Problem with -burnin LogCombiner 1.10.3

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Ch. Julian

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Nov 5, 2018, 1:59:54 PM11/5/18
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Hi,

Using LogCombiner 1.10.3 in Terminal with the burnin option returns error

logcombiner -burnin 10000 test1.log test2.log combined.log

or 

logcombiner -burnin 0 test1.log test2.log combined.log

Returns

Exception in thread "main" java.lang.ClassCastException: dr.app.util.Arguments$LongOption cannot be cast to dr.app.util.Arguments$IntegerOption 
at dr.app.util.Arguments.getIntegerOption(Unknown Source) 
at dr.app.tools.LogCombiner.main(Unknown Source)

but removing the burning option works fine

logcombiner test1.log test2.log combined.log

returns:

Creating combined log file: 'combined.log' 
Combining file: 'test1.log' without removing burnin 
Combining file: 'test2.log' without removing burnin 
Finished.

Any ideas?

Cheers, 

Michael

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Nov 6, 2018, 11:18:49 AM11/6/18
to beast-users
Hi all,

I also encountered a problem when using LogCombiner v1.10.3.

I used LogCombiner v1.10.3 GUI to combine log files with "Renumber output states" checked. However, the combination failed with following messages:

Combining file: '/Users/Test1.log' removing burnin: 10000000
Finished - Quit program to exit.
Exception: / by zero
java.lang.ArithmeticException: / by zero
    at dr.app.tools.LogCombiner.<init>(Unknown Source)
    at dr.app.tools.LogCombiner.main(Unknown Source)


When I used command line with the -renumber flag, the combination failed again with following messages (the same as what Juliáa got):

Exception in thread "main" java.lang.ClassCastException: dr.app.util.Arguments$LongOption cannot be cast to dr.app.util.Arguments$IntegerOption
    at dr.app.util.Arguments.getIntegerOption(Unknown Source)
    at dr.app.tools.LogCombiner.main(Unknown Source)


Any thoughts about it? Thank you!

Best wishes,
Michael

Andrew Rambaut

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Nov 9, 2018, 9:48:38 AM11/9/18
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This is now fixed in the GitHub repository and a update will be release shortly.

Andrew

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Andrew Rambaut

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Nov 11, 2018, 12:28:11 PM11/11/18
to beast...@googlegroups.com, Michael
This bug has now been fixed in v1.10.4

Best,
Andrew

On 6 Nov 2018, at 16:18, Michael <positi...@gmail.com> wrote:

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