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: =========
/lib64/libc.so.6(+0x81299)[0x7fa32d594299]
[/tools/compilers/gcc/4.9.1/lib64/libstdc++.so.6(_ZNSsD1Ev+0x40)[0x7fa259331920]
/site/tl/app/x86_64/discovery/knime/desktop/4.2.3_cc/plugins/org.rdkit.knime.bin.linux.x86_64_4.0.1.v202002120849/os/linux/x86_64/libGraphMolWrap.so(_ZNSt6vectorISsSaISsEE19_M_range_initializeIN5boost9iterators18transform_iteratorINS3_9algorithm6detail20copy_iterator_rangeFISsN9__gnu_cxx17__normal_iteratorIPcSsEEEENS6_14split_iteratorISC_EENS4_11use_defaultESG_EEEEvT_SI_St18input_iterator_tag+0x5e)[0x7fa1cb421166]
[…]

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?

Best,
-greg

1 Like

Hi Greg,

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

Best
Cyrille

1 Like

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