Re: [Rdkit-discuss] compiling error with C++ on maverick

[Peter S. Shenkin]

I'm not sure how this works with modern linkers, but "back in the old
days", you could kludge it by putting all libraries on the link line twice,
This also resolved circular references.

-P.

On Wed, Mar 16, 2016 at 12:05 AM, Greg Landrum 
wrote:

> Though that would be useful information, I'm afraid that's not something
> I've ever put together.
>
> -greg
>
>
>
> On Tue, Mar 15, 2016 at 6:26 PM, Yingfeng Wang  wrote:
>
>> Greg,
>>
>> Could you please give me an order of all libraries? Say, I want to link
>> all RDKit static libraries. I know most of which could be unnecessary, but
>> I just want to make my situation easy.  So, if I cannot figure out a better
>> plan, this way at least works.
>>
>> Thanks.
>> Yingfeng
>>
>> On Mon, Mar 14, 2016 at 8:16 AM, Greg Landrum 
>> wrote:
>>
>>>
>>>
>>> On Sat, Mar 12, 2016 at 5:00 AM, Yingfeng Wang 
>>> wrote:
>>>
 Greg,

 Thanks. Your suggestion solves my problem. I add the following part in
 my compiling command.

 -L/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib
 -lRDInchiLib  -lInChi -lGraphMol -lRDGeneral

 and the complete compiling command is

 g++ -Wall -O2 -std=c++11  -I
 /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/Code -I
 /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/External -I
 /usr/local/Cellar/boost/1.60.0_1/include
 -L/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib -lRDInchiLib
 -lInChi -lGraphMol -lRDGeneral  -o MYTEST main.cpp

 Is there a way to figure out which library I should link? Actually, my
 backup plan is to link all libraries in
 /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib

>>>
>>> That's one approach, but it's kind of overkill. :-)
>>> The big thing is to know which library the functionality you are calling
>>> comes from. You can generally tell this from the header files (i.e. if you
>>> include something from "DataStructs", then you need to include the
>>> DataStructs library). this isn't perfect because some libraries have
>>> dependencies on others, but it often works The other approach is to look in
>>> the RDKit source code at the CMakeLists.txt file for the libraries you are
>>> using and look to see which extra libraries they include when building the
>>> tests.
>>>
>>> This isn't very well documented. I think this kind of documentation is
>>> tricky to generate, so I don't want to do it unless it's going to help a
>>> large number of people, and it's not at all clear to me how many C++ RDKit
>>> users there are.
>>>
>>> By the way, is there a way to guarantee that users using my binary file
 (e.g. MYTEST in this case) do not need to install RDKit? I tried -static,
 but it didn't work. For example, I hope a user can run MYTEST on another
 Mac without RDKit.

>>>
>>> If you link against the _static version of the libraries (i.e.
>>> -lGraphMol_static instead of -lGraphMol), then you should end up with a
>>> version that doesn't require an RDKit install to run. It can be trickier to
>>> get these commands right because on many (all?) systems, there is an order
>>> dependency to static linkage. So since SmilesParse_static depends on
>>> GraphMol_static, GraphMol_static needs to appear *after* SmilesParse_static
>>> in the link line.
>>>
>>> I hope this helps,
>>> -greg
>>>
>>>
>>>
>>
>
>
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Re: [Rdkit-discuss] compiling error with C++ on maverick

[Greg Landrum]

Though that would be useful information, I'm afraid that's not something
I've ever put together.

-greg



On Tue, Mar 15, 2016 at 6:26 PM, Yingfeng Wang  wrote:

> Greg,
>
> Could you please give me an order of all libraries? Say, I want to link
> all RDKit static libraries. I know most of which could be unnecessary, but
> I just want to make my situation easy.  So, if I cannot figure out a better
> plan, this way at least works.
>
> Thanks.
> Yingfeng
>
> On Mon, Mar 14, 2016 at 8:16 AM, Greg Landrum 
> wrote:
>
>>
>>
>> On Sat, Mar 12, 2016 at 5:00 AM, Yingfeng Wang 
>> wrote:
>>
>>> Greg,
>>>
>>> Thanks. Your suggestion solves my problem. I add the following part in
>>> my compiling command.
>>>
>>> -L/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib
>>> -lRDInchiLib  -lInChi -lGraphMol -lRDGeneral
>>>
>>> and the complete compiling command is
>>>
>>> g++ -Wall -O2 -std=c++11  -I
>>> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/Code -I
>>> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/External -I
>>> /usr/local/Cellar/boost/1.60.0_1/include
>>> -L/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib -lRDInchiLib
>>> -lInChi -lGraphMol -lRDGeneral  -o MYTEST main.cpp
>>>
>>> Is there a way to figure out which library I should link? Actually, my
>>> backup plan is to link all libraries in
>>> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib
>>>
>>
>> That's one approach, but it's kind of overkill. :-)
>> The big thing is to know which library the functionality you are calling
>> comes from. You can generally tell this from the header files (i.e. if you
>> include something from "DataStructs", then you need to include the
>> DataStructs library). this isn't perfect because some libraries have
>> dependencies on others, but it often works The other approach is to look in
>> the RDKit source code at the CMakeLists.txt file for the libraries you are
>> using and look to see which extra libraries they include when building the
>> tests.
>>
>> This isn't very well documented. I think this kind of documentation is
>> tricky to generate, so I don't want to do it unless it's going to help a
>> large number of people, and it's not at all clear to me how many C++ RDKit
>> users there are.
>>
>> By the way, is there a way to guarantee that users using my binary file
>>> (e.g. MYTEST in this case) do not need to install RDKit? I tried -static,
>>> but it didn't work. For example, I hope a user can run MYTEST on another
>>> Mac without RDKit.
>>>
>>
>> If you link against the _static version of the libraries (i.e.
>> -lGraphMol_static instead of -lGraphMol), then you should end up with a
>> version that doesn't require an RDKit install to run. It can be trickier to
>> get these commands right because on many (all?) systems, there is an order
>> dependency to static linkage. So since SmilesParse_static depends on
>> GraphMol_static, GraphMol_static needs to appear *after* SmilesParse_static
>> in the link line.
>>
>> I hope this helps,
>> -greg
>>
>>
>>
>
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Re: [Rdkit-discuss] compiling error with C++ on maverick

