formatC(0.0001, digits = 3, format = "f", zero.print="< 0.01")
Error in strrep(" ", nc - i1) : invalid 'times' value

The problem, if it is one, is in .format.zeros:
.format.zeros("0.000", "xxxxxx")
Error in strrep(" ", nc - i1) : invalid 'times' value

R version 3.5.1.


David

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