Hi Padma
I have attached a copy of my startMZmine script. This is the file Tomas is
asking for. You find it in your MZmine folder. Please rename it from .bat to
.txt before adding it to the email.
Best,
Thomas
-----Original Message-----
From: Tomas Pluskal [mailto:plus...@oist.jp]
Sent: 1. april 2015 09:50
To: padma ramakrishnan
Cc: Developer discussion; sreena...@ccamp.res.in; pad...@ccamp.res.in
Subject: Re: [Mzmine-devel] MZmine troubleshooting
No, this is not what I am looking for.
Tomas
> On Apr 1, 2015, at 16:43, padma ramakrishnan <padma...@yahoo.co.in> wrote:
>
> Hi Tomas,
>
> I hope this is what you're looking for.
>
> Regards,
> Padma
>
>
>
> On Wednesday, 1 April 2015 10:49 AM, Tomas Pluskal <plus...@oist.jp> wrote:
>
>
> Hi,
>
> You attached the output of the script execution.
> I am asking for the contents of the script.
> Please attach the startMZmine_Windows.bat file.
>
> Tomas
>
>
>
> > On Apr 1, 2015, at 14:06, padma ramakrishnan <padma...@yahoo.co.in> wrote:
> >
> > Hi Tomas,
> >
> > Thank you for your reply. I've attached the MZmine start script as
> > requested.
> >
> > Regards,
> > Padma
> >
> >
> >
> > On Tuesday, 31 March 2015 7:30 PM, Tomas Pluskal <plus...@oist.jp> wrote:
> >
> >
> > Hi Padma,
> >
> > Please attach the complete startMZmine script.
> > Your R_LIBS_USER setting looks suspicious.
> >
> > Tomas
> >
> >
> > > On Mar 31, 2015, at 8:58 PM, padma ramakrishnan <padma...@yahoo.co.in>
> > > wrote:
> > >
> > > Hi,
> > >
> > > We are working with untargeted metabolomics data sets and are
> > > eager to try out MZmine for our analyses. However we are stuck at
> > > the raw data filtering step (baseline correction). A screenshot of
> > > the error is attached.
> > >
> > > Some of the details you may require are as follows.
> > >
> > > 1) MZmine 2.13.1
> > > Java version "1.8.0_25"
> > > R 3.1.0
> > >
> > > 2)Java Heap Size set to 1024MB
> > >
> > > 3)We are having a problem running "baseline correction". We tried
> > > configuring these in the R script, but we keep getting a message
> > > that these are incompatible with our version of R. Installing an
> > > older version of R also did not seem to help.
> > >
> > > Details of R in the command line are also attached.
> > >
> > > 4) We are using the 64bit version of R.
> > >
> > > Please advice on what we need to do to overcome this.
> > >
> > > Thank you.
> > >
> > > With regards,
> > > Padma Ramakrishnan
> > > C-CAMP, Bangalore.
> >
> > >
> > >
> > > <R command line.docx><mzmine
> > > error.pptx>-------------------------------------------------------
> > > ----------------------- Dive into the World of Parallel
> > > Programming The Go Parallel Website, sponsored by Intel and
> > > developed in partnership with Slashdot Media, is your hub for all
> > > things parallel software development, from weekly thought
> > > leadership blogs to news, videos, case studies, tutorials and
> > > more. Take a look and join the conversation now.
> > > http://goparallel.sourceforge.net/________________________________
> > > _______________
> > > Mzmine-devel mailing list
> > > Mzmine-devel@lists.sourceforge.net
> > > https://lists.sourceforge.net/lists/listinfo/mzmine-devel
> >
> > ===============================================
> > 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
> >
> >
> >
> > <mzminestartscript.docx>
>
>
> ===============================================
> 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
>
>
> <StartMZminebat.txt>
===============================================
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
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
@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:\R\R-3.1.1
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=%R_HOME%\library
rem Include R DLLs in PATH.
set PATH=%PATH%;%R_HOME%\bin\i386
rem The directory holding the JRI shared library (libjri.so).
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri\i386
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
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
