Could not find or load main class Files.R.R-3.0.1.library.mzmatch.R.java.mzmatch.jar

maria....@gmail.com

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Dec 14, 2013, 1:24:13 PM12/14/13

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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 Files.R.R-3.0.1.library.mzmatch.R.java.mzmatch.jar

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

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Dec 14, 2013, 9:35:46 PM12/14/13

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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 https://java.com/en/download/manual.jsp to manually install the 64bit version - then restart the computer before trying again.

I hope this helps.

regards,

Darren

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