I struggled a little bit with this today and thought  I will post it
to the group in case it helps someone.

To build aggdraw for output from rdkit on 64 bit linux systems  do the
following:
Based on a comment on the aggdraw blog page from osirius , you need to
change a single line of code in the
agg2/include/agg_array.h file as detailed on this post:

http://www.pocketuniverse.ca/archive/2008/december/11/pil-and-aggdraw/

Original solution by Subash chandra
(http://timeless-scripts.blogspot.com/2007/08/patch-to-aggdraw-for-64-bit-machines.html)




Index: agg2/include/agg_array.h
===================================================================
--- agg2/include/agg_array.h    (revision 521)
+++ agg2/include/agg_array.h    (working copy)
@@ -520,7 +520,7 @@
                int8u* ptr = m_buf_ptr;
                if(alignment > 1)
                {
-                    unsigned align = (alignment - unsigned(ptr) %
alignment) % alignment;
+                    unsigned align = (alignment - (unsigned
long)(ptr) % alignment) % alignment;
                    size += align;
                    ptr += align;
                    if(size <= m_rest)


After that aggdraw builds fine with

python setup.py build_ext -i
sudo python setup.py install



Hope this helps

Hari

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