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