Hi,

After install KNIME extensitons and update KNIME, R Source(Table) can't configure...it show error message in Console as:

R cannot be initialized.
Could not find Rserve package. Please install it in your R installation by running "install.packages('Rserve')".

How can I fix this problem?

PS: 

in Preferences, the default Path to R Home :C:\Program Files\KNIME\plugins\org.knime.ext.r3.bin.win32.x86_3.0.3.v201508240951\R-Inst

and default Location of R on your computer: C:\Program Files\R\R-3.3.1\bin/RGui.exe, I changed it to C:\Program Files\R\R-3.3.1\bin\RGui.exe or C:\Program Files\R\R-3.3.1\bin\i386\RGui.exe or C:\Program Files\R\R-3.3.1\bin\x86\RGui.exe, no effectiveness.

Hi,

I am looking for smiles to IUPAC names conversion with KNIME. Can you please guide me with the workflow and nodes in it.

Hi,

I have a column called "date" which is timestamp format:

I want to calculate the distance in weeks between 1st date and 2nd date, then 2nd date and 3rd date then 3rd date and 4th date.. and so on.

After calculating the distance in weeks for each and every one, I want to average the distances.

Is there any way I can do that in Knime. And specifically in the Groupby variable in Pattern based aggregation?

I tried time difference but is not exactly what I need.

I want to create a pipeline that runs without the graphical user interface. I already know how to do this (KNIME batch mode). But this pipeline will be invoked from a web frontend by website visitors who are not familiar with the technical details.

I noticed that when running KNIME from the command line, there are messages of the form <message-type><tab><node-type><tab><message>. Is this a general thing? Would it make sense to filter the output so that I keep all lines that start with message-type=ERROR, message-type=WARN or message-type=INFO and then I present them to the user?

What is the idiomatic way to generate these messages from a Java snippet node? Is there a specific class or method I can call?

Or are there other best practises that I could use to report that something has gone wrong during the execution of a batch job?

Hi

I am having issues using nodes that generate a new structure when the input column has an RDKit or CDK adapter cell representation present. 

I've tried a few nodes:

- Generate 2D coordinates and highlight fail if the RDKit or CDK representation is in the adapter value map 

- Canonical SMILES and Indigo fingerprint work

The problem seems to happen if Indigo outputs a new structure column. 

Error in the console: 

ERROR KNIME-Worker-5 Highlighter Execute failed: Runtime class of object "

  -INDIGO-10141614272D

  0  ..." (index 0) in row "Row0" is Molfile and does not comply with its supposed superclass Molfile

Cheers

Sam

Dear KNIMErs,

Small (but crucial?) feature request:

Please consider to offer the option of sorting by "Rowindex" without having to create one explicitly. The current sorter only offers to sort by "RowKey" (called RowID everywhere else), and in the current string-based row naming scheme without leading zeroes this leads to the "order" of Row1, Row10, Row1000, Row2, ...

#-(

Thanks for considering it!

Cheers
E

How can i apply CHAID decision tree algorithm in Knime? Can you offer an open source solution?

When I update KNIME,  an error occurred while installing the items
session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Install, operand=[R]de.openms.win32.x86_64 2.0.0.201607151403 --> [R]de.openms.win32.x86_64 2.0.0.201609092116, action=org.eclipse.equinox.internal.p2.touchpoint.eclipse.actions.ChmodAction).
The action chmod failed - file C:\Program Files\KNIME\plugins\de.openms.win32.x86_64_2.0.0.201609092116\payload\bin\DigestorMotif.exe does not exist.

Anyone knows how to resolve this problem? appreciate your advice in advance!

When I update KNIME,  an error occurred while installing the items
session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Install, operand=[R]de.openms.win32.x86_64 2.0.0.201607151403 --> [R]de.openms.win32.x86_64 2.0.0.201609092116, action=org.eclipse.equinox.internal.p2.touchpoint.eclipse.actions.ChmodAction).
The action chmod failed - file C:\Program Files\KNIME\plugins\de.openms.win32.x86_64_2.0.0.201609092116\payload\bin\DigestorMotif.exe does not exist.

Anyone knows how to resolve this problem? appreciate your advice in advance!

need to know regarding availability of   documentation  for database query node

Please see the screenshots attached to this post.

Cheers,
Marc

Hi,

I have a pretty easy problem, I just dont know how to right properly the Regex.

