Knime 2.3.0 update problem on Mac OS X

 

I installed Knime 2.3.0 on a Mac OS X 10.6.5 with java 1.6.0_22 (JavaForMacOSX10.6Update3).  This should be the latest version of java (?).  However, when I try to update knime or install extensions via the online Software sites I get this error: 

 

An internal error occurred during: "Contacting Software Sites".

java.lang.NullPointerException

 

What can I do?  I need to install CDK and WEKA...

Thanks, Herbert.

Please have a look at <workspace>/.metadata/.log and check if there are any messages indicating why and where the NullPointerException occurs. You may also send me the log file.

Thank you for your reply and help.   There are errors in the .log file, but they don't mean much to me.  Here is the contents of the .log file for the last session: 

 

!SESSION 2010-12-20 14:42:29.319 -----------------------------------------------
eclipse.buildId=unknown
java.version=1.6.0_22
java.vendor=Apple Inc.
BootLoader constants: OS=macosx, ARCH=x86_64, WS=cocoa, NL=en_US
Framework arguments:  -keyring /Users/herbert/.eclipse_keyring -showlocation
Command-line arguments:  -os macosx -ws cocoa -arch x86_64 -clean -keyring /Users/herbert/.eclipse_keyring -showlocation
 
!ENTRY org.eclipse.core.net 1 0 2010-12-20 14:43:00.762
!MESSAGE System property http.nonProxyHosts has been set to local|*.local|169.254/16|*.169.254/16 by an external source. This value will be overwritten using the values from the preferences
 
!ENTRY org.eclipse.core.jobs 4 2 2010-12-20 14:43:05.787
!MESSAGE An internal error occurred during: "Contacting Software Sites".
!STACK 0
java.lang.NullPointerException
at org.eclipse.equinox.internal.p2.repository.RepositoryTransport.download(RepositoryTransport.java:75)
at org.eclipse.equinox.internal.p2.repository.RepositoryTransport.download(RepositoryTransport.java:127)
at org.eclipse.equinox.internal.p2.repository.helpers.AbstractRepositoryManager.loadIndexFile(AbstractRepositoryManager.java:718)
at org.eclipse.equinox.internal.p2.repository.helpers.AbstractRepositoryManager.loadRepository(AbstractRepositoryManager.java:639)
at org.eclipse.equinox.internal.p2.metadata.repository.MetadataRepositoryManager.loadRepository(MetadataRepositoryManager.java:96)
at org.eclipse.equinox.internal.p2.metadata.repository.MetadataRepositoryManager.loadRepository(MetadataRepositoryManager.java:92)
at org.eclipse.equinox.p2.ui.LoadMetadataRepositoryJob.doLoad(LoadMetadataRepositoryJob.java:115)
at org.eclipse.equinox.p2.ui.LoadMetadataRepositoryJob.runModal(LoadMetadataRepositoryJob.java:100)
at org.eclipse.equinox.p2.operations.ProvisioningJob.run(ProvisioningJob.java:177)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54)
!SESSION 2010-12-20 14:42:29.319 -----------------------------------------------
eclipse.buildId=unknown
java.version=1.6.0_22
java.vendor=Apple Inc.
BootLoader constants: OS=macosx, ARCH=x86_64, WS=cocoa, NL=en_US
Framework arguments:  -keyring /Users/herbert/.eclipse_keyring -showlocation
Command-line arguments:  -os macosx -ws cocoa -arch x86_64 -clean -keyring /Users/herbert/.eclipse_keyring -showlocation
 
!ENTRY org.eclipse.core.net 1 0 2010-12-20 14:43:00.762
!MESSAGE System property http.nonProxyHosts has been set to local|*.local|169.254/16|*.169.254/16 by an external source. This value will be overwritten using the values from the preferences
 
