Hi Julian,
Strangely enough, I don't see any problem in your configuration.
Can you double check the %JRI_LIB_PATH% folder exists?
(%R_LIBS_USER%\rJava\jri\x64)
Since many people report problems with the R integration in MZmine, we
have recently switched to a different library - RServe. The new
library does not require any configuration parameters. It will be
included in the next release of MZmine (2.15).
Best regards,
Tomas
On Thu, Jun 18, 2015 at 10:03 PM, Julian Avila Pacheco
<jravi...@broadinstitute.org> wrote:
> Hello,
>
> I am having a problem with mzMine when I try to use the XCMS package, I am
> getting: "XCMS requires R but it couldn't be loaded (Could not start R.
> Please check if R is installed and path to the libraries is set properly in
> the startMZmine script. (R_HOME = C:\Program Files\R\R-3.2.0))
>
> Here is the information for my mzMine, R, and XCMS:
>
>
>> .libPaths()
>
> [1] "C:/Users/jravilap/Documents/R/win-library/3.2"
>
> [2] "C:/Program Files/R/R-3.2.0/library"
>
>
> C:\> java -version
>
> java version "1.8.0_45"
>
> Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
>
> Hava HotSpot(TM) Client VM (build 25.45-b02, mixed mode)
>
>
> XCMS
>
>
>> packageDescription("xcms")
>
> Package: xcms
>
> Version: 1.44.0
>
> Date: 2015-03-16
>
> 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: Steffen Neumann <sneum...@ipb-halle.de>
>
> Depends: R (>= 2.14.0), methods, mzR (>= 1.1.6), BiocGenerics,
>
> ProtGenerics, 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
>
> NeedsCompilation: yes
>
> Packaged: 2015-04-17 02:38:50 UTC; biocbuild
>
> Built: R 3.2.0; i386-w64-mingw32; 2015-04-17 14:12:12 UTC; windows
>
>
>
> -- File: C:/Users/jravilap/Documents/R/win-library/3.2/xcms/Meta/package.rds
>
>
> ptw
>
>
>> 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 3.2.0; x86_64-w64-mingw32; 2015-04-18 00:54:08 UTC; windows
>
>
>
> -- File: C:/Users/jravilap/Documents/R/win-library/3.2/ptw/Meta/package.rds
>
>
>
> rJAVA
>
>>packageDescription("rJava")
>
> Package: rJava
>
> Version: 0.9-6
>
> Title: Low-level R to Java interface
>
> Author: Simon Urbanek <simon.urba...@r-project.org>
>
> Maintainer: Simon Urbanek <simon.urba...@r-project.org>
>
> Depends: R (>= 2.5.0), methods
>
> Description: Low-level interface to Java VM very much like .C/.Call and
>
> friends. Allows creation of objects, calling methods and
>
> accessing fields.
>
> License: GPL-2
>
> URL: http://www.rforge.net/rJava/
>
> SystemRequirements: java
>
> Packaged: 2013-12-23 15:17:13 UTC; svnuser
>
> NeedsCompilation: yes
>
> Repository: CRAN
>
> Date/Publication: 2013-12-24 00:16:48
>
> Built: R 3.2.0; i386-w64-mingw32; 2015-04-18 00:46:16 UTC; windows
>
>
>
> -- File:
> C:/Users/jravilap/Documents/R/win-library/3.2/rJava/Meta/package.rds
>
>>
>
>
> MZMINE SETTINGS:
>
>
>
>
> @echo off
>
>
>
> rem This is necessary to access the TOTAL_MEMORY and ADDRESS_WIDTH variables
> inside the IF block
>
> setlocal enabledelayedexpansion
>
>
>
> rem Obtain the physical memory size and check if we are running on a 32-bit
> system.
>
> if exist C:\Windows\System32\wbem\wmic.exe (
>
> echo Checking physical memory size...
>
> rem Get physical memory size from OS
>
> for /f "skip=1" %%p in ('C:\Windows\System32\wbem\wmic.exe os get
> totalvisiblememorysize') do if not defined TOTAL_MEMORY set /a
> TOTAL_MEMORY=%%p / 1024
>
> for /f "skip=1" %%x in ('C:\Windows\System32\wbem\wmic.exe cpu get
> addresswidth') do if not defined ADDRESS_WIDTH set ADDRESS_WIDTH=%%x
>
> echo Found !TOTAL_MEMORY! MB memory, !ADDRESS_WIDTH!-bit system
>
> ) else (
>
> echo Skipping memory size check, because wmic.exe could not be found
>
> set ADDRESS_WIDTH=32
>
> )
>
>
>
> 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 1024 MB on 32-bit systems, or
>
> rem half of the physical memory on 64-bit systems.
>
> rem Feel free to adjust the HEAP_SIZE according to your needs.
>
> if %ADDRESS_WIDTH%==32 (
>
> set HEAP_SIZE=1024
>
> ) else (
>
> set /a HEAP_SIZE=%TOTAL_MEMORY% / 2
>
> )
>
> echo Java heap size set to %HEAP_SIZE% MB
>
>
>
> 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-3.2.0
>
> 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:\Users\jravilap\Documents\R\win-library\3.2
>
>
>
>
>
>
>
> 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="C:\Program Files\Java\jre7\bin\javaw.exe"
>
>
>
> rem It is not necessary to modify the following section
>
> set JAVA_PARAMETERS=-showversion -classpath lib\* -Djava.ext.dirs=
> -XX:+UseParallelGC -Djava.io.tmpdir=%TMP_FILE_DIRECTORY% -Xms%HEAP_SIZE%m
> -Xmx%HEAP_SIZE%m -Djava.library.path="%JRI_LIB_PATH%"
>
> set MAIN_CLASS=net.sf.mzmine.main.MZmineCore
>
>
>
> rem This command starts the Java Virtual Machine
>
> %JAVA_COMMAND% %JAVA_PARAMETERS% %MAIN_CLASS% %*
>
>
>
> rem If there was an error, give the user chance to see it
>
> IF ERRORLEVEL 1 pause
>
>
> Thanks,
>
>
>
> Julian
>
>
> ------------------------------------------------------------------------------
>
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> Mzmine-devel@lists.sourceforge.net
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>
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