Re: [Rdkit-devel] Install RDKit

2015-01-30 Thread Soren Wacker
No, there is no boost 1.54 on my system. I have a 1.57. Apparently, that was 
build by conda.
I have found a 
./anaconda/conda-bld/linux-64/boost-1.56.0-py27_0.tar.bz2

but no anaconda/pkgs/boost-1.56... only 1.57.

I tried to generate a symbolic link from the 1.57 version to the 1.54 file, but 
that did not work. 
rdBase was still complaining that it could not find it. 


What is about the env. variables LD_LIBRARY_PATH and RDBASE ? 
I pointed them to 

RDBASE=.../anaconda/pkgs/rdkit-2014.09.2-np19py27_0/lib/python2.7/site-packages/rdkit
and 
LD_LIBRARY_PATH=$RDBASE/lib

is that right?

Do I have to activate an anaconda enviroment before I can use it??


kind regards
Sören

--
Dr. Soeren Wacker
Centre For Molecular Simulation, BI # 547
The University of Calgary
2500 University Drive (NW)
Calgary, Alberta
Canada, T2N 1N4

Tel.:   ++1 (403) 210 7860
Email:  swac...@ucalgary.ca


From: Riccardo Vianello [riccardo.viane...@gmail.com]
Sent: Friday, January 30, 2015 4:44 AM
To: Soren Wacker
Cc: Greg Landrum; RDKit Developers List
Subject: Re: [Rdkit-devel] Install RDKit

Hi Soren,

until recently, boost packages were not provided by the anaconda distribution, 
and this is basically the reason we provide recipes to build boost too. When a 
few weeks ago boost packages targeting version 1.57.0 have been added to the 
conda default channels (for linux and windows at least, I couldn't find any 
boost package in the osx repository last time I checked), they caused some 
confusion because the rdkit recipe doesn't specify a version for the boost 
package, and version 1.57.0 is by default installed because it's more recent 
than the version we build locally.

When executed, the boost recipe from the rdkit github repository should have 
built boost 1.56.0 (you could probably find the package in the local channel at 
./Programme/anaconda/conda-bld/linux-64), but the rdkit build probably used 
boost version 1.57.0 (based on the info from your last message it most likely 
did so when testing the rdkit package and in istalling it into envs/rdkit-env). 
I tried building the rdkit with the boost package provided by anaconda in a 
couple of linux environments and it worked ok for me, so in principle I think 
it could work for you too.

But I have no explanation for the reference to boost 1.54.0. Is there any boost 
package matching that version and installed as part of the system linux 
distribution?

Best,
Riccardo



On Fri, Jan 30, 2015 at 12:09 AM, Soren Wacker 
swac...@ucalgary.camailto:swac...@ucalgary.ca wrote:
I tried that. I was able to compile rdkit, apparently just by typing

conda build boost
conda build rdkit

but, when I use that build I get

from rdkit import rdBase

 ImportError: libboost_python.so.1.54.0: cannot open shared object file: No 
 such file or directory

strange thing is, that anaconda build 1.57 version... 1.54 does not exist on my 
system.

./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so
./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so.1.57.0
./Programme/anaconda/envs/_test/lib/libboost_python.so
./Programme/anaconda/envs/_test/lib/libboost_python.so.1.57.0
./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so
./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so.1.57.0

kind regards
Soren
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Re: [Rdkit-devel] Install RDKit

2015-01-30 Thread Soren Wacker
OK, there was a problem with the environment variables. 
I can now import rdBase, however it seems to be outdated?

I would like to find out my old version. I went to the location of my old 
version.
imported rdkit 
and -to find out the version- I have to import rdBase first... which did not 
work.
It is my old version that complains about not finding libboost_python.so.1.54.0

Why is there still no function rdkit.version()? I have seen such discussion 
from 4 years ago. Such a function would be really useful sometimes. Especially, 
if you have no internet connection to find out that you have to look at
rdBase.rdkitVersion or if you know that, but cannot load rdBase, like in my 
case.

It is not even possible to grep the version apparently, since rdBase is a 
binary file.
How can I find out the version then??


For example the function dkit.Chem.Descriptors.fr_Al_COO is not present.

Now, my old version is messed up, and I cannot use the new version :-(

kind regards
Sören


From: Soren Wacker [swac...@ucalgary.ca]
Sent: Friday, January 30, 2015 12:26 PM
To: Riccardo Vianello
Cc: RDKit Developers List; Greg Landrum
Subject: Re: [Rdkit-devel] Install RDKit

No, there is no boost 1.54 on my system. I have a 1.57. Apparently, that was 
build by conda.
I have found a
./anaconda/conda-bld/linux-64/boost-1.56.0-py27_0.tar.bz2

but no anaconda/pkgs/boost-1.56... only 1.57.

I tried to generate a symbolic link from the 1.57 version to the 1.54 file, but 
that did not work.
rdBase was still complaining that it could not find it.


What is about the env. variables LD_LIBRARY_PATH and RDBASE ?
I pointed them to

RDBASE=.../anaconda/pkgs/rdkit-2014.09.2-np19py27_0/lib/python2.7/site-packages/rdkit
and
LD_LIBRARY_PATH=$RDBASE/lib

is that right?

