Could not find or load main class

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Dec 14, 2013, 1:24:13 PM12/14/13
Dear all,

I am now trying to analyze Agilent 6550 Q-TOF data using mzmatch in R version 3.0.1 (2013-05-16) on Platform: x86_64-w64-mingw32/x64 (64-bit).

I have been able to extract peaks using centwave on xcms and write files as peakML. However, when trying to combine such files according to my experimental groups using mzmatch.ipeak.Combine the following error appears

Error: Could not find or load main class

running command 'java -da -dsa -Xmn1g -Xss228k -XX:+UseParallelGC -XX:ParallelGCThreads=10 -Xms1425m -Xmx1425m -cp C:/Program Files/R/R-3.0.1/library/mzmatch.R/java/mzmatch.jar mzmatch.ipeak.Combine -….

I guess that it might be related to a java problem. I do need to fix it in order to proceed with the analysis pipeline for such samples. Any suggestion or workaround?

Thank you very much in advance

Darren Creek

Dec 14, 2013, 9:35:46 PM12/14/13
Hi Maria,
A few common causes of Java errors are:
1) either your files, or the R package are located in a folder with spaces in the name (e.g. 'My documents' or 'Program Files'). 
2) Running 64-bit version of R with the 32bit version of Java. NB the default Java on most machines is 32bit. You need to go to to manually install the 64bit version - then restart the computer before trying again.

I hope this helps.


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Dr Darren Creek

NHMRC CJ Martin Fellow
Department of Biochemistry and Molecular Biology, Bio21 Institute
University of Melbourne

Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences
Monash University, Parkville campus
381 Royal Parade, Parkville, Vic, 3052

Dec 15, 2013, 2:50:34 PM12/15/13
Dear Darren,

Thanks a lot for your fast response

I have installed my R package in other local than Program Files avoiding spaces in the name and the error get fix

Best wishes,

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