[SOLVED] Indigo nodes cannot be installed in KNIME v2.10.1

Hi guys,

It seems that indigo nodes cannot be installed in KNIME 2.10. When I try to do that using the standard procedure (File -> Install KNIME extensions...) I obtain the following error:

​An error occurred while collecting items to be installed
session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Collect, operand=, action=).
No repository found containing: org.eclipse.update.feature,com.ggasoftware.indigo.knime.feature,1.1.4.201308021053
No repository found containing: osgi.bundle,com.ggasoftware.indigo.knime.plugin,1.1.4.201308021053

Please, do you have any clue?

Are you using KNIME 2.10.0 or 2.10.1? The former may have problems installing certain extensions.

Hi Thor,

Thanks for your quick answer. I was using KNIME 2.10.0. So after you suggestion I updated the software to version 2.10.1 and I tried again to install indigo nodes. Unfortunately I obtain the same error message.

Moreover I have similar errors also when I try installing other community nodes (Erl wood cheminformatics, Enalos, etc.). Please do you have other suggestions? I was having no problems before passing to KNIME 2.10 (using KNIME 2.9).

Gio

Go to File->Preferences->Install/Update->Available Update Sites. Remove the community entries, apply the settings, and then add the community site(s) again (all links can also be found at http://tech.knime.org/community). Then it should work.

I'm with Gio.

Since KNIME 2.10, installing community extensions has become an impossible task, I've wasted hours trying to get Indigo, CDK, and RDKit working in KNIME 2.10.1 on my MAC and have now just given up. Constant error messages when the stable and trusted release goes on are displayed in the console box, and failed installation messages when trying to use the Nightly releases. I've had to give up on the matter.

I do think installing extensions on KNIME has been a tricky affair for some number of versions now, with messages of conflicting dependencies and having to tick and untick installation boxes etc... but has reached even harder levels of difficulty now. The installation procedure could do with a major rethink in my opinion...

Simon.

Hi Simon,

RDKit and Indigo use native libraries and those are known to potentially cause problems. In this case MacOS was affected (and only MacOS!). RDKit should works now, for Indigo I'm not sure, there haven't been any updates for quite some time. CDK should never have been an issue, since it's pure Java.

As for the installation problem: this was an issue in 2.10.0 that was only triggered if the user entered additional update sites manually or reloaded the existing update sites. The standard setup worked at any time.

Are there any open issues you are facing? Then we should definitly have a look.

Cheers,

Thorsten

Well, updating to KNIME 2.10.1 has helped in that I have now put the nightly installs on for Indigo and RDKit, so these are working, as is CDK too. But I now load KNIME with lots of error messages about the imaging nodes with this as an example error "ERROR     RepositoryManager                  Node org.knime.knip.base.nodes.proc.ProcNodeSetFactory' from plugin 'org.knime.knip.base' could not be created."

If I now go to Update KNIME, and I just have the same issues again of having to tick and untick extensions to try and find a combination which allows the updates to be passed. It just says conficting dependencies with these errors below in the updater window. It just makes the whole updating process so painful!

