Hi,
I downloaded mzmine 2 for my mac and it worked immediately, great software and
does what I need, many thanks. But now I try on my Win7 in the office and
followed the instructions to modify the .bat file, but trying to start through
the file, the console window pops up for less than a second and then nothing is
happening, no error message. All the required R files are present, all paths
are set. I tried the .bat lines in cmd and get errors from these lines:
for /f "skip=1" %%p in ('wmic os get totalvisiblememorysize') do if not defined
TOTAL_MEMORY=set TOTAL_MEMORY=%%p : %%p was unexpected this time
for /f "skip=1" %%x in ('wmic cpu get addresswidth') do if not defined
ADDRESS_WIDTH set ADDRESS_WIDTH=%%x : %%x was unexpected this time
I overcame these lines by just setting the variables to fixed numbers, the bat
now stops at java - telling me that java is not recognized as command, when I
add a path it ends with "C:/Program is no command" , I have both java 32 and 64
bit on the installed.
I am very out of batch writing, any help welcome
Many thanks
Manfred
Manfred Raida PhD
Senior Research Fellow
Singapore Lipidomics Incubator (SLING)
Center for Life Sciences (CeLS)
28 Medical Drive, Level 03-03A, Singapore 117456
Phone +65 9638 7692
www.sling.edu.sg
Full .bat
@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-3.0.0
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=-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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