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waldronlab / lefser

R implementation of the LEfSe method
https://waldronlab.io/lefser/
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vignette not building #7

Closed lwaldron closed 10 months ago

lwaldron commented 3 years ago

See: https://github.com/waldronlab/lefser/runs/1078939897#step:8:12

* creating vignettes ... ERROR
--- re-building ‘lefser.Rmd’ using rmarkdown
Quitting from lines 66-68 (lefser.Rmd) 
Error: processing vignette 'lefser.Rmd' failed with diagnostics:
Group classification is not binary:
Expected (0, 1) but found (0)
lwaldron commented 3 years ago

It's a different error now. Also should understand these warnings.

results <- lefserAnalysis(exampledata)
##  Error in UseMethod("group_vars") : 
##  no applicable method for 'group_vars' applied to an object of class ##  "logical"

warnings() ##variables are collinear, conditional covariance matrix has zero diagonal elements - maybe need a different example, or to explain what the collinear variables are and the consequences
LiNk-NY commented 10 months ago

This seems to be an old issue. Currently the vignette builds (in version 1.11.1).