Hello:
I have problems with MZmine installations in the past 2 weeks although I
installed MZmine 2.1 last year on my laptop, Win7Pro x64, and there were no
problems then (although it also stopped working now).
Current problems:
MZmine version 2.14.2
Windows7Pro 64bit
C:\Users\ICBDD TOF>java -version
java version "1.8.0_45"
Java<TM> SE Runtime Environment <build 1.8.0_45-b14>
Java HotSpot<TM> Client VM <build 25.45-b02, mixed mode, sharing>
C:\Users\ICBDD TOF>R --version
'R' is not recognized as an internal or external command, operable program
or batch file
Attached is the modified startMZmine_Windows batch file (suffix .bat
renamed .txt to allow attachment in gmail).
When this batch file is run the following error message occurs,
"Checking physical memory size...
Found 8175 MB memory, 64-bit system
Java heap size set to 4087 MB
Error occurred during initialization of VM
Could not reserve enough space for 4186112KB object heap
Press any key to continue..."
Thanks for your help
Bela Ruzsicska, Ph.D
Director - Analytical Laboratory
Institute for Chemical Biology & Drug Discovery
Chemistry Dept. Rm.573, Labs 570,576
SUNY-Stony Brook
Stony Brook, NY, 11794-3400
631-632-7937
http://www.stonybrook.edu/commcms/icbdd/
@echo off
rem This is necessary to access the TOTAL_MEMORY and ADDRESS_WIDTH variables
inside the IF block
setlocal enabledelayedexpansion
rem Obtain the physical memory size and check if we are running on a 32-bit
system.
if exist C:\Windows\System32\wbem\wmic.exe (
echo Checking physical memory size...
rem Get physical memory size from OS
for /f "skip=1" %%p in ('C:\Windows\System32\wbem\wmic.exe os get
totalvisiblememorysize') do if not defined TOTAL_MEMORY set /a TOTAL_MEMORY=%%p
/ 1024
for /f "skip=1" %%x in ('C:\Windows\System32\wbem\wmic.exe cpu get
addresswidth') do if not defined ADDRESS_WIDTH set ADDRESS_WIDTH=%%x
echo Found !TOTAL_MEMORY! MB memory, !ADDRESS_WIDTH!-bit system
) else (
echo Skipping memory size check, because wmic.exe could not be found
set ADDRESS_WIDTH=32
)
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 1024 MB on 32-bit systems, or
rem half of the physical memory on 64-bit systems.
rem Feel free to adjust the HEAP_SIZE according to your needs.
if %ADDRESS_WIDTH%==32 (
set HEAP_SIZE=1024
) else (
set /a HEAP_SIZE=%TOTAL_MEMORY% / 2
)
echo Java heap size set to %HEAP_SIZE% MB
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-3.2.0
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=%R_HOME%\library
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=-showversion -classpath lib\* -Djava.ext.dirs=
-XX:+UseParallelGC -Djava.io.tmpdir=%TMP_FILE_DIRECTORY% -Xms%HEAP_SIZE%m
-Xmx%HEAP_SIZE%m -Djava.library.path="%JRI_LIB_PATH%"
set MAIN_CLASS=net.sf.mzmine.main.MZmineCore
rem This command starts the Java Virtual Machine
%JAVA_COMMAND% %JAVA_PARAMETERS% %MAIN_CLASS% %*
rem If there was an error, give the user chance to see it
IF ERRORLEVEL 1 pause
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