My column is the following:

I want to extract only the trial (x), actually only the numbers that are in trial in a separate column. that means...

?

?

18

2

5

11

I tried regex split or string manipulation (remove chars), or string replacer or cell splitter, but I dont get it right.

Would you please help!

Hi,

I'm trying to use the Report function to show the result of a workflow in a Pie chart. I've followed this video:

https://www.youtube.com/watch?v=jKWQhFrBuzQ

step by step, but when I click on "Finish", the Pie Chart appears for a few seconds and then it disappears. It seems to be something, but I can't show it. Plus, the report items icons are gray, even the report icon.

As attached, I include the workflow and an Image to show the result of report.

Hi,

I have the following integer column with 376000 rows, the content looks like that:

I want to calculate the average including only the values <=52.  How can I do that?

Hi,

I am working on KNIME 3.2.1 with 16G heap space, manipulating a matrix containing 300 rows and 125000 columns. Very often KNIME gives a deadlock error and freezes, and most of the times I have to kill the process from the task manager - at the bottom you'll find the trace taken from the log file after it recovered by itself.

Do you have any clue on what's happening?

Thanks,

Sonia

2016-10-17 11:57:38,362 : WARN  : pool-2-thread-1 : KNIMEApplication$4 :  :  : Potential deadlock in AWT Event Queue detected. Full thread dump will follow as debug ouput.

2016-10-17 11:57:38,362 : DEBUG : pool-2-thread-1 : KNIMEApplication$4 :  :  : "KNIME-TableIO-2" Id=103 TIMED_WAITING on java.util.concurrent.SynchronousQueue$TransferStack@7a838ec5
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.SynchronousQueue$TransferStack@7a838ec5
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
    at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362)
    at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1066)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"Worker-17" Id=102 TIMED_WAITING on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:52)

"OutPortView-Updater-3" Id=101 TIMED_WAITING on java.util.concurrent.SynchronousQueue$TransferStack@2cf55d3a
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.SynchronousQueue$TransferStack@2cf55d3a
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
    at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362)
    at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1066)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"Worker-16" Id=100 TIMED_WAITING on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:52)

"Worker-14" Id=98 TIMED_WAITING on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.core.internal.jobs.WorkerPool@52ebe266
    at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:188)
    at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:220)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:52)

"KNIME Memory Alert Distributor" Id=86 WAITING on java.lang.Object@77f6aa8f
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.Object@77f6aa8f
    at java.lang.Object.wait(Object.java:502)
    at org.knime.core.data.util.memory.MemoryAlertSystem$3.run(MemoryAlertSystem.java:270)

"AWT-EventQueue-0" Id=81 RUNNABLE
    at java.util.ArrayList.indexOf(ArrayList.java:317)
    at java.util.ArrayList.contains(ArrayList.java:300)
    at org.knime.core.node.util.filter.NameFilterPanel.update(NameFilterPanel.java:611)
    at org.knime.core.node.util.filter.NameFilterPanel.setNameFilter(NameFilterPanel.java:839)
    at org.knime.core.node.util.filter.column.DataColumnSpecFilterPanel.loadConfiguration(DataColumnSpecFilterPanel.java:184)
    at org.knime.base.node.preproc.filter.column.DataColumnSpecFilterNodeDialogPane.loadSettingsFrom(DataColumnSpecFilterNodeDialogPane.java:94)
    at org.knime.core.node.NodeDialogPane.loadSettingsFrom(NodeDialogPane.java:564)
    at org.knime.core.node.NodeDialogPane.callDerivedLoadSettingsFrom(NodeDialogPane.java:473)
    at org.knime.core.node.NodeDialogPane$3.run(NodeDialogPane.java:426)
    at org.knime.core.node.util.ViewUtils$3.run(ViewUtils.java:351)
    at org.knime.core.node.util.ViewUtils$2.run(ViewUtils.java:153)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

"AWT-Shutdown" Id=82 WAITING on java.lang.Object@7fa0eb8e
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.Object@7fa0eb8e
    at java.lang.Object.wait(Object.java:502)
    at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295)
    at java.lang.Thread.run(Thread.java:745)

"KNIME-WFM-Parent-Notifier" Id=79 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@31d8c7be
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@31d8c7be
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
    at java.util.concurrent.ArrayBlockingQueue.take(ArrayBlockingQueue.java:403)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"TimerQueue" Id=78 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@15abfccc
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@15abfccc
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
    at java.util.concurrent.DelayQueue.take(DelayQueue.java:211)
    at javax.swing.TimerQueue.run(TimerQueue.java:171)
    at java.lang.Thread.run(Thread.java:745)

