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 <[email protected]> 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 <[email protected]>, Ralf Tautenhahn
> <[email protected]>, Steffen Neumann <[email protected]>,
> Paul Benton <[email protected]>, Christopher Conley
> <[email protected]>
> Maintainer: Ralf Tautenhahn <[email protected]>
> 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 <[email protected]>, Paul Eilers
> <[email protected]>, Hans Wouters, Tom Bloemberg
> <[email protected]>, Ron Wehrens <[email protected]>
> and The R Development Core Team
> Maintainer: Tom Bloemberg <[email protected]>
> 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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