Hello,
I have heard a lot about MZmine and find it very interesting. However I
got stock with a few problems and I hope you will be able to help me
solve them.
My first problem is that I have problems allocating enough memory to
MZmine. I can force MZmine to allocate 1 GB but (as in the attached .bat
file), but if I try to allocate more I get the following error:
And if I try to run the original script (where half the memory should be
allocated to MZmine) I get this result:
Do you have any idea on how I can get more memory allocated? 1 GB is not
enough for my dataset and I get memory problems when I run the
chromatogram builder.
My second problem is that MZmine have problems communicating with R when
I try to do baseline correction.
The output you request in your manual from the command prompt are:
.libPaths()
   [1] "C:/Users/Lea/Documents/R/win-library/3.1"
   [2] "C:/Programmer/R/R-3.1.2/library"
When I try to run the packageDescriptions I get an error: " Could not
find function "packageDescription" " - So I probably have a problem with
my R installation, but I do not know how to fix this. I you could give
me a hint I would very much appreciate it :-)
Some system information:
MZmine: is the newest version just downloaded a week ago.
R (64 bit):
version: 3.1.2
Location on computer: C:\Programmer\R\R-3.1.2
rJava location: C:\Users\Lea\Documents\R\win-library\3.1\rJava\jri\x64
My computer:
64-bit processor, 32 GB RAM, Windows 8.
Kind regards
Lea Johnsen
@echo off
rem Obtain the physical memory size
rem for /f "skip=1" %%p in ('wmic os get totalvisiblememorysize') do if not rem
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.
rem set /a HEAP_SIZE=%TOTAL_MEMORY% / 1024 / 2
set HEAP_SIZE=1024
rem Check if we are running on a 32-bit system.
rem If yes, force the heap size to 1024 MB.
rem for /f "skip=1" %%x in ('wmic cpu get addresswidth') do if not defined rem
ADDRESS_WIDTH set ADDRESS_WIDTH=%%x
rem if %ADDRESS_WIDTH%==32 (
rem set HEAP_SIZE=1024
rem )
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 variamer Files\R\R-3.1.2
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\3.1
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-2.11.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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