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Java Error with DEseq analysis in RobiNA

Hello, I am running RobiNA 1.2.4_Build609 on a Mac with OSX 10.6.8. I am trying to analyze some RNAseq data but after inputing a 'counts table' and selecting the type (EdgeR or DEseq) and parameters (FDR etc...) for differential expression analysis I get the error message displayed below. It looks to me like the analysis proceeds OK but then the system can't write any of the summary files (I.e. The R.session.info.txt file). I am guessing that this is either a Java permission problem or a firewall issue (I work for the US government and we often have firewall troubles). Any help that you could give would be deeply appreciated.

Thanks,
AVilla



-- 04/25/2013@10:16:59:810 -- java.io.FileNotFoundException: /Users/villarinoav/Desktop/TempDesk/source/R.session.info.txt (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:120)
at de.mpimp.golm.robin.GUI.RNASeq.RNASeqPDFSummaryGenerator.addSessionInfo(RNASeqPDFSummaryGenerator.java:302)
at de.mpimp.golm.robin.GUI.RNASeq.RNASeqPDFSummaryGenerator.<init>(RNASeqPDFSummaryGenerator.java:96)
at de.mpimp.golm.robin.GUI.RNASeq.RNASeqWorkflowPanel$67.doInBackground(RNASeqWorkflowPanel.java:4432)
at de.mpimp.golm.robin.GUI.RNASeq.RNASeqWorkflowPanel$67.doInBackground(RNASeqWorkflowPanel.java:4403)
at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at javax.swing.SwingWorker.run(SwingWorker.java:316)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)

System Information
==================

java.runtime.name=Java(TM) SE Runtime Environment
java.vm.version=20.6-b01-415
mrj.build=10M3635
java.vm.vendor=Apple Inc.
java.vendor.url=http://www.apple.com/
java.vm.name=Java HotSpot(TM) 64-Bit Server VM
file.encoding.pkg=sun.io
java.vm.specification.name=Java Virtual Machine Specification
java.runtime.version=1.6.0_31-b04-415-10M3635
os.arch=x86_64
java.vm.specification.vendor=Sun Microsystems Inc.
os.name=Mac OS X
java.specification.name=Java Platform API Specification
java.class.version=50.0
os.version=10.6.8
os.version=10.6.8
user.timezone=America/New_York
file.encoding=MacRoman
java.specification.version=1.6
java.vm.specification.version=1.0
sun.arch.data.model=64
java.specification.vendor=Sun Microsystems Inc.
java.vm.info=mixed mode
java.version=1.6.0_31
java.vendor=Apple Inc.
java.vendor.url.bug=http://bugreport.apple.com/
sun.cpu.endian=little
mrj.version=1060.1.6.0_31-415

RE: Java Error with DEseq analysis in RobiNA
Answer
4/26/13 12:09 PM as a reply to Alejandro Villarino.
Hi Alejandro,

it would be great if you could send me the counts table that you had imported so
i can reproduce and examine the error you reported. I would, of course, only use
the file for debugging and delete it afterwards.

best greetings,
Marc

RE: Java Error with DEseq analysis in RobiNA
Answer
4/26/13 2:23 PM as a reply to Marc Lohse.
HI Marc, thanks for the reply.

Turns out that there was a problem with R. I Downloaded the latest version and now everything is running smoothly.

Also, it seems that R and RobiNA must be in the same folder (i.e. the 'applications folder' on a Mac).

Thanks again,

Alejandro Villarino



Hi Alejandro,

i am happy to hear that the problem went away - i am a bit surprised, though, that
installing and external R on your system was the solution. If you did not reconfigure
RobiNA internally to use the newly installed R, it would continue using the R engine
that is included in the RobiNA package (and hidden deeply within the guts of the actual
RobiNA.app mac application bundle).

Hence i fear the installation of R and disappearance of the problem were just coincidental.
Since the Mac version of RobiNA is distributed as a completely self-contained and self-sufficient
bundle, it does not matter where on your Mac file system you put it (as long as you have
write permission) and what else is installed in the same folder.

Should the problem choose to reoccur, please don't hesitate to contact me again.

cheers,
Marc

RE: Java Error with DEseq analysis in RobiNA
Answer
10/22/13 4:28 AM as a reply to Marc Lohse.
Hello,

Initially I will thank you for RobiNA! It is a great tool!

I have a very similar problem when I try to run RobiNA. I tried the suggestions presented here, by Villarino, but it did not work.
I ran RobiNA (1.2.4_build656) in a server with Ubuntu 12.04 and Java (java version "1.7.0_40")
Java(TM) SE Runtime Environment (build 1.7.0_40-b43)
Java HotSpot(TM) 64-Bit Server VM (build 24.0-b56, mixed mode).

Any help that you could give me would be deeply appreciated.

Thank you very much!

Leomar Woyann

RE: Java Error with DEseq analysis in RobiNA
Answer
11/4/13 1:36 AM as a reply to leomar guilherme woyann.
Unfortunately, I still receive the same error when conducting DGE analysis with RobiNA. I already download and fresh install latest R from their main pages as suggested above but still making no progress. Any suggestion on this ?


-- 11/04/2013@10:34:43:239 -- java.io.FileNotFoundException: C:\New Folder (3)\source\R.session.info.txt (The system cannot find the file specified)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(Unknown Source)
at de.mpimp.golm.robin.GUI.RNASeq.RNASeqPDFSummaryGenerator.addSessionInfo(RNASeqPDFSummaryGenerator.java:302)
at de.mpimp.golm.robin.GUI.RNASeq.RNASeqPDFSummaryGenerator.<init>(RNASeqPDFSummaryGenerator.java:96)
at de.mpimp.golm.robin.GUI.RNASeq.RNASeqWorkflowPanel$67.doInBackground(RNASeqWorkflowPanel.java:4436)
at de.mpimp.golm.robin.GUI.RNASeq.RNASeqWorkflowPanel$67.doInBackground(RNASeqWorkflowPanel.java:4407)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

System Information
==================

java.runtime.name=Java(TM) SE Runtime Environment
java.vm.version=24.45-b08
java.vm.vendor=Oracle Corporation
java.vendor.url=http://java.oracle.com/
java.vm.name=Java HotSpot(TM) 64-Bit Server VM
file.encoding.pkg=sun.io
java.vm.specification.name=Java Virtual Machine Specification
java.runtime.version=1.7.0_45-b18
os.arch=amd64
java.vm.specification.vendor=Oracle Corporation
os.name=Windows 7
java.specification.name=Java Platform API Specification
java.class.version=51.0
os.version=6.1
os.version=6.1
user.timezone=Australia/Brisbane
file.encoding=Cp1252
java.specification.version=1.7
java.vm.specification.version=1.7
sun.arch.data.model=64
java.specification.vendor=Oracle Corporation
java.vm.info=mixed mode
java.version=1.7.0_45
java.vendor=Oracle Corporation
java.vendor.url.bug=http://bugreport.sun.com/bugreport/
sun.cpu.endian=little

RE: Java Error with DEseq analysis in RobiNA
Answer
11/4/13 9:26 AM as a reply to Tuan Viet Nguyen.
Dear Tuan Viet Nguyen,

thank for your report - according to the stack trace you've attached i would say that R must have
failed for some unknown reason. In order to understand better why that might have happened, it would
be great if you could send me the ".log" file from the log subfolder of the project folder. This file
contains more detailed information on the program workflow and should help me find out what causes
the problem you've reported.

You can send the file as an email attachment directly to me (lohse_at_mpimp-golm.mpg.de)

cheers,
Marc