SEQUOIA (R) - error when running parentage assignment step sequoia()

Question

When running the following duplicate check & parentage assignment within the sequoia package:

ParOUT <- sequoia(GenoM = Geno, LifeHistData = LH, Err=0.005, Module="ped", 
                  UseAge = "no",
                  quiet = FALSE, Plot = TRUE)

I get the following output and error (last two lines):

Warning:  There are 2111 SNPs scored for <5% of individuals, these will be excluded 

Warning:  There are 1 monomorphic (fixed) SNPs, these will be excluded 

Warning:  In addition, there are 52874 SNPs scored for <50% of individuals 

Warning:  *********** There are 8 individuals scored for <5% of SNPs, these WILL BE IGNORED *********** 

After exclusion, There are  40  individuals and  185843  SNPs.

Ageprior: Flat 0/1, overlapping generations, MaxAgeParent = 4,4
Error in if (!is.double(MAF) || any(MAF < 0 | MAF > 1)) { : 
  missing value where TRUE/FALSE needed

What is if (!is.double(MAF) || any(MAF < 0 | MAF > 1)) {} checking for that might be missing from my data?

I tried the above as well as running Module= as both "ped" and "par" with no difference in results.

Answer 1

This was a bug in the package: if a SNP is scored for zero individuals the minor allele frequency (MAF) is , which broke the check to see if all MAF's are between 0 and 1. It should work in the version currently on CRAN.