Hi All, In Windows 7 , R installation: R version 3.1.1 Patched (2014-07-14 r66149) -- "Sock it to Me" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) it doesn't recognize shortcuts in path :> list.files(path = "cygwin")character(0) cygwin is a shortcut, in properties window Target shows : C:\Users\me\cygwin64\home\me Real path works : list.files(path = "C:/Users/me/cygwin64/home/me") [1] "1010week.sh" "10week.sh" "a.R" "aa.sh" ....