Every time I try to view the output of the RDKit from Inchi node, KNIME crashes. Also, trying to view output of ANY subsequent node crashes KNIME. I've tried all 3 memory policies in the "RDKit from Inchi" node and it still crashes.
The entire workflow does work but I really need to see the output tables before writing to my database because I've had a few cases where the nodes generated "junk" that I didn't want in my database.
Note: I can view the output tables for both the "Molecule to CDK" and "Molecule Type Cast" nodes so that's why I think it's specific to the RDKit nodes.
KNIME Build 3.2.1 (8/19/2016) Java JRE 1.8 on OSX 10.8.5
Error output below
Crashed Thread: 61 Java: AWT-EventQueue-0
Exception Type: EXC_BREAKPOINT (SIGTRAP)
Exception Codes: 0x0000000000000002, 0x0000000000000000
Dyld Error Message:
Symbol not found: ___sincos_stret
Referenced from: /Applications/KNIME 3.1.0.app/Contents/Eclipse/plugins/org.rdkit.knime.bin.macosx.x86_64_3.0.0.v201606050430/os/macosx/x86_64/libGraphMolWrap.jnilib
Expected in: /usr/lib/libSystem.B.dylib
I'm suprised that KNIME still runs on this old MacOS version. But apparently it is too old for RDKit. Afaik the missing function ___sincos_stret is only available in 10.9 onwards.
Apologies for the slow reply, I've been on vacation for the past couple of weeks.
As Thorsten already pointed out, this is a quite old verson of OS/X. Unfortunately, due to the way Apple aggressively deprecates libraries and APIs it is more or less impossible to provide a single binary that supports both modern and ancient versions of the OS.
Your best bet would be to either "go backwards" and find the newest version of the RDKit nodes that work for you or to discontinue use of the RDKit nodes (it, of course, pains me to suggest that, but there's not really anything I can do).
Thanks Greg for giving me some direction to a solution. I was able to successfully do just that.
I rolled back manually 3 files from RDKit 2014 (I first renamed/backed up the newer 2016 versions):
In folder [org.rdkit.knime.bin.macosx.x86_64_3.0.0.v201606050430], I replaced one file:
With the one from [org.rdkit.knime.bin.macosx.x86_64_188.8.131.52411121516]
In folder [org.rdkit.knime.types_3.0.0.v201606061028], I replaced two files:
org.RDKitDoc.jar and org.RDKit.jar
With the one from [org.rdkit.knime.types_184.108.40.206411251652]
I guess the only question is what functionality would I lose by using a 2014 version instead of the 2016 version.
WARNING: I imagine this may cause some undesirable effects for some newer features of RDKit. Perhaps, someone else may know the full extent of risk this method may cause with regard to compatibility.
It would be safer to install the old versions of the nodes rather than manually replacing dependencies. You should be able to do this from the update site I believe if you uncheck the option for showing only the latest.