[Rdkit-discuss] Conda install of postgres cartrdige on Mac OS; was: Latest Mac Conda installation advice; was: Boost 1.61 and the RDKit work together.

[Peter S. S. <sh...@gm...>]

Hi,

Here's the resolution of the difficulties I was having installing
rdkit-postgresql95 on Mac OS X.

The problem turned out to be that the package originally posted used Py
3.5, and I'm still using 2.7. I may change to 3.5 at some point, but Greg
was kind enough to add a 2.7 version of the package.

So, the following invocations work to set up rdkit with the cartridge in a
new env on Mac OS X. I'm on El Capitan, by the way, and for clarity, I've
not tested the installation, but only checked that it completed
successfully.

conda create -n rdk1 -c rdkit rdkit
. activate rdk1
conda install -c greglandrum rdkit-postgresql95

(The last command also installs postgresql  9.5.4-0.)

Thanks, Greg, for your help on this.

-P.

On Tue, Aug 30, 2016 at 7:05 AM, Peter S. Shenkin <sh...@gm...> wrote:

> Hi, Greg,
>
> Thanks. That worked and gave me 3.4.
>
> But when I then tried to install rdkit-postgresq95, that failed;
>
> The command "conda install -c greglandrum rdkit-postgresql95" gave:
>
> The following specifications were found to be in conflict:
>   - rdkit-postgresql95
> Use "conda info <package>" to see the dependencies for each package.
>
>
> Then the command "conda info rdkit-postgresql95" gave:
>
> Error: Package missing in current osx-64 channels:
>   - rdkit-postgresql95
>
>
> So it seems the problem is that there is no mac build of that package. I
> don't need the cartridge immediately, so there's no need to put this
> together right away for my sake. OTOH, if this does get together, I'm happy
> to try out the installation.
>
> Best,
> -P.
>
> On Tue, Aug 30, 2016 at 6:38 AM, Greg Landrum <gre...@gm...>
> wrote:
>
>> conda install -c rdkit rdkit
>>
>>
>> On Tue, Aug 30, 2016 at 12:27 PM, Peter S. Shenkin <sh...@gm...>
>> wrote:
>>
>>> Hi, Greg,
>>>
>>> What invocation should I use?
>>>
>>> "conda install -c greglandrum rdkit-postgresql95" still complains that I
>>> need rdkit 3.4.
>>>
>>> "conda update rdkit" fails to update rdkit from 3.1, whether or not I
>>> specify "-c greglandrum".
>>>
>>> Thanks,
>>> -P.
>>>
>>> On Tue, Aug 30, 2016 at 12:30 AM, Greg Landrum <gre...@gm...>
>>> wrote:
>>>
>>>> grrr, I uploaded the rdkit binaries to the wrong place.
>>>> That's taken care of now too.
>>>>
>>>> please try again.
>>>> -greg
>>>>
>>>>
>>>> On Tue, Aug 30, 2016 at 5:59 AM, Peter S. Shenkin <sh...@gm...>
>>>> wrote:
>>>>
>>>>> Hi, Greg,
>>>>>
>>>>> That fails for me because it requires rdkit 3.4 at minimum.
>>>>>
>>>>> Earlier, I installed 3.1 using conda. There doesn't appear to be a way
>>>>> to install 3.4 using conda. (I tried the default anaconda and also "-c
>>>>> grelandrum".)
>>>>>
>>>>> -P.
>>>>>
>>>>> On Mon, Aug 29, 2016 at 10:55 PM, Greg Landrum <gre...@gm...
>>>>> > wrote:
>>>>>
>>>>>> Sorry about that. The command I sent was wrong, and I had made a
>>>>>> mistake when I uploaded the file.
>>>>>>
>>>>>> Please try this one:
>>>>>> conda install -c greglandrum rdkit-postgresql95
>>>>>>
>>>>>> -greg
>>>>>>
>>>>>>
>>>>>> On Mon, Aug 29, 2016 at 10:47 PM, Peter S. Shenkin <sh...@gm...
>>>>>> > wrote:
>>>>>>
>>>>>>> Hi, Greg,
>>>>>>>
>>>>>>> Thanks. I tried your invocation, but conda cannot find the package:
>>>>>>>
>>>>>>> (rdk0) > conda install -c https://conda.anaconda.org/greglandrum
>>>>>>> rdkit-postgresql95 2>&1 | tee install_rdkit-postresql_fr_gre
