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
At 2014-10-30 08:32:30, "Tomas Pluskal" <plus...@oist.jp> wrote:
Hi,
PeakInvestigator is a modified version of MZmine provided by different authors.
I cannot help you with your R problem if you provide no information. Please
follow the 'How to report problems' section of the MZmine 2 manual.
Best,
Tomas
On Oct 29, 2014, at 21:37, GY <gzql...@163.com> wrote:
Hi Tomas,
I'm still trying to figure out the r problem and I found that a MZmine
PeakInvestigator software. This software seems similar to MZmine and I can use
r using this software while for MZmine cannot. I'm wondering if it's the same
developer for these two software.
sorry to trouble you.
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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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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