    Number of locked synchronizers = 1
    - java.util.concurrent.locks.ReentrantLock$NonfairSync@73b8b1d8

"Unknown Progress Timer" Id=71 WAITING on java.util.ArrayList@6daf996c
    at java.lang.Object.wait(Native Method)
    -  waiting on java.util.ArrayList@6daf996c
    at java.lang.Object.wait(Object.java:502)
    at org.knime.workbench.editor2.figures.ProgressFigure$UnknownProgressTimer.run(ProgressFigure.java:554)

"KNIME Sync Exec Dispatcher-1" Id=70 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@1abd5650
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@1abd5650
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
    at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"[ThreadPool Manager] - Idle Thread" Id=66 WAITING on org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor@2cbd12ae
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor@2cbd12ae
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.equinox.internal.util.impl.tpt.threadpool.Executor.run(Executor.java:106)

"KNIME Progress Updater" Id=63 TIMED_WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@66bac669
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@66bac669
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"Thread-8" Id=54 TIMED_WAITING
    at java.lang.Thread.sleep(Native Method)
    at org.eclipse.equinox.internal.p2.updatechecker.UpdateChecker$UpdateCheckThread.run(UpdateChecker.java:68)

"EventAdmin Async Event Dispatcher Thread" Id=52 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@774f572b
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@774f572b
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"pool-3-thread-3" Id=49 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
    at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"pool-3-thread-2" Id=48 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
    at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"pool-3-thread-1" Id=47 WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7b09044
    at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
    at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:442)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"ServerSpace Update Timer" Id=44 TIMED_WAITING on java.util.TaskQueue@435cda7e
    at java.lang.Object.wait(Native Method)
    -  waiting on java.util.TaskQueue@435cda7e
    at java.util.TimerThread.mainLoop(Timer.java:552)
    at java.util.TimerThread.run(Timer.java:505)

"Java indexing" Id=36 WAITING on org.eclipse.jdt.internal.core.search.indexing.IndexManager@7365c5f2
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.jdt.internal.core.search.indexing.IndexManager@7365c5f2
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.jdt.internal.core.search.processing.JobManager.run(JobManager.java:382)
    at java.lang.Thread.run(Thread.java:745)

"pool-2-thread-1" Id=32 RUNNABLE
    at sun.management.ThreadImpl.dumpThreads0(Native Method)
    at sun.management.ThreadImpl.dumpAllThreads(ThreadImpl.java:446)
    at org.knime.core.util.GUIDeadlockDetector.createStacktrace(GUIDeadlockDetector.java:162)
    at org.knime.core.util.GUIDeadlockDetector$CheckTask.run(GUIDeadlockDetector.java:145)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

    Number of locked synchronizers = 1
    - java.util.concurrent.ThreadPoolExecutor$Worker@3d53e876

"pool-1-thread-1" Id=31 TIMED_WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7e1e32ba
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@7e1e32ba
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"Provisioning Event Dispatcher" Id=30 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@7dafaf8d
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@7dafaf8d
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"AWT-Windows" Id=26 RUNNABLE (in native)
    at sun.awt.windows.WToolkit.eventLoop(Native Method)
    at sun.awt.windows.WToolkit.run(WToolkit.java:306)
    at java.lang.Thread.run(Thread.java:745)

"Java2D Disposer" Id=24 WAITING on java.lang.ref.ReferenceQueue$Lock@5805056c
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.ref.ReferenceQueue$Lock@5805056c
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
    at sun.java2d.Disposer.run(Disposer.java:148)
    at java.lang.Thread.run(Thread.java:745)

"Bundle File Closer" Id=23 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@51211cb
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@51211cb
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"EMF Reference Cleaner" Id=22 WAITING on java.lang.ref.ReferenceQueue$Lock@a967831
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.ref.ReferenceQueue$Lock@a967831
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
    at org.eclipse.emf.common.util.CommonUtil$1ReferenceClearingQueuePollingThread.run(CommonUtil.java:70)

"Worker-JM" Id=18 WAITING on java.util.ArrayList@a456d29
    at java.lang.Object.wait(Native Method)
    -  waiting on java.util.ArrayList@a456d29
    at org.eclipse.core.internal.jobs.InternalWorker.run(InternalWorker.java:59)

