Erlwood Nodes can not be installed in KNIME 3.7 – RDKit dependency missing

Community Extensions
1

Hi guys,

Trying to install the Erlwood nodes in KNIME 3.7.2 from the trusted community update site

http://update.knime.com/community-contributions/trusted/3.7

leads to the following exception:

Cannot complete the install because one or more required items could not be found.
  Software being installed: Erlwood Knime Open Source Cheminformatics 3.3.0.v201701271222 (org.erlwood.features.cheminformatics.base.feature.group 3.3.0.v201701271222)
  Missing requirement: Erlwood Knime Open Source Cheminformatics 3.3.0.v201701271213 (org.erlwood.knime.cheminformatics 3.3.0.v201701271213) requires 'bundle org.rdkit.knime.nodes [2.4.0,4.0.0)' but it could not be found
  Cannot satisfy dependency:
    From: Erlwood Knime Open Source Cheminformatics 3.3.0.v201701271222 (org.erlwood.features.cheminformatics.base.feature.group 3.3.0.v201701271222)
    To: org.erlwood.knime.cheminformatics [3.3.0.v201701271213]

Obviously there is a dependency to the missing plugin org.rdkit.knime.nodes [2.4.0,4.0.0). NodePit lists this plugin as part of feature org.rdkit.knime.feature.feature.group.

Unfortunately, on the update site for KNIME 3.7, the version of the RDKit feature is 4.0.0.v201912021105. This does not match the expected version range.

Any plans to get this fixed? Mentioning @James, @greglandrum and @manuelschwarze for visibility. Hopefully I picked the right persons. Otherwise please just ignore the mention :grin:

Best regards,
Daniel

3 Likes
2

We also noticed this at @Vernalis just before Christmas. I think one work around is to install the Erlwood nodes from the nightly / trunk build rather than the trusted site.

Steve

3 Likes
3

Thanks for the confirmation and the proposed workaround, @s.roughley. This might also work by installing the nodes from 4.0 or 4.1 update sites.

But indeed just a workaround as – by adding these update sites – the user will constantly get update notifications for all newer plugins hosted on these sites (e.g., KNIME product, …). In my opinion, this should definitely be fixed by (1) increase the upper boundary of the dependency or (2) hosting a compatible RDKit version for KNIME 3.7 on this update site (in case RDKit follows the KNIME versioning).

Best regards,
Daniel

1 Like
4

I had emailed with Thorsten Meinl shortly before Christmas asking to help implementing your option (1), and he suggested that anybody in the community could make the change in the Erlwood nodes. I also had emailed with the Eli Lilly folks, but they currently did not have the time to do the change. Although the change is minimal, I was hesitating to do this myself as I am not the owner of the code (and I was on vacation :slight_smile: ). I will have a look.

4 Likes
5

I made the necessary changes in the Erlwood 3.7 community branch (simply copied what was done for KNIME 4.x) and increased the feature version now from 3.3.0 to 3.3.1. The nightly version is already on 4.0.0. After the next community build the version 3.3.1 should be available on the 3.7 community update site.

Please let me know after you installed 3.3.1, if this solved the issue.

Kind regards,
Manuel

2 Likes
6

Thanks @manuelschwarze - I had similar reservations about changing the Erlwood code myself (and also other pressing things to finish!)

Steve

7

Just gave it a try with version 3.3.1 and I was able to install them from the KNIME 3.7 update site. Thanks @manuelschwarze.

2 Likes
8

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