When I added /opt/hdf5/include to the Includes for my project, the IDE was flagging my #include statements as errors but make executed just fine. If I used C:\cygwin\opt\hdf5\include The IDE didn't flag errors but the make was broken as I would get these "*** multiple target patterns".
Apararently this is a bug in the make that comes with cygwin. In 3.81, make cannot resolve windows style paths. The problem went away when I replaced /usr/bin/make.exe with http://www.cmake.org/files/cygwin/make.exe.
Source: http://www.cygwin.com/ml/cygwin/2009-04/msg00007.html
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