I can't give you the answer for sure, but I'm having trouble getting them to build in cygwin too. It looks like a missing symbol issue. This is the first place it fails, when it can't find the symbol __int64. I don't quite understand this because this is all Linux code and I thought __int64 was a Microsoft VC++-only symbol. Anyway, I've tried sticking a "long long" def for it in various places and it's not taking. The best I can figure is that ImageMagick's libraries are designed to work with Visual C++ as well as Linux, and when then see the WINDOWS definition, they try to use VC++ specific symbols (and who knows what else), even though we're not actually compiling with VC++, and KABOOM!
$ make
make all-recursive
make[1]: Entering directory /home/Ben/pfstools-1.8.2'
Making all in src
make[2]: Entering directory/home/Ben/pfstools-1.8.2/src'
Making all in pfs
make[3]: Entering directory /home/Ben/pfstools-1.8.2/src/pfs'
make[3]: Nothing to be done forall'.
make[3]: Leaving directory /home/Ben/pfstools-1.8.2/src/pfs'
Making all in fileformat
make[3]: Entering directory/home/Ben/pfstools-1.8.2/src/fileformat'
g++ -DHAVE_CONFIG_H -I. -I../.. -I./../pfs -fopenmp -I/usr/include/ImageMagick
-O3 -MT pfsinimgmagick.o -MD -MP -MF .deps/pfsinimgmagick.Tpo -c -o pfs
inimgmagick.o pfsinimgmagick.cpp
In file included from /usr/include/ImageMagick/magick/MagickCore.h:147,
from /usr/include/ImageMagick/Magick++/Include.h:47,
from /usr/include/ImageMagick/Magick++/Image.h:11,
from /usr/include/ImageMagick/Magick++.h:9,
from pfsinimgmagick.cpp:29:
/usr/include/ImageMagick/magick/magick-type.h:129: error: `__int64' does not nam
e a type
[and so on]