Hi Greg, This is probably pretty straightforward.
You were correct there!
In order to build the cartridge you need to have $RDBASE pointing to the
directory containing the RDKit source distribution
(/usr/local/Cellar/rdkit/2012.03.1 in the example above from Hans). You're
looking for the directory that contains the RDKit's Code directory. You don't
have to change this globally or in your .bashrc file; you can just set the
appropriate value of RDBASE in the shell where you want to build the cartridge
and then try running make.
I couldn't get it to work by playing with RDBASE but instead I altered the
Makefile so that all the -L${RDKIT}/lib were changed to -L/usr/local/lib and
similarly with -I${RDKIT}/Code to -I/usr/local/include/rdkit.
Thanks for the help.
Best,
Nick
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On 15 May 2013, at 05:10, Greg Landrum
<[email protected]<mailto:[email protected]>> wrote:
Hi Nick,
On Tue, May 14, 2013 at 12:19 PM, Nicholas Firth
<[email protected]<mailto:[email protected]>> wrote:
Hi RDKitters (in particular Hans),
I have an issue with the installation of the RDKit postgres cartridge using the
brewed version of RDKit. I got an email from Eddie yesterday (below) with some
instruction from Hans about how to do it. However I'm experiencing some
problems.
My issue starts at step 2) (it's worth noting that I'm doing this with the
latest release of RDKit). I started by following the instructions as they were
but when I got to the make stage I get the error below,
adapter.cpp:32:10: fatal error: 'GraphMol/RDKitBase.h' file not found
#include <GraphMol/RDKitBase.h>
So I then went back and checked a few things and it seems that my $RDBASE
variable is in a different place to the instructions mine is
/usr/local/share/RDKit
I then created the link from the source to this RDBASE and I get the same error
when I try to make.
This is about where my knowledge of UNIX runs out, so I thought I should ask
the forum before I end up breaking it all!
This is probably pretty straightforward.
The cartridge is built, as you've seen, with a separate makefile - it does not
use the cmake environment that the rest of the rdkit build does.
That makefile uses the value of the environment variable $RDBASE to tell the
compiler where to find the rdkit's header files.
In order to build the cartridge you need to have $RDBASE pointing to the
directory containing the RDKit source distribution
(/usr/local/Cellar/rdkit/2012.03.1 in the example above from Hans). You're
looking for the directory that contains the RDKit's Code directory. You don't
have to change this globally or in your .bashrc file; you can just set the
appropriate value of RDBASE in the shell where you want to build the cartridge
and then try running make.
Hope this helps,
-greg
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