Invalid pointer with RDKit From Molecule

Hello all,

We have an issue with the RDKit From Molecule node when a V3000 Molecule is used as input. Then Knime exits and we can see a pointer error in Linux terminal:

*** Error in `/site/tl/app/x86_64/discovery/knime/desktop/4.2.3_cc//plugins/org.knime.binary.jre.linux.x86_64_1.8.0.252-b09/jre/bin/java’: free(): invalid pointer: 0x00007fa1e17ac820 ***
======= Backtrace: =========

We don’t have this issue with V2000 format, you will find an example here pb_RDKit-node.knwf (22.2 KB)

Do you know why we have this issue / is it possible to fix it?

Best regards

Cyrille with @lcollia
Knime 4.2.4 / RDKit 4.0.1

cc @greglandrum

Hi @Cyrille,

I’m not able to reproduce this with a more recent version of the RDKit nodes. Could you please try updating the RDKit nodes and see if that helps?


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Hi Greg,

Thanks for the reply, you’re right. The RDKit update (4.0.1 → 4.2.0) fixed this issue :slight_smile:


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