rdkit installs libboost 1.67.0 rdkit-postgresql wants 1.65.1

[dpwildboar]

doing the following install as of today on an ubuntu 18.04.2 LTS

bash /tmp/Anaconda3-2019.03-Linux-x86_64.sh conda create -c rdkit -n my-rdkit rdkit conda activate my-rdkit conda install -c rdkit rdkit-postgresql mkdir postgres mkdir postgres/data mkdir postgres/log anaconda3/envs/my-rdkit/bin/initdb -D /home/username/postgres/data/ anaconda3/envs/my-rdkit/bin/pg_ctl -D /home/username/postgres/data/ -l /home/username/postgres/log/logfile start createdb my_rdkit_db

you end up with the following happening: psql my_rdkit_db psql (11.2) Type "help" for help.

my_rdkit_db=# create extension rdkit; ERROR: could not load library "/home/username/anaconda3/envs/my-rdkit/lib/rdkit.so": libboost_system.so.1.65.1: cannot open shared object file: No such file or directory my_rdkit_db=# \q

if you look in said directory:

anaconda3/envs/my-rdkit/lib/libboost_system.so.1.67.0

if you downgrade with the following:

conda install -y boost-cpp=1.65.1 boost=1.65.1 py-boost=1.65.1

<<< snip >>>

The following NEW packages will be INSTALLED:

boost pkgs/main/linux-64::boost-1.65.1-py36_4 boost-cpp pkgs/main/linux-64::boost-cpp-1.65.1-h14c3975_4

The following packages will be REMOVED:

rdkit-2019.03.3.0-py36hc20afe1_1

The following packages will be DOWNGRADED:

libboost 1.67.0-h46d08c1_4 --> 1.65.1-habcd387_4 py-boost 1.67.0-py36h04863e7_4 --> 1.65.1-py36hf484d3e_4

<<< snip >>>

psql at that point is happy... but... it removed rdkit... so... there is dissonance between what the two packages want.

[greglandrum]

Confirmed. The requirements listed for building the cartridge are inconsistent with those for the python extensions.

[greglandrum]

@dpwildboar : a workaround until this is fixed would be to just use separate conda environments for the cartridge and the python install