From the ggm docs, it looks like the pcor() function, pcor(u, S)
takes arguments:

u
: a vector of integers of length > 1. The first two integers are the indices of variables the correlation of which must be computed. The rest of the vector is the conditioning set. 
S
: a symmetric positive definite matrix, a sample covariance matrix.
Not knowing what your data looks like, it's hard to say, but NAs by coersion occur when, for example, you try to convert a character to numeric.
as.numeric("a")
#> Warning: NAs introduced by coercion
#> [1] NA
Given that the arguments for pcor()
are numeric, you might be passing character strings where the function requires numeric.
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