Re: [Rdkit-discuss] Compilation Errors on RHEL7

2018-10-24 Thread Markus Sitzmann

Re: [Rdkit-discuss] Compilation Errors on RHEL7

2018-10-24 Thread Dimitri Maziuk via Rdkit-discuss 
On 10/24/2018 12:10 PM, Dimitri Maziuk via Rdkit-discuss wrote:
> Yes. I once spent a couple of hours trying and ended up installing docer

docker

-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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Re: [Rdkit-discuss] Compilation Errors on RHEL7

2018-10-24 Thread Dimitri Maziuk via Rdkit-discuss 
On 10/24/2018 11:32 AM, Oellien, Frank wrote:
> Hi,
> 
> I am trying to compile RDKit on a RHEL7 system using Python 2.7 and Boost 
> 1.68 
...
> Has somebody already seen this error?

Yes. I once spent a couple of hours trying and ended up installing docer
and pulling a conda/rdkit container instead. I strongly recommend doing
that, or finding a singularity version of the same.

-- 
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Re: [Rdkit-discuss] Chembience

2018-10-24 Thread Markus Sitzmann 
Feedback was so far kind words and Twitter likes :-). And looking on my github 
stats I also see some clones. 

However, I am happy so far with it - I know it is still a bit heady and I have 
to improve documentation a lot. And I also want to build some easily 
distributable open chemoinformatics projects on top of it which I hope creates 
more interest. From my Chemical Identifier Resolver days I know you have to 
patient.

Markus

-
|  Markus Sitzmann
|  markus.sitzm...@gmail.com

> On 24. Oct 2018, at 17:56, Greg Landrum  wrote:
> 
> Glad that update went ok.
> 
> Have you gotten any feedback about this yet?
> 
>> On Wed, 24 Oct 2018 at 14:10, Markus Sitzmann  
>> wrote:
>> 
>> Hello,
>> 
>> I have released Chembience 0.2.5:  it updates the Docker images of the 
>> Django and the Jupyter notebook app in Chembience + the Postgres extension 
>> of the Chembience database image to RDKit 2018.09 (and it went really smooth 
>> :-) )  
>> 
>> https://twitter.com/markussitzmann/status/1055047319660490753
>> 
>> https://github.com/chembience/chembience/releases  
>> 
>> https://www.chembience.com
>> 
>> Best,
>> Markus
>> 
>>> On Fri, Aug 31, 2018 at 11:20 PM Markus Sitzmann 
>>>  wrote:
>>> Hello,
>>> 
>>> I have put together another Chembience release (0.2.3): update of RDKit to 
>>> version 2018.03.4, Postgres to version 10.5, and Django to 2.1
>>> 
>>> https://github.com/chembience/chembience
>>> 
>>> https://twitter.com/markussitzmann/status/1035629283736264704
>>> 
>>> Best,
>>> Markus
>>> 
 On Sun, Jun 10, 2018 at 4:41 PM Markus Sitzmann 
  wrote:
 Hello,
 
 I have just released Chembience 0.2.1: it updates RDKit to version 
 2018.03.2 and switches Postgres from the 9.x series to version 10.4 
 
 https://github.com/chembience/chembience
 
 Best,
 Markus
 
 
> On Mon, May 14, 2018 at 1:49 AM Markus Sitzmann 
>  wrote:
> Hello,
> 
> I have released Chembience 0.2.0: it includes an update to RDKit 2018.03 
> and also provides Jupyter as new base App container type.
> 
> https://github.com/chembience/chembience
> 
> (so, assuming you have Docker and docker-compose installed on your 
> computer, you are a few, easy commands away from your personal Jupyter 
> notebook server with all RDKit 2018.03 goodness readily available).
> 
> Best,
> Markus
> 
> 
>> On Tue, Apr 24, 2018 at 10:44 AM Markus Sitzmann 
>>  wrote:
>> Hello,
>> 
>> since it includes RDKit as one of its major components I am happy to 
>> announce the first release of my new open-source project Chembience:
>> 
>> A Docker-based, cloudable platform for the development of 
>> chemoinformatics-centric web applications and microservices. 
>> 
>> https://github.com/chembience/chembience
>> 
>> (unfortunately it is still on RDKit 2017.09_3, I failed releasing it 
>> before 2018.03 :-) ).
>> 
>> Best,
>> Markus
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Re: [Rdkit-discuss] Compilation Errors on RHEL7

2018-10-24 Thread Paolo Tosco 

Dear Frank,

I am just guessing here, mostly based on a quick Google search, so 
please bear with me if I am wrong.


Could it be that Boost 1.68 and the RDKit were built with different 
versions of gcc, i.e. the built-in 4.7 and a devtoolset version? I would 
make sure that both Boost and the RDKit were built with the latest 
devtoolset-7 
 toolchain.


I hope the above helps; if not, please reply to me off-list with details 
on the compiler toolchain that you used and I will try to reproduce the 
issue.