!ENTRY org.eclipse.core.jobs 4 2 2010-12-20 14:43:05.787
!MESSAGE An internal error occurred during: "Contacting Software Sites".
!STACK 0
java.lang.NullPointerException
at org.eclipse.equinox.internal.p2.repository.RepositoryTransport.download(RepositoryTransport.java:75)
at org.eclipse.equinox.internal.p2.repository.RepositoryTransport.download(RepositoryTransport.java:127)
at org.eclipse.equinox.internal.p2.repository.helpers.AbstractRepositoryManager.loadIndexFile(AbstractRepositoryManager.java:718)
at org.eclipse.equinox.internal.p2.repository.helpers.AbstractRepositoryManager.loadRepository(AbstractRepositoryManager.java:639)
at org.eclipse.equinox.internal.p2.metadata.repository.MetadataRepositoryManager.loadRepository(MetadataRepositoryManager.java:96)
at org.eclipse.equinox.internal.p2.metadata.repository.MetadataRepositoryManager.loadRepository(MetadataRepositoryManager.java:92)
at org.eclipse.equinox.p2.ui.LoadMetadataRepositoryJob.doLoad(LoadMetadataRepositoryJob.java:115)
at org.eclipse.equinox.p2.ui.LoadMetadataRepositoryJob.runModal(LoadMetadataRepositoryJob.java:100)
at org.eclipse.equinox.p2.operations.ProvisioningJob.run(ProvisioningJob.java:177)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54)
 
 
 
Best wishes,
Herbert
 

This looks as if it could be a problem with network access. Are you behind a firewall or something? Nevertheless KNIME should not throw a NullPointerException but that seems to be an isssue in the Eclipse core.

Another question: did you install "KNIME Image Processing" from the community contributions before you encountered the problem? Or any other features that contain org.slf4j (have a look in the plugins-folder of the KNIME installation)?

I have the Mac firewall on, but java is allowed to receive internet connections.  Anyway, when I turn the firewall off, I still have the same problem.  

As to your second question, I had the previous knime versions for Mac installed, but removed them before I installed 2.3.  The current installation is just the one I downloaded from the knime web site. 

Are there any other preferences I should remove?  

Thanks,

Herbert

I have updated my knime installation now using the downloaded UpdateSite.zip file. After I finally worked out how to use the file (unzipping it and moving the contents to a directory "knime" under the "dropins" directory it has the CDK and Weka installed. It seems to work so far.   The online updates still won't work, though.  Same error message as before.  

Cheers,Herbert

 

PS: It would be great to have a readme in the UpdateSite.zip file to let people know how to use it.  Thank you.

Hi all,

When using the zipped update site, we highly recommend using the update procedure as described on our website: http://knime.org/downloads/update

Regards, Thomas

Hi Herbert,

the Mac firewall only blocks incoming connections. Outgoing connections are not affected. Therefore it cannot be reason for your update problems.

I tried to reproduce your problem under the same system configuration (Mac OS X 10.6.5 with java 1.6.0_22) by installing a new KNIME 2.3.0 and then installing various plugins via the update site. But everything worked smoothly.

Do you have any special network setup or can you access the internet directly from your machine?

Best regards,
Dominik

The reason why I could not use the update instructions for zip files on your website was that I get the same java NullPointer Exception when I use "File" -> "Install KNIME Extensions" as well.  

To answer Dominik's question: As far as I know, I have a standard internet connection.  And I have the same problems connecting to the update site when I connect from the office or from home.  In both locations I connect using wireless AirPort and I did not specify anything unusual. 

I do not notice any problem with the internet from any other software I have installed.  Maybe it some leftover weird preference from some other software... 

At least now that I installed CDK and Weka, I can use knime again. 

Thank you for your help.

Herbert

Hi,

I think had a similar problem in my mac and I couldn't update any plugin in eclipse. The problem seem to be from eclipse itself and nothing to do with KNIME. I found some interesting posts on this problem here. I simply commented the line mentioned (...org.apache.commons.httpclient_3.1.0.xxx.jar) in the bundles.info file and I got the software updates up and running. I updated all the plugins and everything seems to be working properly.

I hope this is of any help, though a little bit late...

Cheers,

Luis