[Rdkit-discuss] Building RDKit on Windows

[James D. <J.D...@ve...>]

Dear All,

As part of a New Year's resolution, I decided I should try to enjoy the benefits of a cutting-edge version of RDKit built from source(!)  So far this has proven to be much more realistic than eg 'not drinking for January' - as I now have a working build to show for my efforts.

However, I wonder if I could quickly list the steps I took; and also ask a couple of questions (relating to InChi and Avalon)?  For reference I am running on Windows7 64-bit, but use python 2.7.6 32bit, so am building 32-bit RDKit.  I essentially followed the guide on the wiki (https://code.google.com/p/rdkit/wiki/BuildingOnWindows) but thought the version info of boost, etc may be of use to others, and the steps may help put my questions into context:


1.       Downloaded Visual Studio Express 2012 for Desktop, installed, and accepted the updates

2.       Downloaded matching version of Windows boost binaries (boost_1_55_0-msvc-11.0-32.exe) from http://sourceforge.net/projects/boost/files/boost-binaries/ and extracted to the default path

3.       Used TortoiseSVN to add a repository link to https://github.com/rdkit/rdkit.git/trunk (and not the SF path as currently shown in the wiki guide) in C:/RDKit

4.       Set the environment variables as described on the wiki.

5.       Downloaded the INCHI src as described in the wiki and set the RDK_BUILD_INCHI_SUPPORT option later in cmake.  Incidentally, the location for the downloads from IUPAC have changed (ie the info in the README is out of date): http://www.iupac.org/home/publications/e-resources/inchi/download.html

6.       Ran CMake configure (GUI) following the wiki, and based on the output, made some boost-related additions to environment variables

a.       Added C:\local\boost_1_55_0\lib32-msvc-11.0 to PATH

b.      Created BOOST_ROOT=C:\local\boost_1_55_0

c.       Created BOOST_LIBRARYDIR=C:\local\boost_1_55_0\lib32-msvc-11.0

7.       Re-ran configure, then generate, then followed the rest of the wiki instructions to build and test - all tests passed except the dbCli one.


So now for the questions:
I thought I did everything right for adding INCHI support.  However, I see the following:



In [1]: from rdkit import Chem

In [2]: Chem.inchi.INCHI_AVAILABLE

Out[2]: False



CMake shows:


Could NOT find InChI in system locations (missing:  INCHI_LIBRARY INCHI_INCLUDE_DIR)

Found InChI software locally



Do I also need to download the InChi binary and set these two variables appropriately in CMake?



Also, I am struggling to build with Avalon support...  Choosing the RDK_BUILD_AVALON_SUPPORT appears to configure fine, but when I try to 'Generate' I see the following error:



CMake Error at Code/cmake/Modules/RDKitUtils.cmake:26 (add_library):
Cannot find source file:

/common/layout.c

Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
.hxx .in .txx
Call Stack (most recent call first):
External/AvalonTools/CMakeLists.txt:43 (rdkit_library)

Any thought on how to get around this?  Do I need to download the Avalon project src and put it somewhere?

And final question - can I happily ignore the CMake messages about not finding FLEX and BISON, or are these needed when incorporating any of the non-default entries (SWIG wrappers, etc)?


Kind regards

James

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