Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-15 Thread Loris Bennett
Greg Landrum writes: > On Fri, Sep 15, 2017 at 1:37 PM, Loris Bennett > wrote: > > When I did > > make test > > some of the tests failed: > > 61% tests passed, 46 tests failed out of 117 > > but most of the failures seemed to have been

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-15 Thread Greg Landrum
On Fri, Sep 15, 2017 at 1:37 PM, Loris Bennett wrote: > > When I did > > make test > > some of the tests failed: > > 61% tests passed, 46 tests failed out of 117 > > but most of the failures seemed to have been caused by > > ImportError: No module named rdkit >

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-15 Thread Loris Bennett
Hi Greg, Greg Landrum writes: > One thing that may help is this (somewhat older, but I believe still > accurate) post from Riccardo: > https://sourceforge.net/p/rdkit/mailman/message/30074971/ > > It's been a while since I looked at this (since I mainly use conda these

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-15 Thread Greg Landrum
One thing that may help is this (somewhat older, but I believe still accurate) post from Riccardo: https://sourceforge.net/p/rdkit/mailman/message/30074971/ It's been a while since I looked at this (since I mainly use conda these days), but I just did a quick experiment with: mkdir build

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-15 Thread Markus Sitzmann
Well, if you have python 2.7 and 3.5 already running ,you can use (mini)conda for the RDKit installation (conda is anaconda but instead of one huge package you can install the packages you want including RDKit) On Fri, Sep 15, 2017 at 9:12 AM, Loris Bennett wrote: >

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-15 Thread Markus Sitzmann
BTW, python 3.6 is out since last Christmas ;-) (and made it to sub-release .2) On Fri, Sep 15, 2017 at 8:36 AM, Greg Landrum wrote: > I'll provide a more detailed answer in a bit, but since you aren't using > the system python anyway, is there any chance that you

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-15 Thread Greg Landrum
I'll provide a more detailed answer in a bit, but since you aren't using the system python anyway, is there any chance that you could switch to anaconda python on your machines? Anaconda is a great python distribution for scientific applications and it makes many things (including system

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-15 Thread Loris Bennett
Hi Greg, Greg Landrum writes: > Hi Loris, > > On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett > wrote: > > I am trying to install RDKit on a university cluster running Linux from > source. The build seem to go OK and 'make install' copied

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Greg Landrum
On Thu, Sep 14, 2017 at 9:58 PM, Andrew Dalke wrote: > On Sep 14, 2017, at 19:26, Dimitri Maziuk wrote: > > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > > linux distros that will be officially with us until June 30,

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Dimitri Maziuk
On 09/14/2017 03:04 PM, Markus Sitzmann wrote: > Not on Centos 6 - Docker requires Centos 7 for the host system. You can't win... :( -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Markus Sitzmann
Not on Centos 6 - Docker requires Centos 7 for the host system. On Thu, Sep 14, 2017 at 10:01 PM, Dimitri Maziuk wrote: > On 09/14/2017 02:58 PM, Andrew Dalke wrote: > > > If only Greg got as much money for long term RDKit support as Red Hat > > gets for long term RHEL

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Dimitri Maziuk
On 09/14/2017 02:58 PM, Andrew Dalke wrote: > If only Greg got as much money for long term RDKit support as Red Hat > gets for long term RHEL support. :) Yep. But an rdkit docker container might be feasible. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison --

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Andrew Dalke
On Sep 14, 2017, at 19:26, Dimitri Maziuk wrote: > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > linux distros that will be officially with us until June 30, 2024. If only Greg got as much money for long term RDKit support as Red Hat gets for

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Riccardo Vianello
On Thu, Sep 14, 2017 at 9:07 PM, Dimitri Maziuk wrote: > > All great when it's one computer and that one's your own personal laptop. > > > # yum ls \*python27\* > > ... > > python27.x86_642.7.13-2.ius.el6 > @salt-2015.8 > >

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Greg Landrum
On Thu, Sep 14, 2017 at 7:26 PM, Dimitri Maziuk wrote: > On 09/14/2017 10:43 AM, Greg Landrum wrote: > > > Just to do some expectation management: python 2.6 is pretty ancient and > > there's no guarantee that all of the RDKit code will work with it. Python > > 2.7 is the

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Dimitri Maziuk
On 09/14/2017 01:41 PM, Riccardo Vianello wrote: > True, but there shouldn't be any strong need for using the system python > for running application software. Python 2.7 (together with python 3) has > been available to RHEL6 subscribers since almost five years, as part of the > Red Hat Software

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Riccardo Vianello
On Thu, Sep 14, 2017 at 7:26 PM, Dimitri Maziuk wrote: > Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of > linux distros that will be officially with us until June 30, 2024. > True, but there shouldn't be any strong need for using the system

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Dimitri Maziuk
On 09/14/2017 10:43 AM, Greg Landrum wrote: > Just to do some expectation management: python 2.6 is pretty ancient and > there's no guarantee that all of the RDKit code will work with it. Python > 2.7 is the minimum version that we "officially" support. It's a very good > idea to update. Just

Re: [Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Greg Landrum
Hi Loris, On Thu, Sep 14, 2017 at 2:25 PM, Loris Bennett wrote: > > I am trying to install RDKit on a university cluster running Linux from > source. The build seem to go OK and 'make install' copied the > directories > > lib > rdkit > > to the NFS share where

[Rdkit-discuss] ImportError: No module named rdkit

2017-09-14 Thread Loris Bennett
Hi, I am trying to install RDKit on a university cluster running Linux from source. The build seem to go OK and 'make install' copied the directories lib rdkit to the NFS share where the software should reside. I then do export RDBASE=/cm/shared/apps/rdkit/rdkit_2017_03_3 export