"[Timer] - Main Queue Handler" Id=17 TIMED_WAITING on java.lang.Object@7a1b2768
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.Object@7a1b2768
    at org.eclipse.equinox.internal.util.impl.tpt.timer.TimerImpl.run(TimerImpl.java:141)
    at java.lang.Thread.run(Thread.java:745)

"Start Level: Equinox Container: 60b432c2-5694-0016-1df5-88f44e40f4e7" Id=15 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@1d7e3af2
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@1d7e3af2
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"Framework Event Dispatcher: Equinox Container: 60b432c2-5694-0016-1df5-88f44e40f4e7" Id=14 WAITING on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@6f12fda9
    at java.lang.Object.wait(Native Method)
    -  waiting on org.eclipse.osgi.framework.eventmgr.EventManager$EventThread@6f12fda9
    at java.lang.Object.wait(Object.java:502)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextEvent(EventManager.java:400)
    at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:336)

"Active Thread: Equinox Container: 60b432c2-5694-0016-1df5-88f44e40f4e7" Id=12 TIMED_WAITING on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@56fc478a
    at sun.misc.Unsafe.park(Native Method)
    -  waiting on java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject@56fc478a
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
    at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
    at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
    at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

"Attach Listener" Id=5 RUNNABLE

"Signal Dispatcher" Id=4 RUNNABLE

"Finalizer" Id=3 WAITING on java.lang.ref.ReferenceQueue$Lock@77f14459
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.ref.ReferenceQueue$Lock@77f14459
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
    at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"Reference Handler" Id=2 WAITING on java.lang.ref.Reference$Lock@54720da8
    at java.lang.Object.wait(Native Method)
    -  waiting on java.lang.ref.Reference$Lock@54720da8
    at java.lang.Object.wait(Object.java:502)
    at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)

"main" Id=1 RUNNABLE
    at org.eclipse.swt.internal.win32.OS.WaitMessage(Native Method)
    at org.eclipse.swt.widgets.Display.sleep(Display.java:4728)
    at org.knime.core.node.util.ViewUtils.invokeAndWaitInEDT(ViewUtils.java:164)
    at org.knime.core.node.NodeDialogPane.internalLoadSettingsFrom(NodeDialogPane.java:432)
    at org.knime.core.node.Node.getDialogPaneWithSettings(Node.java:2000)
    at org.knime.core.node.workflow.NativeNodeContainer.getDialogPaneWithSettings(NativeNodeContainer.java:1103)
    at org.knime.core.node.workflow.NodeContainer.getDialogPaneWithSettings(NodeContainer.java:949)
    at org.knime.workbench.ui.wrapper.WrappedNodeDialog.<init>(WrappedNodeDialog.java:133)
    at org.knime.workbench.editor2.editparts.NodeContainerEditPart.openNodeDialog(NodeContainerEditPart.java:820)
    at org.knime.workbench.editor2.editparts.NodeContainerEditPart.openDialog(NodeContainerEditPart.java:729)
    at org.knime.workbench.editor2.editparts.NodeContainerEditPart.performRequest(NodeContainerEditPart.java:331)
    at org.eclipse.gef.tools.SelectEditPartTracker.performOpen(SelectEditPartTracker.java:194)
    at org.eclipse.gef.tools.SelectEditPartTracker.handleDoubleClick(SelectEditPartTracker.java:137)
    at org.knime.workbench.editor2.WorkflowSelectionDragEditPartsTracker.handleDoubleClick(WorkflowSelectionDragEditPartsTracker.java:112)
    at org.eclipse.gef.tools.AbstractTool.mouseDoubleClick(AbstractTool.java:1069)
    at org.eclipse.gef.tools.SelectionTool.mouseDoubleClick(SelectionTool.java:527)
    at org.eclipse.gef.EditDomain.mouseDoubleClick(EditDomain.java:231)
    at org.eclipse.gef.ui.parts.DomainEventDispatcher.dispatchMouseDoubleClicked(DomainEventDispatcher.java:291)
    at org.eclipse.draw2d.LightweightSystem$EventHandler.mouseDoubleClick(LightweightSystem.java:518)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:196)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
    at org.eclipse.swt.widgets.Display.sendEvent(Display.java:4362)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1113)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:4180)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3769)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$4.run(PartRenderingEngine.java:1127)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:337)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1018)
    at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:156)
    at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:654)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:337)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:598)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
    at org.knime.product.rcp.KNIMEApplication.start(KNIMEApplication.java:137)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:380)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:235)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:669)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:608)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1515)

Unable to open/execute Knime workflow with Spark Linear/Logistic Regression node. Facing below issue.

