Unfortunately the error message doesn't stay on screen for more than a split
second so I cannot read it fully or I would have given a more accurate
description. I have tried changing the path, setting the environmental
variables and using the .exe as you just suggested and still get the same
message. Is there anything else it may be? Is there a way for me to get the
error message to stay on screen so I can give you the full description?
-Scott
Sent from my iPhone
On Aug 5, 2013, at 11:29 PM, Tomáš Pluskal <plus...@oist.jp> wrote:
> Hi Scott,
>
> "an error regarding classFactory and something about missing operand" is not
> a very precise description of the error. Next time please send an accurate
> description.
>
> Your problem is most likely in the JAVA_COMMAND variable. This variable is
> supposed to contain the path of the java program (java.exe if you're on
> Windows), so in your case should be probably like this:
>
> set JAVA_COMMAND=C:\Program Files\Java\jre7\bin\java.exe
>
>
> Cheers,
>
> Tomas
>
>
>
> On Aug 6, 2013, at 9:47 AM, srjhogan <srjho...@gatech.edu> wrote:
>
>> I cannot run the batch file to start mzmine. I receive an error regarding
>> classFactory and something about missing operand. I have the current java
>> installed and the proper environmental variable path. Please let me know
>> where my problem is. My source code is:
>>
>> @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=C:\Users\scott\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=C:\Users\KAA FLB\Documents\R\win-library\2.15\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\jre7\bin
>>
>> 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
>>
>>
>> --
>> Scott Hogan
>> Georgia Institute of Technology
>> School of Chemistry and Biochemistry
>> LaPlaca Research Group
>> email: srjho...@gatech.edu
>>
>>
>>
>> --
>> View this message in context:
>> http://mzmine-devel-developer-discussion.970458.n3.nabble.com/Help-Installing-MZmine-tp4024280.html
>> Sent from the Mzmine-devel -- Developer discussion mailing list archive at
>> Nabble.com.
>>
>> ------------------------------------------------------------------------------
>> Get your SQL database under version control now!
>> Version control is standard for application code, but databases havent
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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
>
------------------------------------------------------------------------------
Get your SQL database under version control now!
Version control is standard for application code, but databases havent
caught up. So what steps can you take to put your SQL databases under
version control? Why should you start doing it? Read more to find out.
http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
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