Dear Tomas,
please find below for the script.
@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-3.1.1\library
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:\Program Files\R\R-3.1.1\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-2.11.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
Thanks.
Gao Yan
At 2014-10-28 14:31:24, "Tomas Pluskal" <plus...@oist.jp> wrote:
>Hi Gao,
>
>Did you change the R-related paths in your startMZmine script? Please send us
>the script together with your problem report.
>
>Best regards,
>
>Tomas
>
>
>
>On Oct 28, 2014, at 15:22, GY <gzql...@163.com> wrote:
>
>>
>>
>> Hi,
>>
>> I'm using mzmine for data processing and when i'm trying to use the
>> wavelets(XCMS) algorithm, the software shows " Couldn't start R. Please
>> check if R is installed and path to the libraries is set properly in the
>> startMZmine script. can you give me some suggestion on this?
>>
>> please find related information below.
>>
>> The version of R installed is R-3.1.1 and it is installed under C:/Program
>> Files. I’m running the 64-bits version of R.
>>
>> Please refer to the script below
>>
>>
>>
>>
>>
>> R version 3.1.1 (2014-07-10) -- "Sock it to Me"
>>
>> Copyright (C) 2014 The R Foundation for Statistical Computing
>>
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>>
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>
>> You are welcome to redistribute it under certain conditions.
>>
>> Type 'license()' or 'licence()' for distribution details.
>>
>>
>>
>> Natural language support but running in an English locale
>>
>>
>>
>> R is a collaborative project with many contributors.
>>
>> Type 'contributors()' for more information and
>>
>> 'citation()' on how to cite R or R packages in publications.
>>
>>
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>
>> 'help.start()' for an HTML browser interface to help.
>>
>> Type 'q()' to quit R.
>>
>>
>>
>> > .libPaths()
>>
>> [1] "C:/Users/a0068387/Documents/R/win-library/3.1"
>>
>> [2] "C:/Program Files/R/R-3.1.1/library"
>>
>> > packageDescription("xcms")
>>
>> Package: xcms
>>
>> Version: 1.42.0
>>
>> Date: 2014-10-11
>>
>> Title: LC/MS and GC/MS Data Analysis
>>
>> Author: Colin A. Smith <csm...@scripps.edu>, Ralf Tautenhahn
>>
>> <rtaut...@gmail.com>, Steffen Neumann <sneum...@ipb-halle.de>,
>>
>> Paul Benton <hpben...@scripps.edu>, Christopher Conley
>>
>> <cjcon...@ucdavis.edu>
>>
>> Maintainer: Ralf Tautenhahn <rtaut...@gmail.com>
>>
>> Depends: R (>= 2.14.0), methods, mzR (>= 1.1.6), BiocGenerics, Biobase
>>
>> Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>=
>>
>> 1.5.2), RANN, RUnit
>>
>> Enhances: Rgraphviz, Rmpi, XML
>>
>> Description: Framework for processing and visualization of
>>
>> chromatographically separated and single-spectra mass spectral
>>
>> data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML
>>
>> files. Preprocesses data for high-throughput, untargeted
>>
>> analyte profiling.
>>
>> License: GPL (>= 2) + file LICENSE
>>
>> URL: http://metlin.scripps.edu/download/ and
>>
>> https://github.com/sneumann/xcms
>>
>> BugReports: https://github.com/sneumann/xcms/issues/new
>>
>> biocViews: MassSpectrometry, Metabolomics
>>
>> Packaged: 2014-10-14 02:08:49 UTC; biocbuild
>>
>> Built: R 3.1.1; i386-w64-mingw32; 2014-10-14 14:24:49 UTC; windows
>>
>>
>>
>> -- File: C:/Users/a0068387/Documents/R/win-library/3.1/xcms/Meta/package.rds
>>
>> > package
>>
>>
>> Thanks a lot.
>>
>> Gao Yan
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> 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
>
------------------------------------------------------------------------------
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