"Cannot complete the install because of a conflicting dependency.
  Software being installed: KNIME Image Processing - Tess4J Integration 1.0.0.201409151345 (org.knime.knip.tess4j.feature.feature.group 1.0.0.201409151345)
  Software currently installed: KNIME Image Processing - OMERO Integration 0.8.2.201407092003 (org.knime.knip.omero.feature.feature.group 0.8.2.201407092003)
  Only one of the following can be installed at once: 
    KNIP - KNIME Image Processing 1.3.0.201409131900 (org.knime.knip.core 1.3.0.201409131900)
    KNIP - KNIME Image Processing 1.2.1.201409091700 (org.knime.knip.core 1.2.1.201409091700)
    KNIP - KNIME Image Processing 1.2.1.201409031452 (org.knime.knip.core 1.2.1.201409031452)
    KNIP - KNIME Image Processing 1.2.0.201407021244 (org.knime.knip.core 1.2.0.201407021244)
  Cannot satisfy dependency:
    From: OmeroConnector-Node extension for KNIME Workbench 0.8.2.201407041339 (org.knime.knip.omero 0.8.2.201407041339)
    To: bundle org.knime.knip.core [1.2.0,1.3.0)
  Cannot satisfy dependency:
    From: KNIME Image Processing - OMERO Integration 0.8.2.201407092003 (org.knime.knip.omero.feature.feature.group 0.8.2.201407092003)
    To: org.knime.knip.omero [0.8.2.201407041339]
  Cannot satisfy dependency:
    From: KNIME Image Processing - Tess4J Integration 1.0.0.201409151345 (org.knime.knip.tess4j.base 1.0.0.201409151345)
    To: bundle org.knime.knip.core [1.3.0,1.4.0)
  Cannot satisfy dependency:
    From: KNIME Image Processing - Tess4J Integration 1.0.0.201409151345 (org.knime.knip.tess4j.feature.feature.group 1.0.0.201409151345)
    To: org.knime.knip.tess4j.base [1.0.0.201409151345]"

Dear Thor, I've tried what you suggested: removed community entries and added their sites again.

Unfortunately in mi case the problems persists. If this is relevant I'm running KNIME in a Linux machine (Ubuntu 14.04_64).

Please, do you have other suggestions?

It is sad but I'm considering to go back to KNIME 2.9 as I didn't experienced such a problems with that version.

What follows are the errors I obtain while trying to install node from Indigo, Enalos and ErlWood, respectively:

 

INDIGO:

An error occurred while collecting items to be installed

session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Collect, operand=, action=).

No repository found containing: org.eclipse.update.feature,com.ggasoftware.indigo.knime.feature,1.1.13.201306201403

No repository found containing: osgi.bundle,com.ggasoftware.indigo.knime.plugin,1.1.13.201306201403



ENALOS

An error occurred while collecting items to be installed

session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Collect, operand=, action=).

No repository found containing: osgi.bundle,com.novamechanics.apd,1.0.0.201301301156

No repository found containing: org.eclipse.update.feature,com.novamechanics.feature,1.0.0.201301301156


ERLWOOD

An error occurred while collecting items to be installed

session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Collect, operand=, action=).

No repository found containing: org.eclipse.update.feature,org.erlwood.knime.feature,2.3.1.201212171301

No repository found containing: org.eclipse.update.feature,org.erlwood.knime.gpl.feature,2.3.1.201212171301

No repository found containing: osgi.bundle,org.erlwood.knime.gpl.nodes,2.3.1.201212171301

No repository found containing: osgi.bundle,org.erlwood.knime.nodes,2.3.1.201212171301

 

Thanks in advance,

Gio

Try restarting KNIME between removing the community update sites and re-adding them again. This has always worked so far.

Dear Thor,

Thank you so much for your help! Finally With the trick you suggested in your last reply I finally achieved to install Indigo, Enalos and Erl Wood cheminformatics nodes in KNIME 2.10.1.

It seems they are not in the "Trusted Community Contributions" but in the "Stable Community Contribution" site.

I hope this can help other users.

Thanks again.

I am using Knime 2.10.2 on Mac 10.9.

While I was able to access the Nodes vie the "Stable" contribution site, they don't load.

Errors are, e.g.:

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.combchem.IndigoReactionGeneratorNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.combchem.IndigoReactionGeneratorNodeFactory The corresponding plugin bundle could not be activated!

Do I suspect correctly that it has to do with Mac? I will be switching to PC again soon, so it's not a big deal for me personally (at the moment at least, never know about future).

Hi Docminus,

I don't know if Mac version gives extra-problems, anyway I have to say that it is quite tricky to install some of the Community Contribuition nodes. I In summary what you have to do is:

  1. Update all the system to KNIME 2.10.1 (at least)
  2. Remove community entries (from File->Preferences->Install/Update->Available Update Sites)
  3. Restart KNIME!!
  4. Add community entries "Stable Community Contribution"
  5. Install Indigo/Erl Wood/Enalos/etc nodes in the standard way (File -> Install KNIME extensions...)

