Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

2015-11-22 Thread Huw Jones 
Hi Greg,

Many thanks. I’ll take a look.

Huw

> On 20 Nov 2015, at 16:02, Greg Landrum  wrote:
> 
> Hi Huw,
> 
> This is not directly responsive to your question, but if you're working with 
> anaconda, it is probably easier to just build and install the RDKit using the 
> conda-rdkit recipes here:
> https://github.com/rdkit/conda-rdkit 
> The development branch there pulls from master.
> 
> -greg
> 
> 
> On Fri, Nov 20, 2015 at 4:26 PM, Huw Jones  > wrote:
> Hi there,
> 
> I’ve been building the Python RDKit modules direct from the GitHub repository 
> recently on an Ubuntu 14.04 LTS VM (i.e. git clone 
> https://github.com/rdkit/rdkit.git ).
> 
> I use the following aptitude packages for the build process:
> 
> flex  2.5.35-10.1ubuntu2
> bison 2:3.0.2.dfsg-2
> build-essential 11.6ubuntu6
> cmake 2.8.12.2-0ubuntu3
> libboost-dev 1.54.0.1ubuntu1
> libboost-regex-dev 1.54.0.1ubuntu1
> python-dev 2.7.5-5ubuntu3
> libboost-python-dev 1.54.0.1ubuntu1
> python-numpy 1:1.8.2-0ubuntu0.1
> 
> The build process is as follows:
> 
> git clone https://github.com/rdkit/rdkit.git 
>  rdkit-latest
> source /opt/virtualenv/current/bin/activate
> export RDBASE=/path/to/rdkit-latest
> cd rdkit-latest
> mkdir build
> cd build
> cmake ..
> make -j 2
> make install
> cd ..
> cp -r rdkit /opt/virtualenv/current/lib/python2.7/site-packages
> mkdir /opt/virtualenv/current/lib/python2.7/lib-rdkit
> cp lib/* /opt/virtualenv/current/lib/python2.7/lib-rdkit
> 
> I have recently been experiencing this error:
> 
> Python 2.7.10 (default, Nov 20 2015, 07:14:39)
> [GCC 4.8.4] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from rdkit import rdBase
> Traceback (most recent call last):
>   File "", line 1, in 
> ImportError: /opt/virtualenv/current/lib/python2.7/lib-rdkit/libRDBoost.so.1: 
> undefined symbol: _ZN5boost6python23throw_error_already_setEv
> 
> It looks like this error starts appearing from this commit onwards:
> 
> https://github.com/rdkit/rdkit/commit/9965702691b039c936c3fcca579fbd9ded8f5331
>  
> 
> 
> Any ideas?
> 
> Many thanks as ever.
> 
> Huw Jones
> 
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[Rdkit-discuss] New problem compiling RDKit on Windows

2015-11-22 Thread James Davidson 
Dear All,

For quite some time I have been successfully compiling RDKit on Windows using 
Visual Studio 2012.
However, recently (and perhaps triggered by a recent VS update that I accepted) 
I am getting errors.

The problem seems to be in Wrap.h (line 133):

<<< .mine


VS is complaining "error C2059: syntax error:'<<'"  and the corresponding error 
when inspecting the code is "Error: expected a declaration".
Does anyone have any suggestions for working through this?

Kind regards

James

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Re: [Rdkit-discuss] New problem compiling RDKit on Windows

2015-11-22 Thread Greg Landrum 
Hi James,

That looks like a leftover from a source-control conflict. I can't find it
in github:
https://github.com/rdkit/rdkit/blob/master/Code/RDBoost/Wrap.h#L133

Could it be that you are pulling from github and that you had local
modifications to the file that lead to a conflict?

Best,
-greg


On Mon, Nov 23, 2015 at 1:52 AM, James Davidson 
wrote:

> Dear All,
>
>
>
> For quite some time I have been successfully compiling RDKit on Windows
> using Visual Studio 2012.
>
> However, recently (and perhaps triggered by a recent VS update that I
> accepted) I am getting errors.
>
>
>
> The problem seems to be in Wrap.h (line 133):
>
>
>
> <<< .mine
>
>
>
>
>
> VS is complaining “error C2059: syntax error:’<<’”  and the corresponding
> error when inspecting the code is “Error: expected a declaration”.
>
> Does anyone have any suggestions for working through this?
>
>
>
> Kind regards
>
>
>
> James
>
> __
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> intended for the named addressee(s) only and access to it by anyone else is
> unauthorised. If you are not an addressee, any disclosure or copying of the
> contents of this email or any action taken (or not taken) in reliance on it
> is unauthorised and may be unlawful. If you have received this email in
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> responsibility for the accuracy or completeness of this message or any
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> Company accepts no responsibility. If verification of this email is sought
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> opinions presented are solely those of the author and do not represent
> those of the Company.
>
> The Vernalis Group of Companies
> 100 Berkshire Place
> Wharfedale Road
> Winnersh, Berkshire
> RG41 5RD, England
> Tel: +44 (0)118 938 
>
> To access trading company registration and address details, please go to
> the Vernalis website at www.vernalis.com and click on the "Company
> address and registration details" link at the bottom of the page..
> __
>
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