We recently found that we had an rdkit conda channel and any attempt to update or install the newest rdkit from conda would use that channel which was out of date. Removing the channel let us install the up to date distribution. You should check your .condarc file and see if removing any of the channels in there will let you get the most recent rdkit.
On Sun, Oct 11, 2020 at 10:59 AM Ling Chan <lingtrek...@gmail.com> wrote: > Thank you Taka and Dennis for the suggestions. > > I tried conda update but it does not work. My rdkit is still stuck at > 2018.03.2.0. > > Then I made a new environment > > conda create -c rdkit -n new_env rdkit=2019.09.2.0 > > Now the new environment has 2019.09.2.0 instead of 2018.03.2.0. But when I do > conda update, it's still stuck at 2019.09.2.0. > > Hence somehow my rdkit version was locked. I took a look at > > https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-pkgs.html#updating-packages > > to see what could have happened. But there is no pinned file found in any of > my conda-meta directories. Moreover, even "conda update rdkit --no-pin" does > not update my rdkit. > > Any idea what mechanism could have locked my rdkit version? > > Ling > > > Dennis Moccia <den...@cognitivedataworks.com> 於 2020年10月11日週日 上午5:34寫道： > >> Ling >> >> I ran into something similar installing an older version of rdkit >> recently, the temporary fix to get you able to install a new is adding >> "python=3.7" to your create statement >> >> conda create -c rdkit -n my-rdkit-env rdkit python=3.7 >> >> Or specify the version of rdkit you would like... >> >> conda create -c rdkit -n my-rdkit-env rdkit-2020.03.6 >> >> However this will not solve the longer term issue that your conda >> environment is now looking for an older URL for rdkit. >> >> Dennis >> >> >> >> On Sat, Oct 10, 2020 at 6:47 PM Ling Chan <lingtrek...@gmail.com> wrote: >> >>> Dear colleagues, >>> >>> I am trying to install RDKit using conda. According to the manual at >>> https://www.rdkit.org/docs/Install.html#how-to-install-rdkit-with-conda >>> >>> it is very simple. I just need to do >>> >>> conda create -c rdkit -n my-rdkit-env rdkit >>> >>> It used to work. Somehow when I try this again, things are not working. >>> When I investigated, it turns out that somehow the 2018.03.2.0 version of >>> rdkit was installed instead of the most current one. It seems to me that I >>> have screwed up my conda setup. Just wonder what have I screwed up? How can >>> I repair it? >>> >>> One hint could be found at the message when I did conda create. The line >>> for rdkit looks different from the other lines, as indicated below. >>> Unfortunately I still could not figure it out. >>> >>> Thank you for your insight. >>> >>> Ling >>> >>> >>> ================================================= >>> >>> > conda create -c rdkit -n tempenv rdkit >>> >>> The following NEW packages will be INSTALLED: >>> >>> _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main >>> blas pkgs/main/linux-64::blas-1.0-mkl >>> bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 >>> .... >>> python pkgs/main/linux-64::python-3.6.12-hcff3b4d_2 >>> python-dateutil pkgs/main/noarch::python-dateutil-2.8.1-py_0 >>> pytz pkgs/main/noarch::pytz-2020.1-py_0 >>> rdkit rdkit/linux-64::rdkit-2018.03.2.0-py36h6bb024c_1 >>> readline pkgs/main/linux-64::readline-8.0-h7b6447c_0 >>> setuptools pkgs/main/linux-64::setuptools-50.3.0-py36hb0f4dca_1 >>> six pkgs/main/noarch::six-1.15.0-py_0 >>> .... >>> >>> >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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