[Yingfeng Wang]

Greg,

Could you please give me an order of all libraries? Say, I want to link all
RDKit static libraries. I know most of which could be unnecessary, but I
just want to make my situation easy.  So, if I cannot figure out a better
plan, this way at least works.

Thanks.
Yingfeng

On Mon, Mar 14, 2016 at 8:16 AM, Greg Landrum 
wrote:

>
>
> On Sat, Mar 12, 2016 at 5:00 AM, Yingfeng Wang  wrote:
>
>> Greg,
>>
>> Thanks. Your suggestion solves my problem. I add the following part in my
>> compiling command.
>>
>> -L/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib
>> -lRDInchiLib  -lInChi -lGraphMol -lRDGeneral
>>
>> and the complete compiling command is
>>
>> g++ -Wall -O2 -std=c++11  -I
>> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/Code -I
>> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/External -I
>> /usr/local/Cellar/boost/1.60.0_1/include
>> -L/Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib -lRDInchiLib
>> -lInChi -lGraphMol -lRDGeneral  -o MYTEST main.cpp
>>
>> Is there a way to figure out which library I should link? Actually, my
>> backup plan is to link all libraries in
>> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/lib
>>
>
> That's one approach, but it's kind of overkill. :-)
> The big thing is to know which library the functionality you are calling
> comes from. You can generally tell this from the header files (i.e. if you
> include something from "DataStructs", then you need to include the
> DataStructs library). this isn't perfect because some libraries have
> dependencies on others, but it often works The other approach is to look in
> the RDKit source code at the CMakeLists.txt file for the libraries you are
> using and look to see which extra libraries they include when building the
> tests.
>
> This isn't very well documented. I think this kind of documentation is
> tricky to generate, so I don't want to do it unless it's going to help a
> large number of people, and it's not at all clear to me how many C++ RDKit
> users there are.
>
> By the way, is there a way to guarantee that users using my binary file
>> (e.g. MYTEST in this case) do not need to install RDKit? I tried -static,
>> but it didn't work. For example, I hope a user can run MYTEST on another
>> Mac without RDKit.
>>
>
> If you link against the _static version of the libraries (i.e.
> -lGraphMol_static instead of -lGraphMol), then you should end up with a
> version that doesn't require an RDKit install to run. It can be trickier to
> get these commands right because on many (all?) systems, there is an order
> dependency to static linkage. So since SmilesParse_static depends on
> GraphMol_static, GraphMol_static needs to appear *after* SmilesParse_static
> in the link line.
>
> I hope this helps,
> -greg
>
>
>
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Re: [Rdkit-discuss] rdkit installation problem

[kapil dhingra]

Hi Riccardo,

Thanks for the solution.
Problem is solved now. This time I installed by explicitly mentioning the
versions of rdkit and boost (2015.09.2 and 1.56.0 resp.)
I think the problem with the previously mentioned command is that,  it was
installing rdkit (2014.09.2) and boost (1.60.0)
Thanks again..

On Tue, Mar 15, 2016 at 1:37 PM, Riccardo Vianello <
riccardo.viane...@gmail.com> wrote:

> Hi Kapil,
>
> I was able to reproduce the problem, I'm having the impression that this
> might be a regression due to changes implemented in conda 4.0+. I couldn't
> find a way to use 'conda update' to upgrade the initial configuration to
> the latest rdkit package, so - as a shortest term solution - I would
> suggest reinstalling the environment from scratch. You should be able to
> remove the existing environment with something like
>
> > deactivate my-rdkit-env
> > conda remove -n my-rdkit-env --all
>
> and then create it again, but this time specifying the desired rdkit
> version:
>
> >conda create -n my-rdkit-env -c rdkit rdkit=2015.*
>
> this should select rdkit 2015.09.2, numpy 1.10 and boost 1.56
>
> I hope that helps, ​please let me know if the problems persist,
>
> Best,
> Riccardo
>
>


-- 

Best Regards

Kapil Dhingra

Research Scholar, M.S.(Pharm.),

Department of Pharmacoinformatics,

NIPER, S.A.S. Nagar (*Mohali*), Punjab (India)- 160 062,

Mob. No.: +91 - 7508076738
E-mail id: kapil.dhing...@gmail.com
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Re: [Rdkit-discuss] rdkit installation problem

[Riccardo Vianello]

Hi Kapil,

I was able to reproduce the problem, I'm having the impression that this
might be a regression due to changes implemented in conda 4.0+. I couldn't
find a way to use 'conda update' to upgrade the initial configuration to
the latest rdkit package, so - as a shortest term solution - I would
suggest reinstalling the environment from scratch. You should be able to
remove the existing environment with something like

> deactivate my-rdkit-env
> conda remove -n my-rdkit-env --all

and then create it again, but this time specifying the desired rdkit
version:

>conda create -n my-rdkit-env -c rdkit rdkit=2015.*

this should select rdkit 2015.09.2, numpy 1.10 and boost 1.56

I hope that helps, ​please let me know if the problems persist,

Best,
Riccardo
--
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