Do I have to activate an anaconda enviroment before I can use it??


kind regards
Sören

--
Dr. Soeren Wacker
Centre For Molecular Simulation, BI # 547
The University of Calgary
2500 University Drive (NW)
Calgary, Alberta
Canada, T2N 1N4

Tel.:   ++1 (403) 210 7860
Email:  swac...@ucalgary.ca


From: Riccardo Vianello [riccardo.viane...@gmail.com]
Sent: Friday, January 30, 2015 4:44 AM
To: Soren Wacker
Cc: Greg Landrum; RDKit Developers List
Subject: Re: [Rdkit-devel] Install RDKit

Hi Soren,

until recently, boost packages were not provided by the anaconda distribution, 
and this is basically the reason we provide recipes to build boost too. When a 
few weeks ago boost packages targeting version 1.57.0 have been added to the 
conda default channels (for linux and windows at least, I couldn't find any 
boost package in the osx repository last time I checked), they caused some 
confusion because the rdkit recipe doesn't specify a version for the boost 
package, and version 1.57.0 is by default installed because it's more recent 
than the version we build locally.

When executed, the boost recipe from the rdkit github repository should have 
built boost 1.56.0 (you could probably find the package in the local channel at 
./Programme/anaconda/conda-bld/linux-64), but the rdkit build probably used 
boost version 1.57.0 (based on the info from your last message it most likely 
did so when testing the rdkit package and in istalling it into envs/rdkit-env). 
I tried building the rdkit with the boost package provided by anaconda in a 
couple of linux environments and it worked ok for me, so in principle I think 
it could work for you too.

But I have no explanation for the reference to boost 1.54.0. Is there any boost 
package matching that version and installed as part of the system linux 
distribution?

Best,
Riccardo



On Fri, Jan 30, 2015 at 12:09 AM, Soren Wacker 
swac...@ucalgary.camailto:swac...@ucalgary.ca wrote:
I tried that. I was able to compile rdkit, apparently just by typing

conda build boost
conda build rdkit

but, when I use that build I get

from rdkit import rdBase

 ImportError: libboost_python.so.1.54.0: cannot open shared object file: No 
 such file or directory

strange thing is, that anaconda build 1.57 version... 1.54 does not exist on my 
system.

./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so
./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so.1.57.0
./Programme/anaconda/envs/_test/lib/libboost_python.so
./Programme/anaconda/envs/_test/lib/libboost_python.so.1.57.0
./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so
./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so.1.57.0

kind regards
Soren
--
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net

Re: [Rdkit-devel] Install RDKit

2015-01-30 Thread Riccardo Vianello
Hi Soren,

until recently, boost packages were not provided by the anaconda
distribution, and this is basically the reason we provide recipes to build
boost too. When a few weeks ago boost packages targeting version 1.57.0
have been added to the conda default channels (for linux and windows at
least, I couldn't find any boost package in the osx repository last time I
checked), they caused some confusion because the rdkit recipe doesn't
specify a version for the boost package, and version 1.57.0 is by default
installed because it's more recent than the version we build locally.

When executed, the boost recipe from the rdkit github repository should
have built boost 1.56.0 (you could probably find the package in the local
channel at ./Programme/anaconda/conda-bld/linux-64), but the rdkit build
probably used boost version 1.57.0 (based on the info from your last
message it most likely did so when testing the rdkit package and in
istalling it into envs/rdkit-env). I tried building the rdkit with the
boost package provided by anaconda in a couple of linux environments and it
worked ok for me, so in principle I think it could work for you too.

But I have no explanation for the reference to boost 1.54.0. Is there any
boost package matching that version and installed as part of the system
linux distribution?

Best,
Riccardo



On Fri, Jan 30, 2015 at 12:09 AM, Soren Wacker swac...@ucalgary.ca wrote:

 I tried that. I was able to compile rdkit, apparently just by typing

 conda build boost
 conda build rdkit

 but, when I use that build I get

 from rdkit import rdBase

  ImportError: libboost_python.so.1.54.0: cannot open shared object file:
 No such file or directory

 strange thing is, that anaconda build 1.57 version... 1.54 does not exist
 on my system.

 ./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so
 ./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so.1.57.0
 ./Programme/anaconda/envs/_test/lib/libboost_python.so
 ./Programme/anaconda/envs/_test/lib/libboost_python.so.1.57.0
 ./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so
 ./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so.1.57.0

 kind regards
 Soren

 --
 Dive into the World of Parallel Programming. The Go Parallel Website,
 sponsored by Intel and developed in partnership with Slashdot Media, is
 your
 hub for all things parallel software development, from weekly thought
 leadership blogs to news, videos, case studies, tutorials and more. Take a
 look and join the conversation now. http://goparallel.sourceforge.net/
 ___
 Rdkit-devel mailing list
 Rdkit-devel@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-devel

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Re: [Rdkit-devel] Install RDKit

2015-01-29 Thread Soren Wacker
Uh! Wow!
Awesome news!!
Good work ;-)

--
Dr. Soeren Wacker
Centre For Molecular Simulation, BI # 547
The University of Calgary
2500 University Drive (NW)
Calgary, Alberta
Canada, T2N 1N4

Tel.:   ++1 (403) 210 7860
Email:  swac...@ucalgary.ca

From: Greg Landrum [greg.land...@gmail.com]
Sent: Wednesday, January 28, 2015 10:32 PM
To: Soren Wacker
Cc: RDKit Developers List
Subject: Re: [Rdkit-devel] Install RDKit

Hi Soren,

On Thu, Jan 29, 2015 at 2:03 AM, Soren Wacker 
swac...@ucalgary.camailto:swac...@ucalgary.ca wrote:

I would highly appreciate a
conda install rdkit

way of doing it, but that is probably not so easy to realize.

It wasn't easy to realize but fortunately Riccardo has already done the work:
https://github.com/rdkit/conda-rdkit
We have a binstar channel available with some pre-built binaries too:
https://conda.binstar.org/rdkit

Best,
-greg
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