>>>>>>> glandrum.log
>>>>>>>
>>>>>>> Fetching package metadata .........
>>>>>>> Solving package specifications: .
>>>>>>> Error: Package missing in current osx-64 channels:
>>>>>>>   - rdkit-postgresql95
>>>>>>>
>>>>>>> Close matches found; did you mean one of these?
>>>>>>>     rdkit-postgresql95: postgresql
>>>>>>>
>>>>>>> You can search for packages on anaconda.org with
>>>>>>>     anaconda search -t conda rdkit-postgresql95
>>>>>>>
>>>>>>> On Mon, Aug 29, 2016 at 2:52 AM, Greg Landrum <
>>>>>>> gre...@gm...> wrote:
>>>>>>>
>>>>>>>> Hi Peter,
>>>>>>>>
>>>>>>>> Thanks for pointing out the conda postgresql build; it's great that
>>>>>>>> they are providing this now (though it's a bit irritating that it doesn't
>>>>>>>> have readline support). I was able to do a Mac build of the RDKit cartridge
>>>>>>>> against that postgresql install this morning.
>>>>>>>>
>>>>>>>> Since this uses a different set of dependencies, I'm not
>>>>>>>> comfortable pushing this to the main rdkit channel until after Riccardo and
>>>>>>>> I have had a chance to talk about how we want to handle PostgreSQL going
>>>>>>>> forward. In the meantime there is a Mac build in my channel at
>>>>>>>> anaconda.org. It would be great if you could try this out and let
>>>>>>>> me know if it works for you:
>>>>>>>> conda install -c https://conda.anaconda.org/greglandrum
>>>>>>>> rdkit-postgresql95
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> -greg
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sat, Aug 27, 2016 at 7:49 AM, Peter S. Shenkin <
>>>>>>>> sh...@gm...> wrote:
>>>>>>>>
>>>>>>>>> Thanks, Greg. I assumed that because the installation manager gave
>>>>>>>>> a conda invocation for rdkit-postgresql, it must exist. Perhaps a bad
>>>>>>>>> assumption, but that's why I guessed that it's just not been ported to OS X.
>>>>>>>>>
>>>>>>>>> FWIW, there is a conda build of PostgreSQL, called "postgresql".
>>>>>>>>>
>>>>>>>>> Thanks again,
>>>>>>>>> -P.
>>>>>>>>>
>>>>>>>>> -P.
>>>>>>>>>
>>>>>>>>> On Sat, Aug 27, 2016 at 12:56 AM, Greg Landrum <
>>>>>>>>> gre...@gm...> wrote:
>>>>>>>>>
>>>>>>>>>> There just isn't a conda build (yet) for the cartridge (or, I
>>>>>>>>>> believe, for PostgreSQL itself).
>>>>>>>>>>
>>>>>>>>>> I did a bit of looking this morning and it is going to require
>>>>>>>>>> some work to get things working.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Sat, Aug 27, 2016 at 6:25 AM +0200, "Peter S. Shenkin" <
>>>>>>>>>> sh...@gm...> wrote:
>>>>>>>>>>
>>>>>>>>>> Well, actually, thought I'd try the conda install of
>>>>>>>>>>> rdkit-postgresql, using:
>>>>>>>>>>>
>>>>>>>>>>> conda install -c https://conda.binstar.org/rdkit rdkit-postgresql
>>>>>>>>>>>
>>>>>>>>>>> I get the message:
>>>>>>>>>>>
>>>>>>>>>>> Error: Package missing in current osx-64 channels:
>>>>>>>>>>>   - rdkit-postgresql
>>>>>>>>>>> Close matches found; did you mean one of these?
>>>>>>>>>>>     rdkit-postgresql: postgresql
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Is the cartridge not supported on OS X?
>>>>>>>>>>>
>>>>>>>>>>> -P.
>>>>>>>>>>>
>>>>>>>>>>> On Sat, Aug 27, 2016 at 12:10 AM, Greg Landrum <
>>>>>>>>>>> gre...@gm...> wrote:
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Sat, Aug 27, 2016 at 5:23 AM, Peter S. Shenkin <
>>>>>>>>>>>> sh...@gm...> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Lazy execution rules.
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> :-)
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>