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the downloads from IUPAC have changed (ie the info in the README is out of
date): http://www.iupac.org/home/publications/e-resources/inchi/download.html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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