Best,
Paolo


On 10/24/18 17:32, Oellien, Frank wrote:


Hi,

I am trying to compile RDKit on a RHEL7 system using Python 2.7 and 
Boost 1.68 and I retrieve the following issue:


64%] Linking CXX executable testReaction

../../../lib/libRDKitChemReactions.so.1.2019.03.1dev1: undefined 
reference to 
`boost::archive::text_iarchive_impl::load_override(boost::archive::class_name_type&)'


../../../lib/libRDKitChemReactions.so.1.2019.03.1dev1: undefined 
reference to 
`boost::archive::archive_exception::archive_exception(boost::archive::archive_exception 
const&)'


../../../lib/libRDKitChemReactions.so.1.2019.03.1dev1: undefined 
reference to 
`boost::archive::text_iarchive_impl::load(std::__cxx11::basic_stringstd::char_traits, std::allocator >&)'


../../../lib/libRDKitChemReactions.so.1.2019.03.1dev1: undefined 
reference to 
`boost::archive::text_oarchive_impl::save(std::__cxx11::basic_stringstd::char_traits, std::allocator > const&)'


collect2: error: ld returned 1 exit status

make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1

make[1]: *** 
[Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] Error 2


make: *** [all] Error 2

Has somebody already seen this error?

Best regards,

Frank



*FRANK OELLIEN, PhD*

LabHead Cheminformatics and Modeling

Computer-Aided Drug Design (CADD) / Medicinal Chemistry

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[Rdkit-discuss] Compilation Errors on RHEL7

2018-10-24 Thread Oellien, Frank 
Hi,

I am trying to compile RDKit on a RHEL7 system using Python 2.7 and Boost 1.68 
and I retrieve the following issue:
64%] Linking CXX executable testReaction
../../../lib/libRDKitChemReactions.so.1.2019.03.1dev1: undefined reference to 
`boost::archive::text_iarchive_impl::load_override(boost::archive::class_name_type&)'
../../../lib/libRDKitChemReactions.so.1.2019.03.1dev1: undefined reference to 
`boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
 const&)'
../../../lib/libRDKitChemReactions.so.1.2019.03.1dev1: undefined reference to 
`boost::archive::text_iarchive_impl::load(std::__cxx11::basic_string, std::allocator >&)'
../../../lib/libRDKitChemReactions.so.1.2019.03.1dev1: undefined reference to 
`boost::archive::text_oarchive_impl::save(std::__cxx11::basic_string, std::allocator > const&)'
collect2: error: ld returned 1 exit status
make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] 
Error 2
make: *** [all] Error 2
Has somebody already seen this error?


Best regards,
Frank


FRANK OELLIEN, PhD
LabHead Cheminformatics and Modeling
Computer-Aided Drug Design (CADD) / Medicinal Chemistry

[cid:image001.gif@01D1640E.6AC721D0]

AbbVie Deutschland GmbH & Co KG
Neuroscience Discovery
Knollstr.
67061 Ludwigshafen
OFFICE+49 621-589-4683
FAX  +49 621-589-63449
EMAIL frank.oell...@abbvie.com
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Wiesbaden HRB 26371
Gesch?ftsf?hrer: Dr. Patrick Horber, Thomas Scheidmeir, Dr. Stefan Simianer, 
William J. Chase
Vorsitzende des Aufsichtsrats: Dr. Azita Saleki-Gerhardt

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Re: [Rdkit-discuss] Chembience

2018-10-24 Thread Markus Sitzmann 
Hello,

I have released *Chembience 0.2.5*: it updates the Docker images of the
Django and the Jupyter notebook app in Chembience + the Postgres extension
of the Chembience database image to *RDKit 2018.09* (and it went really
smooth :-) )

https://twitter.com/markussitzmann/status/1055047319660490753

https://github.com/chembience/chembience/releases

https://www.chembience.com

Best,
Markus

On Fri, Aug 31, 2018 at 11:20 PM Markus Sitzmann 
wrote:

> Hello,
>
> I have put together another Chembience release (0.2.3): update of RDKit to
> version 2018.03.*4, *Postgres to version 10.5, and Django to 2.1
>
> https://github.com/chembience/chembience
>
> https://twitter.com/markussitzmann/status/1035629283736264704
>
> Best,
> Markus
>
> On Sun, Jun 10, 2018 at 4:41 PM Markus Sitzmann 
> wrote:
>
>> Hello,
>>
>> I have just released Chembience 0.2.1: it updates RDKit to version
>> 2018.03.2 and switches Postgres from the 9.x series to version 10.4
>>
>> https://github.com/chembience/chembience
>>
>> Best,
>> Markus
>>
>>
>> On Mon, May 14, 2018 at 1:49 AM Markus Sitzmann <
>> markus.sitzm...@gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I have released Chembience 0.2.0: it includes an update to RDKit 2018.03
>>> and also provides Jupyter as new base App container type.
>>>
>>> https://github.com/chembience/chembience
>>>
>>> (so, assuming you have Docker and docker-compose installed on your
>>> computer, you are a few, easy commands away from your personal Jupyter
>>> notebook server with all RDKit 2018.03 goodness readily available).
>>>
>>> Best,
>>> Markus
>>>
>>>
>>> On Tue, Apr 24, 2018 at 10:44 AM Markus Sitzmann <
>>> markus.sitzm...@gmail.com> wrote:
>>>
 Hello,

 since it includes RDKit as one of its major components I am happy to
 announce the first release of my new open-source project Chembience:

 A Docker-based, cloudable platform for the development of
 chemoinformatics-centric web applications and microservices.

 https://github.com/chembience/chembience

 (unfortunately it is still on RDKit 2017.09_3, I failed releasing it
 before 2018.03 :-) ).

 Best,
 Markus

>>>
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