Well, I think I figured it out: there's a problem with the python 3.5 boost
build on windows that is provided by the anaconda team: it actually depends
on python 3.6.
I reported this back in April:
https://github.com/ContinuumIO/anaconda-issues/issues/9257 but there
haven't been any updates yet.
If the silence from the anaconda team continues, I can try to do an
rdkit-channel build of the relevant conda packages, but I would very much
like to avoid that if possible.
-greg
On Mon, Jul 23, 2018 at 1:27 PM Greg Landrum <[email protected]> wrote:
> Hi Jon,
>
> I can reproduce this problem locally, which is a bit strange since the
> tests passed before I uploaded the 2018.03.1 build. I will take a look and
> see if I can figure out what's going on.
>
> In the meantime, it may work to try installing the rdkit from the
> conda-forge channel:
> "conda install -c conda-forge rdkit"
> The conda-forge builds are quite useful, but they do introduce a different
> set of dependencies and may not work for you.
>
> -greg
>
>
> On Sun, Jul 22, 2018 at 10:26 PM <[email protected]> wrote:
>
>> I downgraded rdkit to 2017.09 and that resolved the problem. I had
>> already downgraded Python to 3.5.4. You need to do both of these
>> downgrades. First downgrade Python, then downgrade rdkit. Now everything is
>> working. Including all the other stuff like pandas, jupyter, etc.
>>
>> If I just want the latest rdkit, it works fine with the Anaconda3 Python
>> 3.6. I have scripts that want to use both rdkit and tensorflow, however.
>>
>> Jon T. Swanson, Ph.D.
>>
>> ChemModeling, LLC
>> Suite 101, 500 Huber Park Ct.
>> Weldon Spring, MO 63304
>>
>> (636) 329-0300
>>
>>
>> -------- Original Message --------
>> Subject: [Rdkit-discuss] Getting rdkit to work with Anaconda Python
>> 3.5.x
>> From: <[email protected]>
>> Date: Sun, July 22, 2018 2:08 pm
>> To: "RDKit Discuss" <[email protected]>
>>
>> Hi,
>>
>> Does anyone have a magic recipe for getting rdkit to work with python 3.5
>> in Anaconda3?
>>
>> I am trying to create a conda environment that will allow me to run rdkit
>> and tensorflow.
>>
>> I have Anaconda3 installed (Windows 10). That installs Python 3.6 by
>> default.
>>
>> So I created an environment for Python 3.5 (which is what tensorflow
>> wants)
>>
>> conda create -n py35 python=3.5
>> activate py35
>> conda install -c anaconda tensorflow
>> conda install -c rdkit rdkit
>>
>> both install.
>>
>> Tensorflow works, but
>>
>> from rdkit import Chem
>>
>> gives
>>
>> Fatal Python error: PyThreadState_Get: no current thread
>>
>> I read some old posts on this and downgraded Python to 3.5.4, then 3.5.3
>> and finally 3.5.0. I've tried removing and recreating the environment. Same
>> error. I've tried just installing rdkit. Same error.
>>
>> I've spent all day on this, I'm hoping someone has tried this and has a
>> solution!
>>
>> Is there a specific rdkit version I should try? People must have run
>> rdkit in Anaconda with Python 3.5 in the past.
>>
>> Jon T. Swanson, Ph.D.
>>
>> ChemModeling, LLC
>> Suite 101, 500 Huber Park Ct.
>> Weldon Spring, MO 63304
>>
>> (636) 329-0300
>> ------------------------------
>>
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