Dear Tomas,
It worked, thanks a lot.
i changed this
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri\x64
to
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri\x64;%R_LIBS%\rJava\jri\x64
--
Regards
GAO Yan
At 2014-10-30 11:05:27, "Tomas Pluskal" <plus...@oist.jp> wrote:
>Hi Gao,
>
>I don't see any obvious problem in your settings. You mentioned that the
>PeakInvestigator edition of MZmine works fine.
>What happens if you copy the settings of the R-related variables from the
>PeakInvestigator's startMZmine script into MZmine's startMZmine script?
>
>I am talking about these variables:
>
> set R_HOME=
> set R_LIBS_USER=
> set R_LIBS=
> set R_SHARE_DIR=
> set R_INCLUDE_DIR=
> set R_DOC_DIR=
> set PATH=
> set JRI_LIB_PATH=
>
>Tomas
>
>
>
>On Oct 30, 2014, at 11:45, GY <gzql...@163.com> wrote:
>
>> Hi Tomas,
>>
>> 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".
>> 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:/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:/Program Files/R/R-3.1.1/library/xcms/Meta/package.rds
>> > packageDescription("ptw")
>> Package: ptw
>> Type: Package
>> Title: Parametric Time Warping
>> Version: 1.0-7
>> Date: 2014-03-29
>> Author: Jan Gerretzen <j.gerret...@science.ru.nl>, Paul Eilers
>> <p.eil...@erasmusmc.nl>, Hans Wouters, Tom Bloemberg
>> <t.bloemb...@science.ru.nl>, Ron Wehrens <ron.wehr...@fmach.it>
>> and The R Development Core Team
>> Maintainer: Tom Bloemberg <t.bloemb...@science.ru.nl>
>> Description: Parametric Time Warping aligns patterns, i.e. it aims to
>> put corresponding features at the same locations. The algorithm
>> searches for an optimal polynomial describing the warping. It
>> is possible to align one sample to a reference, several samples
>> to the same reference, or several samples to several
>> references. One can choose between calculating individual
>> warpings, or one global warping for a set of samples and one
>> reference. Two optimization criteria are implemented: RMS (Root
>> Mean Square error) and WCC (Weighted Cross Correlation).
>> License: GPL (>= 2)
>> Copyright: Copyright for the file src/approx.c is detailed in
>> inst/COPYRIGHT
>> LazyLoad: yes
>> Repository: CRAN
>> Date/Publication: 2014-03-30 00:17:02
>> Packaged: 2014-03-29 20:09:17 UTC; tombloem
>> NeedsCompilation: yes
>> Built: R 3.1.1; x86_64-w64-mingw32; 2014-07-16 10:45:10 UTC; windows
>>
>> -- File: C:/Program Files/R/R-3.1.1/library/ptw/Meta/package.rds
>> > packageDescription("rJava")
>>
>>
>>
>> @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
>> 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
>>
>> --
>> Regards
>> GAO Yan
>>
>>
>
>===============================================
>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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