Dear Joelle,
Thanks a lot for letting us know your solution!
Tomas
On Jun 12, 2014, at 18:44, joelle
<joelle.hour...@unige.ch<mailto:joelle.hour...@unige.ch>> wrote:
Hi!
I had a few problems with the file.bat to define the path of R. My OS is
windows 7, 64bit. I installed MZmine 2.10, R 3.1.0 and JRE8. Finally, we
managed to run it, so I send a copy of our file.bat. Just an observation for
the library: look where is your library, the correct version can be:
set R_LIBS_USER= C:\Program Files\R\R-3.1.0\library (Look where is your
library)
@echo off
rem Obtain the physical memory size
for /f "skip=1" %%p in ('wmic os get totalvisiblememorysize') do if not
defined TOTAL_MEMORY=set TOTAL_MEMORY=%%p
rem The HEAP_SIZE variable defines the Java heap size in MB.
rem That is the total amount of memory available to MZmine 2.
rem By default we set this to the half of the physical memory
rem size, but feel free to adjust according to your needs.
set /a HEAP_SIZE=%TOTAL_MEMORY% / 4096 / 2
rem Check if we are running on a 32-bit system.
rem If yes, force the heap size to 4096 MB.
for /f "skip=1" %%x in ('wmic cpu get addresswidth') do if not defined
ADDRESS_WIDTH set ADDRESS_WIDTH=%%x
if %ADDRESS_WIDTH%==32 (
set HEAP_SIZE=1024
)
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-3.1.0
set R_SHARE_DIR=C:\Program Files\R\R-3.1.0
set R_INCLUDE_DIR=C:\Program Files\R\R-3.1.0\include
set R_DOC_DIR=C:\Program Files\R\R-3.1.0\doc
set R_LIBS_USER=C:\Users\xxxxxx\documents\R\win-library\3.1
rem Include R DLLs in PATH.
set PATH=%PATH%;%R_HOME%\bin\x64
rem The directory holding the JRI shared library (libjri.so).
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri\x64
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 JAVA_PARAMETERS=-XX:+UseParallelGC -Djava.io.tmpdir=%TMP_FILE_DIRECTORY%
-Xms%HEAP_SIZE%m -Xmx%HEAP_SIZE%m -Djava.library.path="%JRI_LIB_PATH%"
set CLASS_PATH=lib\MZmine-2.10.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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===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
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