Please note you have to restart knime after you removed community entries and before to add community entries again (point 3). Otherwise it will not work.

I hope this help.

Gio

Hi,

(freshly installed Knime 2.10.3)

I followed the instructions, removed the commuity contributions, restarted knime, added the community contrubutions, added Erlwood contributions and tried to install it. With the following result:

An error occurred while collecting items to be installed
session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Collect, operand=, action=).
No repository found containing: org.eclipse.update.feature,com.ggasoftware.indigo.knime.feature,1.1.4.201308021053
No repository found containing: osgi.bundle,com.ggasoftware.indigo.knime.plugin,1.1.4.201308021053
No repository found containing: osgi.bundle,com.ggasoftware.indigo.knime.plugin.source,1.1.4.201308021053
No repository found containing: org.eclipse.update.feature,com.ggasoftware.indigo.knime.source.feature,1.1.4.201308021053
No repository found containing: org.eclipse.update.feature,org.erlwood.knime.feature,2.3.1.201212171301
No repository found containing: org.eclipse.update.feature,org.erlwood.knime.gpl.feature,2.3.1.201212171301
No repository found containing: osgi.bundle,org.erlwood.knime.gpl.nodes,2.3.1.201212171301
No repository found containing: osgi.bundle,org.erlwood.knime.gpl.nodes.source,2.3.1.201212171301
No repository found containing: org.eclipse.update.feature,org.erlwood.knime.gpl.source.feature,2.3.1.201212171301
No repository found containing: osgi.bundle,org.erlwood.knime.nodes,2.3.1.201212171301
No repository found containing: osgi.bundle,org.erlwood.knime.nodes.source,2.3.1.201212171301
No repository found containing: org.eclipse.update.feature,org.erlwood.knime.source.feature,2.3.1.201212171301
No repository found containing: org.eclipse.update.feature,org.knime.knip.imagej.feature,0.7.0.201307240656
No repository found containing: org.eclipse.update.feature,org.knime.knip.imagej.source.feature,0.7.0.201307240656
No repository found containing: osgi.bundle,org.knime.knip.imagej1,0.7.0.201307240656
No repository found containing: osgi.bundle,org.knime.knip.imagej1.source,0.7.0.201307240656
No repository found containing: osgi.bundle,org.knime.knip.imagej2.base,0.7.0.201307240656
No repository found containing: osgi.bundle,org.knime.knip.imagej2.base.source,0.7.0.201307240656
No repository found containing: osgi.bundle,org.knime.knip.imagej2.core,0.7.0.201307240656
No repository found containing: osgi.bundle,org.knime.knip.imagej2.core.source,0.7.0.201307240656
No repository found containing: osgi.bundle,org.knime.knip.view3d.base,1.0.4.201307240656
No repository found containing: osgi.bundle,org.knime.knip.view3d.base.source,1.0.4.201307240656
No repository found containing: osgi.bundle,org.knime.knip.view3d.bin.linux.x86_64,1.0.4.201307240656
No repository found containing: org.eclipse.update.feature,org.knime.knip.view3d.feature,1.0.4.201307240656
No repository found containing: org.eclipse.update.feature,org.knime.knip.view3d.source.feature,1.0.4.20130724065

 

How can I solve that issue?

regards

Hi serendip42,

I know this is a tiresome issue to deal with. I spent quite time before succeed.

My suggestion: after you removed the community contributions and restarted knime try to add the "Stable Community Contribution" instead of the "Trusted Community Contributions". This worked for me.

Alternatively, if this does not work neither, you can even try with the "Nightly build" package instead of the "Trusted Community Contributions". But remember always to restart knime after you remove a repository and before to add the substitute one.

I hope this help. Cheers