Answering my own question. This is the command line for cmake that
finally allowed me to compile OB (and pass all the tests in "make
test"!):

../../cmake-2.8.0/bin/cmake.exe   -G"MSYS Makefiles"
-DZLIB_LIBRARY=/usr/local/lib/libz.a
-DZLIB_INCLUDE_DIR=/usr/local/inclulde
-DEIGEN2_INCLUDE_DIR=/usr/local/include/eigen2
-DLIBXML2_LIBRARIES=/usr/local/lib/libxml2.a
-DLIBXML2_INCLUDE_DIR=/usr/local/include/libxml2
-DCMAKE_INSTALL_PREFIX=/usr/local/ -DBUILD_SHARED=OFF
-DCMAKE_CXX_FLAGS=-DLIBXML_STATIC -DCMAKE_C_FLAGS=-DLIBXML_STATIC
-DCMAKE_CXX_STANDARD_LIBRARIES=-lws2_32 ../


Now, for some reason libopenbabel.a gets installed in /usr/local/bin
instead of /usr/local/lib - anybody can comment on this?

Igor

On Fri, 2010-11-12 at 14:01 -0500, Filippov, Igor (NIH/NCI) [C] wrote:
> It seems I have somehow messed up my build system for OB on Windows...Or
> perhaps it was messed up before and worked, and now I try to clean it up
> and it stopped working.
> Has anyone worked out a consistent way to build OB 2.3.0 on MinGW? It
> looks like my own instructions do not work for me anymore after I
> removed old versions of OpenBabel and libxml2:
> http://sourceforge.net/tracker/?func=detail&aid=3095855&group_id=40728&atid=428740
> 
> right now I can compile everything, however "make test" shows 37 failed
> tests out of 52 and trying to run babel.exe gives a weird error:
> "Couldn't reserve space for cygwin's heap. Win32 error 6".
> This is weird because I don't use cygwin at all.
> 
> Igor
> 
> 
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