RDKit Library Loss

I have a problem with the RDKit library. The native
library cannot be loaded as the dependent libraries cannot be located. The
context for this problem is that I was originally using v4.1 which was
upgraded from v4.0.1 in January. However, this resulted in a stack overflow
for my main calculation, an issue which was only resolved when I wiped
everything and reinstalled v4.0.1. The calculation is now stable in v4.0.1,
but RDKit is missing its library! I have upgraded to v4.1.1 to try and
recover the library as well as uninstall and reinstall RDKit and nothing
works. I am running a windows 10 machine. I am happy to provide more
specifications if needed.

Here are some further details for this problem.
The path which is resulting in the lack of dependent libraries is
C:\Program Files\KNIME\plugins\org.rdkit.knime.bin.win32.x86_64_4.0.1.v202002121353\os\win32\x86_64graphmolwrap.dll

Additionally, when I try to use the RDKit fingerprints node, I get an error message that states

The selected node could not be created due to the following reason: Could not initialize class

What do I need to do to fix this?

Hi @tgapo,
I’m not able to reproduce this problem on my Windows 10 KNIME installation.
I have the same version of the RDKit nodes installed and things work fine.
One possible problem is missing system libraries from Microsoft’s VS2017 redistributable; you can install these from here: https://go.microsoft.com/fwlink/?LinkId=746572
Please give that a try and see if that fixes the problem.


1 Like

Hi Greg,

Thanks for taking a stab at this issue. Unfortunately, your fix did not solve the issue. I have some further information which may assist someone in tracking down the problem. When I try to use the RDKit fingerprint node, I get an error which says that the "selected node could not be created due to the following reason: could not initialize class org.rdkit.knime.nodes.rdkfingerprint.RDKitFingerprintNodeModel

The previous error encountered with the salt stripping node still persists as well.

Hi @tgapo,

Would you mind trying to install KNIME into C:\KNIME instead of C:\Program Files\KNIME? Let’s see if this solved the issue. I remember from the past (long time ago) that I had some difficulties when having KNIME installed in a folder with spaces or in a system related folder (not sure anymore what the issue was). Since that time I avoid that by installing it always into the root directory of a drive.

Also, I noticed that the path you posted is incorrect, it is lacking a backspace before the library file. Is that a typo or did you copy and paste the wrong path from somewhere?