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 <[email protected]>, Ralf Tautenhahn
<[email protected]>, Steffen Neumann <[email protected]>,
Paul Benton <[email protected]>, Christopher Conley
<[email protected]>
Maintainer: Steffen Neumann <[email protected]>
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 <[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 3.2.0; 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 <[email protected]>
Maintainer: Simon Urbanek <[email protected]>
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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