Hi Gao, Please follow the 'How to report problems' section of the MZmine 2 manual.
Tomas On Oct 28, 2014, at 16:19, GY <gzql...@163.com<mailto:gzql...@163.com>> wrote: 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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:csm...@scripps.edu>>, >> >> Ralf Tautenhahn >> >> >> >> <rtaut...@gmail.com<mailto:rtaut...@gmail.com>>, Steffen Neumann >> >> <sneum...@ipb-halle.de<mailto:sneum...@ipb-halle.de>>, >> >> >> >> Paul Benton <hpben...@scripps.edu<mailto:hpben...@scripps.edu>>, >> >> Christopher Conley >> >> >> >> <cjcon...@ucdavis.edu<mailto:cjcon...@ucdavis.edu>> >> >> >> >> Maintainer: Ralf Tautenhahn >> >> <rtaut...@gmail.com<mailto: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<mailto: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<mailto: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<mailto: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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