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Error with ./configure and make

Hello  World,

I am trying to install a package on my computer (Windows 7 64) that was written 
primarily for a Linux instillation.  I am using cygwin to accomplish this.  The 
Install notes for the package I am trying to use say I can either run 
make install

or I can use cmake then   
make install

If I just run ./configure  I get the error

line 21: $'\r': command not found 
line 32: syntax error near unexpected token `$'in\r'' 
line 32: `   case   1(set -o) 2>/dev/null` in 

To resolve this I use Vim and run
:set fileformat=unix
I then enter  ./configure  into the terminal and get the following error.

configure: error: cannot run /bin/sh config/config.sub

I have not figured out how to fix this yet.
I then tried using cmake and am able to run that.  However, once it is finished 
I type    make    into the terminal and I get the following error

src/nvec_ser/CMakeFiles/sundials_nvecserial_shared_dir/build.make:53: *** target 
pattern contains no `%'. stop. 
make[1]: *** [src/nvec_ser/CMakeFiles/sundials_nvecserial_shared.dir/all] Error 
make: *** [all] Error 2 

Does anyone have any idea on how I can fix either or both of these issues?  For 
the  configure: error: cannot run /bin/sh config/config.sub  error I tried 
changing /bin/sh to  C:/cygwin/bin/sh (the location of sh on my hard drive) in 
the configure file, but that did not help.

Please help me!  :,(

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