"Workflow could not be loaded. breeze/linalg/Vector"

"Workflow could not be loaded. breeze/generic/UFunc$UImpl2"

I am able to execute only Spark Random Forest Learner, Spark Decision Tree MLIB nodes, for all other Spark MLIB nodes I am encountering above error. I am facing this issue after I did an update.

Please let me know how to resolve this issue.

Hi,

I wanted to use KNIME with OMSSA adapter and I get this error message after a few seconds:

ERROR OMSSAAdapter         0:74       Failing process stdout: [OpenMS data path ('C:/Program Files/KNIME_OpenMSsession/plugins/de.openms.win32.x86_64_2.1.0.201609092116/payload/share/OpenMS') retrieved from OPENMS_DATA_PATH (environment)., OMSSAAdapter took 0.12 s (wall), 0.03 s (CPU), 0.03 s (system), 0.00 s (user).]
ERROR OMSSAAdapter         0:74       Failing process stderr: [Input database 'C:\Users\Dennis\Desktop\Test_KNIME\uniprot_Human_reviewed_concatenated_target_decoy_noX.fasta.psq' not found (the file 'C:\Users\Dennis\Desktop\Test_KNIME\uniprot_Human_reviewed_concatenated_target_decoy_noX.fasta.psq' could not be found). Make sure it exists (and check 'OpenMS.ini:id_db_dir' if you used relative paths. Aborting!, Unable to find database 'C:\Users\Dennis\Desktop\Test_KNIME\uniprot_Human_reviewed_concatenated_target_decoy_noX.fasta.psq' (searched all folders). Did you mistype its name? Is the .psq-formatted version available?]
ERROR OMSSAAdapter         0:74       Execute failed: Failed to execute node OMSSAAdapter

My question is if I really need a .psq db format, and if yes what that looks like/ how I can create that from a database I have on my computer. I found something about ncbi-blast but I think I am handling it wrong.

Thanks for your help!

Hi. For some reason running WebDriver with Chrome isn't working, the browser just opens and closes immediately with an error. I tried reinstalling Chrome and it did not help. Any suggestions? Last week it was working fine. Firefox has never worked for me.

Thanks in advance for your help!

Steps to reproduce:

1. Open WebDriver Factory
2. Select Chrome as WebDriver
3. Click Test WebDriver

Console:
ERROR Start WebDriver      0:3        Execute failed: session not created exception
from unknown error: Runtime.executionContextCreated has invalid 'context': {"auxData":{"frameId":"5880.1","isDefault":true},"id":1,"name":"","origin":"://"}
  (Session info: chrome=54.0.2840.59)
  (Driver info: chromedriver=2.22.397933 (1cab651507b88dec79b2b2a22d1943c01833cc1b),platform=Windows NT 6.1.7601 SP1 x86_64) (WARNING: The server did not provide any stacktrace information)
Command duration or timeout: 2.39 seconds
Build info: version: 'unknown', revision: 'unknown', time: 'unknown'
System info: host: 'MYPC', ip: '172.somenumbers', os.name: 'Windows 7', os.arch: 'amd64', os.version: '6.1', java.version: '1.8.0_60'
Driver info: org.openqa.selenium.chrome.ChromeDriver

Hi,  I am using the DataBase Reaer Node, and I have some doubts

note: I am conectiog to Oracle DB (Exadata) using the Database Conector and oracle.jdbc.OracleDriver

1.- Can I show the database schema?

I have many schemas and tables, and it is not friendley to have all the tables together under the TABLE folder

2.- Can I create folders, to organize my tables ??

-TABLE
-VIEW
-SYNONYM
-FOLDER 1
-FOLDER 2...etc

3.- The SQL generated automatically doesn`t inclue the schema,..so it gives an error. I have to modify it by hand

SELECT * FROM TD_MASTER_PRODUCTS  -->> the correct sql is SELECT * FROM .schema.TD_MASTER_PRODUCTS 

4.- One I click Fetch Metadata, can I search a table....I have thousands of tables...

thanks

ALberto

Hi,

I am new to KNIME, and I am trting to connect KNIME to my SQL Server - without success.

what are the steps I need to do in order to create this connections.

Thanks