You can use colMeans
:
### Sample data
set.seed(1)
m <- data.frame(matrix(sample(100, 20, replace = TRUE), ncol = 4))
### Your error
mean(m)
# [1] NA
# Warning message:
# In mean.default(m) : argument is not numeric or logical: returning NA
### The result using `colMeans`
colMeans(m)
# X1 X2 X3 X4
# 47.0 64.4 44.8 67.8