I recently switched from KNIME AP 4.6 to 4.7 and I realised that the 3D-e-chem extension is no longer available for this KNIME version. The same is true for KNIME 5.1. As this extension is extremely valuable for cheminformatics tasks I’ve tried to install it from the KNIME 4.6 repository (i.e. https://update.knime.com/community-contributions/4.6).
After enabling this repo I can correctly see the 3D-e-Chem extension in the extensions list but if I try to install it, I receive the following error:
“Cannot perform operation”. “Will not be installed”.
Please, does anybody know how to install this extension in KNIME 4.7 and 5.1?
Check the desired extension, click Next and follow the prompts to complete installation.
If you want to install the 3D-e-chem nodes for AP 5.1.0, you need to go to the upper right and click on the settings gear wheel, then check-mark the experimental community extensions for this version as well:
Nickolaus (@NDekay), thanks for your reply!
I confirm you that I can not install 3D-e-chem in KNIME 4.7 nor 5.1.
Installation in KNIME 4.7
The method you mention for the installation on KNIME 4.7 is the one that I tried (this is the standard procedure). Nevertheless, as I wrote in my first message, I cannot complete the installation because I receive the following error:
I receive the following error:
Cannot perform operation. Will not be installed
Installation in KNIME 5.1
I’ve tried the method you suggested for KNIME 5.1 but that neither worked. The following error is triggered in that case:
Cannot complete the install because some dependencies are not satisfiable
org.eclipse.equinox.p2.iu; nl.esciencecenter.e3dchem.collection.feature.feature.group [1.6.0.v202102121219,1.6.0.v202102121219] cannot be installed in this environment because its filter is not applicable.
Were you able to install it in your machine in some of the 2 KNIME versions?
I’m running KNIME AP 4.7.3 on MacOS.
We reached out to the extension owner and have confirmed that updating them for AP 5.1 is planned, but is not yet underway. The current extension URL [1] for 5.1.0 seems to be placeholder.
However, I did install the 3d-e-chem extensions in AP 4.7.6 yesterday as shown in my post, and it completed successfully.
If you are not on 4.7.6 (maybe an earlier version?), let me know what version you are on.
But as long as you enable the Community Extension site (Experimental) in the update sites preferences, it should work.
Is there any additional information other than “Cannot perform operation”? Any logs with additional error info?
I could also install it in 4.7 on MacOS. Adding to Nickolaus’ post: not sure whether there might be information in the KNIME Log, but please have a look whether you can see somewhere (Maybe also in the Error Log? Or somewhere during the installation process?) some more information about the failing installation.
Dear @NDekay and @steffen_KNIME,
Thanks for your help on this. I’ve carefully checked the log (<path-to-knime-workspace>/.metadata/knime/knime.log) activated at DEBUG level but I cannot see anything. Where is the Error Log located?
I’m running KNIME 4.7.3 (I still didn’t update to 4.7.6 because I want to run the same version of the KNIME executors connected with our KNIME Server). May this be the cause of the problem?
This is the screenshot of the installer when I attempt the installation of the 3D-e-Chem extension.
@steffen_KNIME, thanks for this!! I didn’t know this “trick” to see the error. I’ll keep this in mind for the future.
So… the error I got is the following:
Cannot complete the install because some dependencies are not satisfiable
org.eclipse.equinox.p2.iu; nl.esciencecenter.e3dchem.collection.feature.feature.group [1.6.0.v202102121219,1.6.0.v202102121219] cannot be installed in this environment because its filter is not applicable.
Honestly, it’s a bit cryptic to me but maybe informative to you. What does it mean “because its filter is not applicable”?
This error indicates that the extension is not compatible with the target environment. In this case this likely indicates that you are using the Apple Silicon build of KNIME AP, and 3d-e-chem only works on the intel build.
thanks Gabriel!
Gio, could you try with the Intel build? @sverhoeven when you do the update for 3D-e-chem, maybe we can also look on how to enable it for 4.7 and 5.1 for Apple Silicon architecture
@gab1one thank you very much for the clarification! That makes sense.
@steffen_KNIME, I would like to try with the Intel architecture but my current version of KNIME AP 4.7 is the one I use for production and I’m a little worried of getting confused if I install 2 KNIME AP with the same version and different architectures (I’m afraid they will be given the same app name in MacOS). Do you have some recommendations about how to keep them completely separated?
@steffen_KNIME, thank you very much for your suggestion: I was not aware that it was so simple to install 2 versions of KNIME (same-version & different architecture) in parallel.
I can confirm that using KNIME 4.7.4 for macOS x86_64 (Intel) solves the problem: the 3D-e-Chem can be correctly installed with that architecture.
Thanks anybody!
