Hi Gao,
1) R_HOME should be set to C:\Program Files\R\R-3.1.1 (not C:\Program
Files\R\R-3.1.1\library), as described in MZmine manual.
2) According to the output of your command packageDescription("xcms"), the XCMS
library is installed in
C:/Users/a0068387/Documents/R/win-library/3.1/xcms/Meta/package.rds
Therefore, I think you should set R_LIBS_USER to
C:\Users\a0068387\Documents\R\win-library\3.1 (not C:\Program
Files\R\R-3.1.1\library).
Let me know if this helped. If you have any further problems, please check the
manual and make sure you followed all steps properly.
Tomas
On Oct 28, 2014, at 15:42, GY <gzql...@163.com> wrote:
> 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
===============================================
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
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