Errors with RDkit and Vernalis after latest updates

If you update RDKit to the latest version, that should fix the problem. The RDKit problem causes a problem for the Vernalis nodes, because some of the Vernalis nodes use the RDKit toolkit, and if that is not present or broken, then those nodes also become broken.

Steve

Thanks for the reply Steve, however I must plead ignorance. I am not aware of the RDKit, where to source it or how to update it.

Let alone the implications there of.

@Tim_Napier RDkit is a Community extension and installed the same way as any other extension.

If you have the Vernalis extension installed, then you almost certainly have the RDKit extension already installed too. The easiest way to check is if you type ‘rdkit’ in the Node Repository search box - you should then see something like this:

image

Assuming that you have got it, then Choosing ‘Update KNIME’ from the file menu should get you to the latest version. You can check what version of RDKit and Vernalis nodes you have by browsing to your KNIME installation folder, and then looking in the plugins folder. You should see something like this for the Vernalis nodes:

image

The bit that matters of the version string is the bit highlighted - in this case, 1.20.3. Similarly for RDKit:

image

In this case, I have version 3.8.0 installed (and also, for reasons which I’ve never figured, but this seems to happen sometimes and it doesnt seem to cause any problems, bits of version 3.7.0 also installed)

RDKit provides a chemical toolkit (i.e. ‘chemical awareness’) to KNIME. You can read more about it here and here. Some of the Vernalis nodes use that functionality (mainly the ones in the Matched Molecular Pairs (MMP) folder in the node repository) to do their stuff.

Hope that helps?

Steve

It certainly does Steve thankyou. Interestingly I only have the Vernais nodes installed, not RDKit. However the folders for 3.7 of RDKit are in my plug-ins folder so go figure. I’m thinking the easiest way is just install the RDKit nodes and pick up 3.8 that way.

I do appreciate your patience, thank you

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Thankyou acommons

No problem. Actually, I guess what might happen is that the Vernalis nodes only need the RDKit ‘types’ and ‘bin’ plugins, and not the actual RDKit nodes, which probably explains why you have some but not all of the RDKit parts (I think if you install the RDkit nodes, you should see an RDkit ‘nodes’ plugin and possibly ‘wizards’ folder also appear in your KNIME plugins folder)

Steve

Hello,

I have a similar problem which might be related to this. I use KNIME 3.7.2 (and tried KNIME 3.7.1 aswell) and want to use the Chemical Identifier Resolver node https://nodepit.com/node/com.alvascience.cir.CIRNodeFactory

I recieve the following error message:


