There is a difference in how files are stored on these two operating systems.

By default, when files are created on a windows system, the end of the file is marked with a carriage return (\r) and a newline (\n). The user does not insert this, it is done automatically by the software. This is not the case in the linux/unix environment. The end of line in linux is marked only by the newline (\n). When performing text processing, the carriage return (\r) will cause problems in the linux environment.

To see if your file contains carriage returns (\r) use the linux command od. Od stands for Octal Dump and will display the contents of the file in various formats. In this case, you should run od -c filename. This will display each character in the file, with some special characters, like carriage return and newline proceeded by a slash.

In this example, the file foo.cpp has been created on a computer running windows and transferred to a computer running linux. To check the format, the user runs od -c foo.cpp. Note that each line ends in \r and \n.

 
$ more foo.cpp
#include <iostream>

using namespace std;

int main() {
   cout << "Hello World " << endl;

   return 0;
}

$ od -c foo.cpp
0000000   #   i   n   c   l   u   d   e       <   i   o   s   t   r   e
0000020   a   m   >  \r  \n  \r  \n   u   s   i   n   g       n   a   m
0000040   e   s   p   a   c   e       s   t   d   ;  \r  \n  \r  \n   i
0000060   n   t       m   a   i   n   (   )       {  \r  \n            
0000100   c   o   u   t       <   <       "   H   e   l   l   o       W
0000120   o   r   l   d       "       <   <       e   n   d   l   ;  \r
0000140  \n  \r  \n               r   e   t   u   r   n       0   ;  \r
0000160  \n   }  \r  \n
0000164

In the following example, the file bar.cpp was produced on a system that did not add a carriage return (\r) to the end of each line.

$ more bar.cpp
#include <iostream>

using namespace std;

int main() {
   cout << "Hello World " << endl;

   return 0;
}
$ od -c bar.cpp
0000000   #   i   n   c   l   u   d   e       <   i   o   s   t   r   e
0000020   a   m   >  \n  \n   u   s   i   n   g       n   a   m   e   s
0000040   p   a   c   e       s   t   d   ;  \n  \n   i   n   t       m
0000060   a   i   n   (   )       {  \n               c   o   u   t    
0000100   <   <       "   H   e   l   l   o       W   o   r   l   d    
0000120   "       <   <       e   n   d   l   ;  \n  \n               r
0000140   e   t   u   r   n       0   ;  \n   }  \n
0000153

Note in this example that lines end with a newline (\n) but not a carriage return (\r).