Re: [Rdkit-discuss] strange linker error using VC++

2018-01-11 Thread Paolo Tosco 

Hi Jason,

Correct. You'd probably better use std::unique_ptr unless you are 
planning to reference the original pointer from multiple std::shared_ptr's.


Cheers,
p.


On 11/01/2018 14:42, Jason Biggs wrote:


On Thu, Jan 11, 2018 at 8:03 AM, Paolo Tosco > 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 

#include 

#include 


classtestClass{

testClass();

~testClass();

std::string testFunc() {

std::string smi = "CCC";

RDKit::ROMol mol = *(RDKit::SmilesToMol(smi));

std::string res = RDKit::MolToSmiles(mol);

returnres;

};

};


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 

#include 

#include 



classtestClass{

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);

returnres;

};

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

Re: [Rdkit-discuss] strange linker error using VC++

2018-01-11 Thread Jason Biggs 
On Thu, Jan 11, 2018 at 8:03 AM, Paolo Tosco  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 
>
> #include 
>
> #include 
>
>
> 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 
>
> #include 
>
> #include 
>
>
>
> 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
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> ___
> Rdkit-discuss mailing 
>

Re: [Rdkit-discuss] strange linker error using VC++

2018-01-11 Thread Paolo Tosco 

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.


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;

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 

#include 

#include 


classtestClass{

testClass();

~testClass();

std::string testFunc() {

std::string smi = "CCC";

RDKit::ROMol mol = *(RDKit::SmilesToMol(smi));

std::string res = RDKit::MolToSmiles(mol);

returnres;

};

};


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 

#include 

#include 



classtestClass{

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);

returnres;

};

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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engaging tech sites, Slashdot.org! http://sdm.link/slashdot


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