m2 <- c(22,NA,0,NA,42,NA)
m3 <- c(89,38,0,67,0,NA)
df = data.frame(m2,m3)

for (i in nrow(df)){
      if (is.na(df[['m2']][i]) == TRUE | is.na(df[['m3']][i]) == TRUE){df[['result']][i] = NA}
      if (df[['m2']][i] == 0 & df[['m3']][i] == 0) {df[['result']][i] = 9999}
      if (df[['m3']][i] == 0 | df[['m2']][i] != 0) {df[['result']][i] = -9999}
      else {df[['result']][i] = (df[['m2']][i] - df[['m3']][i])/df[['m3']][i]}
    }

Error in if (df[["m2"]][i] == 0 & df[["m3"]][i] == 0) { :
  missing value where TRUE/FALSE need