originally added as a workaround for crashes caused by memory leaks, as then the system can be restarted from the most recent checkpoint.  Those leaks were fixed for version 0.18, so they are no longer needed for that purpose. 

To disable the checkpoints, set the value to -1 (this is the default value).

Regards,
Shawn.
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Shawn Laffan

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Feb 18, 2020, 5:22:35 PM2/18/20
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I have also updated the blog post with a note to recommend not using checkpoint saves unless they are really needed. 

Hopefully that addresses the issue more generally, but please do keep reporting any other problems (or successes) you have with the software. 


Regards,
Shawn.

Andre Alexander

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Feb 19, 2020, 11:18:03 AM2/19/20
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Shawn,

Thank you so much, that worked!

Cheers,
Andre
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Shawn Laffan

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Feb 19, 2020, 4:32:42 PM2/19/20
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Good to hear.

Regards,
Shawn.
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