Hi,
I have got problem to open MZmine.
I have installed Java 7, 64-bit, on my computer. When I use the startup script
(by double clicking on the windows bat file) I get the following message:
'C:\Program' is not recognized as an internal or external command,
operable program or batch file.
'C:\Program' is not recognized as an internal or external command,
operable program or batch file.
Press any key to continue . . .
I have opened and edited my bat file in notepad and save it. Does it
automatically taken in bat file?
I appreciate if you can help me!
Best
Ali
Here is the copy past from notepad:
@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% / 1024 / 2
rem Check if we are running on a 32-bit system.
rem If yes, force the heap size to 1024 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-3.0.1
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%\Documents\R\win-library\3.0
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=C:\Program Files\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
Ali Moazzami (Associate Professor)
Department of Chemistry and Biotechnology
Metabolomics core facilities
Swedish University of Agricultural Sciences
Box 7015, 750 07 Uppsala, Sweden
Tel: +46-18-672048
Mobile:+46-739403240
E-mail: ali.moazz...@slu.se<mailto:ali.moazz...@slu.se>
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