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bundle could not be activated

Member for

6 years 11 months grimbart

Dear all,

today I noticed that on a new Fedora 17 machine the Indigo bundle cannot be loaded, producing a lot of errors like:

ERROR	 RepositoryManager	 Node com.ggasoftware.indigo.knime.IndigoMoleculeLoaderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created. The corresponding plugin bundle could not be activated!

In the .metadata/.log file there is this indigo-related message:

!MESSAGE An error occurred while automatically activating bundle com.ggasoftware.indigo.knime.plugin (368).

org.osgi.framework.BundleException: The activator com.ggasoftware.indigo.knime.plugin.IndigoPlugin for bundle com.ggasoftware.indigo.knime.plugin is invalid
        at com.ggasoftware.indigo.Indigo.loadIndigo(Indigo.java:711)
        at com.ggasoftware.indigo.Indigo.<init>(Indigo.java:725)
        at com.ggasoftware.indigo.Indigo.<init>(Indigo.java:732)
        at com.ggasoftware.indigo.knime.plugin.IndigoPlugin.<clinit>(IndigoPlugin.java:50)
        at com.ggasoftware.indigo.Indigo.loadIndigo(Indigo.java:711)
        at com.ggasoftware.indigo.Indigo.<init>(Indigo.java:725)
        at com.ggasoftware.indigo.Indigo.<init>(Indigo.java:732)
        at com.ggasoftware.indigo.knime.plugin.IndigoPlugin.<clinit>(IndigoPlugin.java:50)

 

What  could be the reason? I have not seen this error before on F14 and F16.

 

Any help appreciated! Thanks a lot !

ingo

Comments
Mon, 07/09/2012 - 10:12

Member for

6 years 9 months

mkvyatkovskiy

Hello ingo,

I have reproduced the problem. We will try to fix it as soon as possible.

Best regards,
Mikhail Kvyatkovskiy,
GGA Software.

Tue, 07/10/2012 - 01:57

Member for

6 years 11 months

grimbart

Dear Mikhail,

at least in my case there seems to be a connection to different user rights, and might not be related directly to F17. The above mentioned problem was first observed for a new user that used a F17 system. However, the same problem occurred when this new user launched KNIME on a F16 system, whereas I do not have this problem, neither on the F17 nor the F16 machine.

That said, on both machines each a local KNIME installation was used, but both up to date.

 

I hope this helps to sort things out.

 

Thanks a lot for the efforts,

best

Ingo

Wed, 07/11/2012 - 11:55

Member for

7 years 1 month

asavelyev

Dear Ingo,

I have finally found the possible reason for the issue. Your suggestion about user rights seems to be correct. Indigo uses JNA library, which creates temporary folder called 'jna' located in /tmp for native libraries. But the folder is not removed at the end. Therefore, different user can not create new instance (and create new folder) since the permission is denied for him.

The simple solution is to remove (by sudo) jna folder from /tmp and create the jna folder with '777' permission.

But we agree that such a behavior is not convinient, because only one user can use jna. Indigo uses JNA as a third-party component and we can not modify it. But we will try to find out how to solve the problem. I hope the issue is resolved in the newest jna version (I saw many similar bug-reports on the forums).

With best regards,

Alexander

GGA Software Services

Wed, 07/11/2012 - 12:47

Member for

7 years 1 month

asavelyev

Dear Ingo,

Yes, the bug with jna temp folder is fixed in the version 3.4.1 - jna creates 'jna-user' folder now. We have updated and have replaced jna by the newest version (Indigo used 3.4.0 by the way). Therefore, the new indigo-nodes will be available soon in nightly builds (the indigo nodes version should be 1.1.5).

Anyway, many thanks for the bug-report. It is very strange that we didn't notice the issue before.

With best regards,

Alexander

GGA Software Services

Wed, 07/11/2012 - 03:51

Member for

6 years 11 months

grimbart

Dear Alexander,

these are good news, thanks a lot for checking and fixing so fast. I guess that at least on the user side people mostly work at "their own" single computer.

 

Always glad to help, and course to have your nodes available!

 

best regards

ingo

Thu, 09/05/2013 - 06:00

Member for

6 years 11 months

lgauthie

Hi,

Strangely, I am experiencing the same problem described by grimbart, but using KNIME 2.8 with the latest stable release of the "Community Contributions" package (2013/08/28).

Am I doing something wrong ? Because when reading your previous posts, I have the feeling that this should have been fixed a long time ago.

Thanks for your help !

Regards,
Luc

Tue, 12/17/2013 - 04:09

Member for

5 years 9 months

George_Nicola

I am receiving similar problems with the latest version of KNIME (2.9) installed on Linux x64, and the "Stable Community Contributions" of Indigo:

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoMoleculeLoaderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.molecule.IndigoMoleculeLoaderNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoMoleculeSaverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.molecule.IndigoMoleculeSaverNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoQueryMoleculeSaverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.molecule.IndigoQueryMoleculeSaverNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoQueryReactionLoaderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.reaction.IndigoQueryReactionLoaderNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoReactionSaverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.reaction.IndigoReactionSaverNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoQueryReactionSaverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.reaction.IndigoQueryReactionSaverNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.compjoin.IndigoComponentCombinerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.compjoin.IndigoComponentCombinerNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.compsep.IndigoComponentSeparatorNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.compsep.IndigoComponentSeparatorNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.murcko.IndigoMurckoScaffoldNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.murcko.IndigoMurckoScaffoldNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoRGroupDecomposerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.rgdecomp.IndigoRGroupDecomposerNodeFactory The corresponding plugin bundle could not be activated!
ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoScaffoldFinderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.scaffold.IndigoScaffoldFinderNodeFactory The corresponding plugin bundle could not be activated!

...

 

Regards,

--George