Can't add Vernalis nodes to new KNIME install

zambernardi · December 14, 2018, 10:29am

I’ve just installed KNIME (3.7.0) on a new computer. In trying to install the extensions I need, I found that I can’t install the Vernalis cheminformatics nodes. (More specifically, they seem to install, but loading a workflow containing some of those nodes says they are missing, and any subsequent attempt to install the nodes fails.)

I found that the problem seems to be that the install site for 3.7 (http://update.knime.com/community-contributions/trusted/3.7) contains only an old version of the Vernalis nodes (1.12.0.v201708101336). After adding the older update site (http://update.knime.com/community-contributions/trusted/3.6) I was able to install a newer version (1.17.3.v201808160901), which works normally.

daria.goldmann · December 18, 2018, 1:57pm

Hi Zambernardi,

Thank you for pointing the issue. I passed it to our developers and we will correct the update site asap.

Best,
Daria

Vernalis · December 18, 2018, 2:15pm

Thanks @daria.goldmann. Please do contact us directly if you run into problems with that.

Steve

thor · December 19, 2018, 12:56pm

Steve, the problem is that there are currently test failures with the 3.7. build and therefore it does not get published.

Vernalis · December 20, 2018, 10:43am

Thanks @thor - We will try to get to the bottom of this today.

Steve

Vernalis · December 20, 2018, 11:34am

This is now fixed. The community update job, which I think publishes our update to the trusted contributions update site (@thor can correct me if I’m wrong on that!) should complete in around 10 minutes time.

Steve

Aldo_Barduco · July 22, 2019, 9:19am

Hi,

I´m experiencing the same with Knime 4.0.
On my Windows Server 2016 installation the Vernalis installation is not working. It apparently has been installed, but an error occurs when the Knime is loading/starting, only showing error messages in the log. In other hand, on my Windows 10 installation it has worked fine.

Cheers,

s Aldo

Vernalis · July 22, 2019, 9:33am

There was another thread over at:

https://forum.knime.com/t/errors-with-rdkit-and-vernalis-after-latest-updates/15572/31

which might help. Could you confirm the version of Vernalis nodes you have installed, and also if you have the RDKit nodes installed, which version of those?

Steve

Aldo_Barduco · July 24, 2019, 12:31pm

Hi Steve,

On Windows Server running Knime 3.7 where the upgrade to version 4.0 did not work it has the following:
Vernalis version 1.20.4.v201907091449 and;
RDKit is not installed.

On my local computer, which was perfectly upgraded, it has the following:
Vernalis version 1.20.4.v201907091450
RDKit is not installed.

Kind regards,

s Aldo

Vernalis · July 24, 2019, 1:08pm

Thats very strange - I’ve checked, and there are no differences between the various versions (3.7, 4.0, nightly) at present.

Could you look in the plugins directory within the knime installation directory, and see what you have by way of folders starting org.rdkit.knime, e.g:

https://forum.knime.com/uploads/default/original/2X/6/6bb00d895ab697811d5cbe7d7e61b4f7c0772d53.png

Thanks

Aldo_Barduco · July 24, 2019, 3:35pm

Thank you for your answer and explanation.
Here they are…
Server files (3.7):
org.rdkit.knime.bin.win32.x86_64_3.8.0.v201906261723
org.rdkit.knime.types_3.8.0.v201906261723

Local (4.0):
org.rdkit.knime.bin.win32.x86_64_3.8.0.v201906261723
org.rdkit.knime.types_3.8.0.v201906261723

s Aldo

Vernalis · July 24, 2019, 3:37pm

Thanks - that all looks OK. Could you show the log error for the server? (It will be a week or two before I can get back to you on this now, but if you leave a copy of the errors here I will pick them up when I’m back)

Steve

Aldo_Barduco · July 24, 2019, 8:51pm

See the log below:
ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RDKitTypesPluginActivator ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager ERROR RepositoryManager Could not load native RDKit library: C:\Program Files\KNIME\plugins\org.rdkit.knime.bin.win32.x86_64_3.8.0.v201906261723\os\win32\x86_64\boost_serialization-vc140-mt-1_65_1.dll: Can’t find dependent libraries
Loading of library boost_serialization-vc140-mt-1_65_1.dll failed: C:\Program Files\KNIME\plugins\org.rdkit.knime.bin.win32.x86_64_3.8.0.v201906261723\os\win32\x86_64\boost_serialization-vc140-mt-1_65_1.dll: Can’t find dependent libraries
The library boost_serialization-vc140-mt-1_65_1.dll is missing.
Loading of library boost_iostreams-vc140-mt-1_65_1.dll failed (possibly a subsequent error): C:\Program Files\KNIME\plugins\org.rdkit.knime.bin.win32.x86_64_3.8.0.v201906261723\os\win32\x86_64\boost_iostreams-vc140-mt-1_65_1.dll: Can’t find dependent libraries
The library boost_iostreams-vc140-mt-1_65_1.dll is missing.
Loading of library boost_system-vc140-mt-1_65_1.dll failed (possibly a subsequent error): C:\Program Files\KNIME\plugins\org.rdkit.knime.bin.win32.x86_64_3.8.0.v201906261723\os\win32\x86_64\boost_system-vc140-mt-1_65_1.dll: Can’t find dependent libraries
The library boost_system-vc140-mt-1_65_1.dll is missing.
Loading of library GraphMolWrap.dll failed (possibly a subsequent error): C:\Program Files\KNIME\plugins\org.rdkit.knime.bin.win32.x86_64_3.8.0.v201906261723\os\win32\x86_64\GraphMolWrap.dll: Can’t find dependent libraries
The library GraphMolWrap.dll is missing.
Suggestion for fix: Please install the VS2017 Redistributables from https://go.microsoft.com/fwlink/?LinkId=746572 and then restart KNIME.
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!
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!
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!
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!
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!
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!
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!
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!
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!
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!
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!
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!

Kind regards,

s Aldo

thor · August 6, 2019, 9:59am

Did you try the suggested fix already?

Aldo_Barduco · August 6, 2019, 4:48pm

@thor, thank you!
It works very fine.

system · August 13, 2019, 4:48pm

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