G'day,
> Here is my start-up batch file for comparison: (I use Win7 64bit).
> You will have to put in your own paths to your R installation
And as we're now using MZmine 2.7 and R 2.15 the bat file now looks like
that given below.
Note also that in R you will need the following installed:
rJava for R integration:
install.packages("rJava")
ptw for baseline correction:
install.packages("ptw")
Regards,
Chris.
-----
@echo off
rem The HEAP_SIZE variable line defines the Java heap size in MB.
rem That is the total amount of memory available to MZmine 2.
rem Please adjust according to the amount of memory of your computer.
rem Maximum value on a 32-bit Windows system is about 1300.
set HEAP_SIZE=4096
rem The TMP_FILE_DIRECTORY parameter defines the location where temporary
rem files (parsed raw data) will be placed. Default is %TEMP%, which
rem represents the system temporary directory.
set TMP_FILE_DIRECTORY=%TEMP%
rem Set R environment variables.
set R_HOME=C:\Program Files\R\R-2.15.0\bin\x64
set R_SHARE_DIR=%R_HOME%\share
set R_INCLUDE_DIR=%R_HOME%\include
set R_DOC_DIR=%R_HOME%\doc
set R_LIBS_USER=%USERPROFILE%\My Documents\R\win64-library\2.15
rem Include R DLLs in PATH.
set PATH=%PATH%;%R_HOME%\bin
rem The directory holding the JRI shared library.
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri
rem It is usually not necessary to modify the JAVA_COMMAND parameter, but
rem if you like to run a specific Java Virtual Machine, you may set the
rem path to the java command of that JVM
set JAVA_COMMAND=java
rem It is not necessary to modify the following section
set LOGGING_CONFIG_FILE=conf/logging.properties
set JAVA_PARAMETERS=-XX:+UseParallelGC
-Djava.io.tmpdir=%TMP_FILE_DIRECTORY%
-Djava.util.logging.config.file=%LOGGING_CONFIG_FILE% -Xms%HEAP_SIZE%m
-Xmx%HEAP_SIZE%m -Djava.library.path="%JRI_LIB_PATH%"
set CLASS_PATH=lib\MZmine-2.8-SNAPSHOT.jar
set MAIN_CLASS=net.sf.mzmine.main.MZmineCore
rem Show java version, in case a problem occurs
%JAVA_COMMAND% -version
rem This command starts the Java Virtual Machine
%JAVA_COMMAND% %JAVA_PARAMETERS% -classpath %CLASS_PATH% %MAIN_CLASS% %*
rem If there was an error, give the user chance to see it
IF ERRORLEVEL 1 pause
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