Hi Sergio,
On Tue, Jul 14, 2015 at 9:53 PM, Wong, Sergio E. <[email protected]
<javascript:_e(%7B%7D,'cvml','[email protected]');>> wrote:
> Dear Greg;
>
> Thank you for the file and the suggestion. I tried following the
> examples and your suggestion and yet, I am still getting some errors. Here
> is my code and below are the errors:
>
> <snip>
>
> Compilation line:
>
> g++ -I${RDBASE}/Code -L/${RDBASE}/lib test.c
>
>
> Error:
>
> In file included from
> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/hash_set:60,
> from /usr/include/boost/graph/adjacency_list.hpp:25,
> from
> /usr/gapps/bbs/rdkit-master//Code/GraphMol/ROMol.h:24,
> from
> /usr/gapps/bbs/rdkit-master//Code/GraphMol/GraphMol.h:19,
> from
> /usr/gapps/bbs/rdkit-master//Code/GraphMol/RDKitBase.h:25,
> from test.c:1:
> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/backward_warning.h:28:2:
> warning: #warning This file includes at least one deprecated or antiquated
> header which may be removed without further notice at a future date. Please
> use a non-deprecated interface with equivalent functionality instead. For a
> listing of replacement headers and interfaces, consult the file
> backward_warning.h. To disable this warning use -Wno-deprecated.
> /var/tmp/swong/ccJYjg6o.o: In function `main':
> test.c:(.text+0x4b): undefined reference to
> `RDKit::SDMolSupplier::SDMolSupplier(std::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&, bool, bool, bool)'
> test.c:(.text+0xcd): undefined reference to `RDKit::SDMolSupplier::next()'
> test.c:(.text+0xe1): undefined reference to `RDKit::SDMolSupplier::atEnd()'
> /var/tmp/swong/ccJYjg6o.o: In function
> `RDKit::ForwardSDMolSupplier::~ForwardSDMolSupplier()':
> test.c:(.text._ZN5RDKit20ForwardSDMolSupplierD2Ev[_ZN5RDKit20ForwardSDMolSupplierD5Ev]+0x16):
> undefined reference to `vtable for RDKit::ForwardSDMolSupplier'
> /var/tmp/swong/ccJYjg6o.o: In function
> `RDKit::SDMolSupplier::~SDMolSupplier()':
> test.c:(.text._ZN5RDKit13SDMolSupplierD2Ev[_ZN5RDKit13SDMolSupplierD5Ev]+0x16):
> undefined reference to `vtable for RDKit::SDMolSupplier'
> collect2: ld returned 1 exit status
>
> Do you think I need to re-install rdkit? The python wrapper works fine.
>
No, you need to link against the required RDKit libraries; you can
generally tell which of these you need by looking at the RDKit headers you
include. Here's an example command line from the demo directory:
https://github.com/rdkit/rdkit/blob/master/Code/Demos/RDKit/GettingStarted/sample.cpp#L11
// g++ -o sample.exe sample.cpp -I$RDBASE/Code -I$RDBASE/Extern \
// -L$RDBASE/lib -lChemReactions -lFileParsers -lSmilesParse
-lDepictor \
// -lSubstructMatch -lGraphMol -lDataStructs -lRDGeometryLib
-lRDGeneral
You probably don't need ChemicalReactions, Depictor, or SubstructMatch.
-greg
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