On Thu, Jan 11, 2018 at 8:03 AM, Paolo Tosco <[email protected]> wrote:
> Hi Jason,
>
> I believe the problem here is that if you are building outside CMake the
> WIN32 preprocessor macro is not defined (_WIN32 is). So, when ROMol.h is
> parsed, the ROMol class definition includes a "private" directive that
> should not be there, hence the error. To fix the issue, you need to add to
> your cl command line a /DWIN32.
>
Thank you! This did the trick. I should learn to use CMake instead of
compiling everything in Mathematica (when all you have is a hammer,
everything looks like a nail)
> As a side note, I am not sure you really want to do:
>
> RDKit::ROMol mol = *(RDKit::SmilesToMol(smi));
> std::string res = RDKit::MolToSmiles(mol);
>
> In fact, this makes a copy of the molecule that the pointer returned by
> SmilesToMol() points to, while leaking the memory pointed to.
> If you are not interested in making a copy of the returned molecule, you
> should probably rather do:
>
> RDKit::RWMol *mol = RDKit::SmilesToMol(smi);
> std::string res = RDKit::MolToSmiles(*mol);
> delete mol;
>
You are definitely correct here, I was trying to make the simplest failing
example and the example without the copy compiled fine - declaring a
pointer to an ROMol is fine but declaring an actual object triggered the
error.
I'm very new to c++, will keep in mind to always delete my pointers. If I
understand correctly, if I always wrap my ROMol objects in a
std::shared_ptr (or the boost equivalent), then the memory will not be
leaked. Is that right?
Best,
Jason
>
>
> If you actually meant to make a copy, you'd better do:
>
> RDKit::RWMol *mol = RDKit::SmilesToMol(smi);
> RDKit::ROMol molCopy(*mol);
> delete mol;
> std::string res = RDKit::MolToSmiles(molCopy);
>
> Cheers,
> p.
>
>
> On 11/01/2018 02:33, Jason Biggs wrote:
>
> I'm trying to use the rdkit as a library in another project, and am having
> trouble getting it to build on windows. I can get the code to compile on
> mac and linux, but it fails for windows, both 32-big and 64-bit varieties.
> I don't know how specific this is to the rdkit, but I have zero experience
> compiling with visual studio (and very little C++ coding background) and I
> am very confused here. The following is just a toy example showing the
> minimum necessary for me to get the error. I get the same error using the
> full code.
>
>
> If I create a test class using this code, I can compile it just fine in
> windows:
>
>
> #include <GraphMol/GraphMol.h>
>
> #include <GraphMol/SmilesParse/SmilesParse.h>
>
> #include <GraphMol/SmilesParse/SmilesWrite.h>
>
>
> class testClass{
>
>
>
> testClass();
>
>
>
> ~testClass();
>
>
>
>
>
> std::string testFunc() {
>
> std::string smi = "CCC";
>
> RDKit::ROMol mol = *(RDKit::SmilesToMol(smi));
>
> std::string res = RDKit::MolToSmiles(mol);
>
> return res;
>
> };
>
>
>
> };
>
>
> testClass::testClass() {
>
> }
>
>
> testClass::~testClass() {
>
> }
>
>
>
> But if I move the definition of the testFunc() function outside of the
> class declaration (which is the normal case, where the definitions are in
> separate files), like this
>
>
> #include <GraphMol/GraphMol.h>
>
> #include <GraphMol/SmilesParse/SmilesParse.h>
>
> #include <GraphMol/SmilesParse/SmilesWrite.h>
>
>
>
> class testClass{
>
>
>
> testClass();
>
>
>
> ~testClass();
>
>
>
> std::string testFunc();
>
>
>
> };
>
>
> testClass::testClass() {
>
> }
>
>
> testClass::~testClass() {
>
> }
>
>
> std::string testClass::testFunc() {
>
> std::string smi = "CCC";
>
> RDKit::ROMol mol = *(RDKit::SmilesToMol(smi));
>
> std::string res = RDKit::MolToSmiles(mol);
>
> return res;
>
> };
>
> then I get the following linker errors:
>
> error LNK2019: unresolved external symbol "private: virtual void
> __thiscall RDKit::ROMol::destroy(void)" (?destroy@ROMol@RDKit@@EAEXXZ)
> referenced in function "public: virtual __thiscall
> RDKit::ROMol::~ROMol(void)" (??1ROMol@RDKit@@UAE@XZ)
> failing.obj : error LNK2019: unresolved external symbol "private: void
> __thiscall RDKit::ROMol::initFromOther(class RDKit::ROMol const
> &,bool,int)" (?initFromOther@ROMol@RDKit@@AAEXABV12@_NH@Z) referenced in
> function "public: __thiscall RDKit::ROMol::ROMol(class RDKit::ROMol const
> &,bool,int)" (??0ROMol@RDKit@@QAE@ABV01@_NH@Z)
> C:\Users\IEUser\Documents\rdkitlink_windows_compile_
> issue\Working-ie11win7-3268-3284-12\RDKitLink.dll : fatal error LNK1120:
> 2 unresolved externals
>
>
> I can't understand why moving the definition of testFunc() causes this
> error.
>
> Any help would be most appreciated. Clearly I can use the workaround of
> making all definitions for testClass in the header file, but I would rather
> not do that.
>
> Thank you,
> Jason
>
>
>
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