Hi Tomas,
I tried to modify the pathway but it didn't work. i got the same problem.
Thanks.
Gao Yan
At 2014-10-28 15:13:16, "Tomas Pluskal" <plus...@oist.jp> wrote:
>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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