*** Welcome to KNIME Analytics Platform v3.7.2.v201904170949 ***
*** Copyright by KNIME AG, Zurich, Switzerland ***


Log file is located at: XXXX\KNIME Version 3.7.2 Workspace.metadata\knime\knime.log
ERROR RDKitTypesPluginActivator Could not load native RDKit library: C:\KNIME 3.7.2\plugins\org.rdkit.knime.bin.win32.x86_64_3.7.0.v201905200540\os\win32\x86_64\boost_iostreams-vc140-mt-x64-1_67.dll: Can’t find dependent libraries
ERROR RDKitTypesPluginActivator Loading of library boost_iostreams-vc140-mt-x64-1_67.dll failed: C:\KNIME 3.7.2\plugins\org.rdkit.knime.bin.win32.x86_64_3.7.0.v201905200540\os\win32\x86_64\boost_iostreams-vc140-mt-x64-1_67.dll: Can’t find dependent libraries
ERROR RDKitTypesPluginActivator The library boost_iostreams-vc140-mt-x64-1_67.dll is missing.
ERROR RDKitTypesPluginActivator Loading of library GraphMolWrap.dll failed (possibly a subsequent error): C:\KNIME 3.7.2\plugins\org.rdkit.knime.bin.win32.x86_64_3.7.0.v201905200540\os\win32\x86_64\GraphMolWrap.dll: Can’t find dependent libraries
ERROR RDKitTypesPluginActivator The library GraphMolWrap.dll is missing.
ERROR RDKitTypesPluginActivator Suggestion for fix: Please install the VS2017 Redistributables from https://go.microsoft.com/fwlink/?LinkId=746572 and then restart KNIME.
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.loop.CutTypeLoopStartNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.loop.CutTypeLoopStartNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.uniquifyids.UniquifyIdsNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.uniquifyids.UniquifyIdsNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.fragutil.maxcuts.rdkit.RDKitMMPMaxCutsNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.fragutil.maxcuts.rdkit.RDKitMMPMaxCutsNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.fragutil.filter.rdkit.RDKitMMPFilterNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.fragutil.filter.rdkit.RDKitMMPFilterNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.fragutil.filter.rdkit.RDKitMMPSplitterNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.fragutil.filter.rdkit.RDKitMMPSplitterNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.fragutil.fragment.rdkit.RDKitMMPFragmentNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.fragutil.fragment.rdkit.RDKitMMPFragmentNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.fragutil.fragment.rdkit.RDKitMulticutMMPFragmentNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.fragutil.fragment.rdkit.RDKitMulticutMMPFragmentNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.pairgen.frag2pair.Frag2Pair3NodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.pairgen.frag2pair.Frag2Pair3NodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.pairgen.frag2pair.ReferenceFrag2Pair3NodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.pairgen.frag2pair.ReferenceFrag2Pair3NodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.fragutil.render.rdkit.RDKitMMPRenderMatchingBondsNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.fragutil.render.rdkit.RDKitMMPRenderMatchingBondsNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.fragutil.render.rdkit.RDKitMMPRenderCuttableBondsNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.fragutil.render.rdkit.RDKitMMPRenderCuttableBondsNodeFactory The corresponding plugin bundle could not be activated!
ERROR RepositoryManager Node com.vernalis.knime.mmp.nodes.transform.rdkit.RWMolApplyTransformNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created: Can’t load factory class for node: com.vernalis.knime.mmp.nodes.transform.rdkit.RWMolApplyTransformNodeFactory The corresponding plugin bundle could not be activated!
ERROR CIR 0:2 error during interpretation of 3-Oxazolidinyloxy, 2-(3-carboxypropyl)-4,4-dimethyl-2-tridecyl-, ammonium sal… as https://cactus.nci.nih.gov/chemical/structure/3-Oxazolidinyloxy,%202-(3-carboxypropyl)-4,4-dimethyl-2-tridecyl-,%20ammonium%20sal.../cas#: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
ERROR CIR 0:2 error during interpretation of Boron, difluoro[(1S)-1-(hydroxymethyl)-2-[(1-oxohexadecyl)oxy]ethyl .lambda.-… as https://cactus.nci.nih.gov/chemical/structure/Boron,%20difluoro[(1S)-1-(hydroxymethyl)-2-[(1-oxohexadecyl)oxy]ethyl%20.lambda.-.../cas#: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
ERROR CIR 0:2 error during interpretation of Poly(oxy-1,2-ethanediyl), .alpha.-[(9R)-6-hydroxy-6-oxido-1,12-dioxo-9-[(1-ox… as https://cactus.nci.nih.gov/chemical/structure/Poly(oxy-1,2-ethanediyl),%20.alpha.-[(9R)-6-hydroxy-6-oxido-1,12-dioxo-9-[(1-ox…/cas#: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target

Hi Alkaline

Installing the RDKit extension got rid of the error messages that reference RDKit for me.

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Thanks Steve

Installing the RDKit nodes got rid of the error messages.

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OK - that’s actually really useful information. I think what has happened is that the RDKit plugins that the Vernalis nodes use wasnt updated because it already set the version requirements we currently have. However, as you and others have seen, version 3.7.0 of the RDKit plugins was broken in some cases. When you installed the RDKit nodes, that has forced the bits of RDKit that Vernalis depend on to update to the newer, fixed, version. In that case, I will update our dependency so that anyone else in the same situation doesnt need to install or manually update RDKit to get rid of the error messages. (You won’t need to do anything, but it should fix this for anyone else as and when their KNIME installation updates the installed plugins)

Steve

Hello,

I am sorry, I do not completely understand the background. I now freshly installed RDKit Version 3.8.0.v201906261723.

I still recieve error messages like (I trunkated the SMILES code):

ERROR CIR 0:2 error during interpretation of OC1=XXX as https://cactus.nci.nih.gov/chemical/structure/OC1=XXX/cas#: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target

I don´t know if this means that at least something was fixed?

This issue is unrelated unrelated to the RDKit issues you were seeing.

This is an SSL certificate issue accessing the CIR resource. Are you behind a proxy?

Hello swebb,

I am working from a company network with restricted user rights (no admin rights).

