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BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
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analyse trees.R Error: evaluation nested too deeply: infinite recursion / options(expressions=)? #40

Closed damientully closed 5 years ago

damientully commented 5 years ago

Hi,

I seem to get the following error when using phyloscanner_analyse_trees.R on a dataset when performing the parsimony reconstruction:

Error: evaluation nested too deeply: infinite recursion / options(expressions=)? Execution halted Any solutions?

Thanks, Damien

mdhall272 commented 5 years ago

Huh. Not seen that before. How many tips does the tree have?

damientully commented 5 years ago

A lot! ~20,000!

mdhall272 commented 5 years ago

See https://stackoverflow.com/questions/22003021/explanation-of-r-optionsexpressions-to-non-computer-scientists - try options(expressions=N) for some large N?

damientully commented 5 years ago

Will take a look. Thanks

damientully commented 5 years ago

That worked. Thanks!