KNIME 3.7.1: requires pyarrow 0.11.0 which is incompatible with rdkit

See title. It doesn’t seem possible to have rdkit and pyarrow 0.11.0 installed in the same anaconda env:

due to boost version.

Hi @beginner,

thank you very much for reporting that issue. Are you planning to use the arrow serialization?

I used it in 3.6 as it’s supposedly faster but it’s not crucial. I can simply change back to flat buffers.

Still I think it’s an important thing to fix due to the tight integration of Knime, rdkit and python.

Hi @beginner,

I’m glad that’s no blocker for you. We’ll look into it.


You hit the nail on the head: this is a problem with the boost versions.
The RDKit builds that I have done use boost 1.65.1 and pyarrow 0.11.0 requires 1.67.0.
I will try to do new RDKit builds that use newer boost versions later this week (v2018.09.2 is overdue anyway), but I’m not sure that’s going to happen.
In the meantime there are a couple of possibilities that still allow the use of arrow:

  1. Install the rdkit from conda-forge instead of the RDKit channel: conda install conda-forge::rdkit This build has been done using newer boost libraries. If you’re using conda-forge for other stuff, this may be the best solution anyway.
  2. Install pyarrow 0.9.0 instead of 0.11.0. I know that the KNIME preferences page says that 0.11.0 is required, but v0.9.0 has been working just fine for me.

I hope this helps,

I uploaded a new conda release of the RDKit yesterday. This one can now be installed together with pyarrow 0.11


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