I’ve seen SunCertPathBuilder exceptions in the past with other nodes - in this case it was due to using an old Java Runtime in KNIME. Check in your plugins folder in the knime installation directory - you should have a folder name starting org.knime.binary.jre.
On my windows install, it is org.knime.binary.jre.win32.x86_64_1.8.0.152-01, which I corresponds to java version 1.8.0_152 - you can check this by opening a command prompt and changing the current directory e.g, on windows:

cd C:\KNIME\plugins\org.knime.binary.jre.win32.x86_64_1.8.0.152-01\jre\bin

and then running

java.exe -version

If this is a much older version then updating KNIME should fix the problem (There was a major purge of internet certificates a while back which I think caused the issue - see e.g. https://www.theregister.co.uk/2018/03/01/trustico_digicert_symantec_spat/ ). Older knime installations had a jre folder in the top level KNIME installation folder, if you cant find it in the plugins. Otherwise, I would guess it is down to a proxy server problem.

You could also try opening the URL indicated in a web browser - i.e. https://cactus.nci.nih.gov/chemical/structure/OC1=XXX/cas# - in this case you will get a ‘404 Page not found’ - because OC1=XXX is not a valid SMILES string - if you try e.g. https://cactus.nci.nih.gov/chemical/structure/O=CC=C/cas# you should get a valid response - in this case the CAS Nos for acrolein:

25314-61-8
107-02-8
25068-14-8

I just tried OC1=XXX as input for the CIR node, and got a successful execution, with the response in the ‘cas’ column error during interpretation of OC1=XXX as https://cactus.nci.nih.gov/chemical/structure/OC1=XXX/cas#, so it looks like the node itself handles broken input OK.

Steve

Hello Steve,

java.exe -version gives me

Java version “1.8.0_152”
Java™ SE Runtime Environmet (build 1.8.0_152-b16)
Java HotSpot™ 64-Bit Server VM (build 25.152-b16, mixed mode)

I installed KNIME 3.7.2 ~1 week ago. I truncated the SMILES by chance, I searched of course with valid SMILES codes. Do you think that this is then a Proxy issue?

I would guess so - what happens if you try to open the URL https://cactus.nci.nih.gov/chemical/structure/O=CC=C/cas# in your web browser?

Steve

Hello Steve,

I see:

25314-61-8
107-02-8
25068-14-8

I also see the CAS numbers when I click on the links from the error messages from the node.

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There is something a bit odd about their server configuration or certificate I think. If I try to open the same URL above in the File Reader node, then in my ‘normal’ copy of KNIME (i.e downloaded/installed from KNIME website, KNIME 3.7.2), it works OK:

image

But, if I try the same thing in KNIME 3.7.2 running from my SDK for node development and testing, the URL does not work in a File Reader:

A bit more digging into the respective java jre folders in each case shows some differences. It may be worth taking a look in the \lib\security subfolder as follows:

cd C:\KNIME\plugins\org.knime.binary.jre.win32.x86_64_1.8.0.152-01\jre\lib\security
dir

In the case of my KNIME install where the file reader accesses the URL OK, the result is as follows:

12/12/2017  12:33    <DIR>          .
12/12/2017  12:33    <DIR>          ..
04/12/2017  14:39             4,054 blacklist
04/12/2017  14:38             1,253 blacklisted.certs
04/12/2017  14:39           115,314 cacerts
04/12/2017  14:38             2,466 java.policy
04/12/2017  14:39            38,397 java.security
04/12/2017  14:39                98 javaws.policy
04/12/2017  14:40             3,035 local_policy.jar
12/12/2017  12:33    <DIR>          policy
04/12/2017  14:38                 0 trusted.libraries
04/12/2017  14:40             3,023 US_export_policy.jar
           9 File(s)        167,640 bytes
           3 Dir(s)  40,361,308,160 bytes free

Whereas in the non-functional installation, the result is:

20/12/2016  17:58    <DIR>          .
20/12/2016  17:58    <DIR>          ..
23/11/2016  21:09             4,054 blacklist
23/11/2016  21:09             1,188 blacklisted.certs
30/11/2018  16:56           105,204 cacerts
23/11/2016  21:09             2,466 java.policy
23/11/2016  21:09            24,633 java.security
23/11/2016  21:09                98 javaws.policy
23/11/2016  21:09             3,035 local_policy.jar
23/11/2016  21:09                 0 trusted.libraries
23/11/2016  21:09             3,023 US_export_policy.jar
           9 File(s)        143,701 bytes
           2 Dir(s)  40,343,908,352 bytes free

Assuming your install looks similar to or the same as the first result, above, then unless your web browser if configured to used a proxy server somehow and KNIME is not, then not sure what else to suggest. Probably worth talking to your IT department to check.

Good luck!

Steve

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