When trying to run ChAMP version 1.8.2 on a data set of 91 samples using the default champ.process command, it got through the SVD step, but then died at the ComBat step:

Preparing files for ComBat
Error in if (min(beta.c) == 0) { : missing value where TRUE/FALSE needed
Calls: champ.process -> champ.runCombat
In addition: Warning messages:
1: In min(beta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
2: In min(nbeta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
3: In min(beta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
4: In min(nbeta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
5: In min(beta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
6: In min(nbeta2.v[selMR.idx]) :
  no non-missing arguments to min; returning Inf
Execution halted

In champ.norm, I see code like this:

if (min(beta.p, na.rm = TRUE) == 0) {

but in champ.runCombat, I see this (which lacks the na.rm option):

if (min(beta.c) == 0) {

I am not sure how to debug this.  

Thank you.