file modified in R produces "unexpected end of file" error

Question

I am modifying the input and bash files of a model that I run using Cygwin. I have no problems when modifying the input files using readLines() and write(). However, for the bash file I get the following error in Cygwin: "Line xx: syntax error, unexpected end of file". The xxx is the final line of the file. Is there a way to open, modify and save these type of files withtout producing any change in the format or does anybody know how to solve this?

Thanks!

G

I have modified other files of the same program (inputs and data) files and saved back using write() in R and the program has run ok. It is just modifying the bash file when I get the error.