OK, I found why MZmine was crashing.
See
http://svn.mesquiteproject.org:8080/repository/MesquiteR/trunk/MesquiteR/Source/org/rosuda/JRI/Rengine.java
Those *** (replace with your favorite insult) call System.exit(1) if the JRI
library is not found!
I added a workaround to our RUtilities class, so it should not crash anymore.
Cheers,
Tomas
On Jun 22, 2012, at 10:02 AM, Tomas Pluskal wrote:
Hi Sandra, Chris,
I can confirm that if R is not installed, the whole MZmine application will
crash when running the heat map plot.
This is certainly not good. We should catch the UnsatisfiedLinkError and
display a sensible error message.
Also, I found two issues with the heat map plot (Sandra?)
1) The documentation does not explicitly say that R must be installed to use
the module
2) If heat map is run on a non-aligned peak list (single column), it shows an
exception:
[9:59:21|SEVERE|WorkerThread]: Unhandled exception
java.lang.ArrayIndexOutOfBoundsException: 0 while processing task Heat map...
(java.lang.ArrayIndexOutOfBoundsException:
0...@net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.groupingDataset<mailto:0...@net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.groupingDataset>(HeatMapTask.java:586))
java.lang.ArrayIndexOutOfBoundsException: 0
at
net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.groupingDataset(HeatMapTask.java:586)
at
net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.run(HeatMapTask.java:113)
at net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60)
Cheers,
Tomas
On Jun 21, 2012, at 12:39 AM, Mischa Vreeburg wrote:
Did you install R? http://cran.r-project.org/bin/windows/base/
and did you install the JRI package and added the location of R in the ini file?
regards,
Mischa Vreeburg
2012/6/20 Hoch, Kathleen
<kathleen.h...@uth.tmc.edu<mailto:kathleen.h...@uth.tmc.edu>>
Attached is screenshot with run information on heat map crashing. Also here is
a dropbox link to the mzmine project file
http://dl.dropbox.com/u/62257560/0hr_vs_0hrexcl1.mzmine. Thank you for your
assistance.
Kathy
Kathleen Hoch
Research Associate
CCTS Proteomics Core
Sarofim Research Building
1825 Pressler St.
Houston, TX 77030
713-500-3666<tel:713-500-3666>
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Tomáš Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
Fax: +81-98-966-2890
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G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
Fax: +81-98-966-2890
------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
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