Hi JP,
From the Docker log you posted it is obvious that the build starts from the
latest miniconda version which than will use python 3.6 as default, however one
of the python packages still relies python 3.5.
One thing you can try is to tell the conda install command in the docker script
to go back to python 3.5 or create a python 3.5 based environment.
Unfortunately I just don’t remember out of my head which option you have to use
for this but you fill find it in the conda documentation.
And as much I like the idea of conda, it is unfortunately one of the biggest
troublemakers in my personal projects.
Another point is, if you look for one of the recent post from Greg here on the
list, there is another problem with the latest conda version you might run into.
Markus
-------------------------------------
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 21. Nov 2017, at 16:53, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>
> I've got some dockerfiles that might be worth a look.
> https://github.com/InformaticsMatters/docker_jupyter
>
> Not sure if they will help.
>
> Tim
>
>
>> On 21/11/2017 15:25, JP wrote:
>> Yo RDKitters,
>>
>> I am running a CADD workshop for a group of MSc students and would like to
>> show them some some RDKit awesomeness.
>>
>> I thought the best way to do this is to use an rdkit enabled docker image +
>> jupyter notebooks (they are comfortable with python).
>>
>> In preparation, I tried building the docker image from the docker file at
>> https://github.com/rdkit/rdkit_containers/tree/master/docker/run_conda3 but
>> this fails on Ubuntu 16.04.3 LTS with the following error:
>>
>> $ docker build -t run_rdkit_conda
>> https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
>> Downloading build context from remote url:
>> https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
>> 357B
>> Sending build context to Docker daemon 2.048kB
>> Step 1/7 : FROM continuumio/miniconda3
>> latest: Pulling from continuumio/miniconda3
>> 85b1f47fba49: Pull complete
>> 6b3cb0c49789: Pull complete
>> fecb432dacf0: Pull complete
>> f461f7e3890d: Pull complete
>> Digest:
>> sha256:604cda0c0be5d40cc26db31912d8b1b7276840a56544b846abef441b32d987fc
>> Status: Downloaded newer image for continuumio/miniconda3:latest
>> ---> f700f7f570c7
>> Step 2/7 : MAINTAINER Greg Landrum <greg.land...@gmail.com>
>> ---> Running in ad6a648c18ba
>> ---> 18e6d6093d5b
>> Removing intermediate container ad6a648c18ba
>> Step 3/7 : ENV PATH /opt/conda/bin:$PATH
>> ---> Running in e21cf8e5332f
>> ---> ddef65292068
>> Removing intermediate container e21cf8e5332f
>> Step 4/7 : ENV LANG C
>> ---> Running in efa12ef17f37
>> ---> 137d7e20350d
>> Removing intermediate container efa12ef17f37
>> Step 5/7 : RUN conda config --add channels https://conda.anaconda.org/rdkit
>> ---> Running in 79566bf4b6e9
>> ---> 032965875391
>> Removing intermediate container 79566bf4b6e9
>> Step 6/7 : RUN conda install -y nomkl rdkit pandas cairo cairocffi jupyter
>> ---> Running in c5aa6417a63a
>> Fetching package metadata .............
>> Solving package specifications: .
>>
>> UnsatisfiableError: The following specifications were found to be in
>> conflict:
>> - cairocffi -> python 3.5* -> xz 5.0.5
>> - python 3.6*
>> Use "conda info <package>" to see the dependencies for each package.
>>
>> The command '/bin/sh -c conda install -y nomkl rdkit pandas cairo cairocffi
>> jupyter' returned a non-zero code: 1
>>
>> Any ideas?
>> JP
>>
>>
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