I really need help in this

I have a file and would like to calculate the cosine similarity of the values in it...

For now I do use R which has an easy function for doing so

test <- as.matrix(read.csv(file="file.csv", sep=",", header=FALSE)) 
result<- cosine(t(test))

dos2unix test.sh test.sh

I think you will have to give more details in order to get some help:
What OS are you on?
explain the R code, and what you want in unix
Where does cygwin intervene in the process
etc...

I have two files each of 6 lines each representing the frequency of specific words
now I wanted to calculate the cosine similarity between these files

for R I simply combine both files and extracted the bits from overall matrix that I needed

test <- as.matrix(read.csv(file="file.csv", sep=",", header=FALSE)) 
result<- cosine(t(test))
result-files <- (result[7:12,1:6])

Solved the problem by working on a Linux machine