Hello,
I have been trying to get R to work in MZmine and have had nothing but
problems. Any R application (easiest one to list is baseline
correction) and MZmine cannot find R. I have tried MZmine 2.10.38
(MZmine PI) and 2.14.2 both encountered the same errors.
The steps I've undergone are simply uploading my files (25 .mzXML files)
and select baseline correction. Regardless of what conditions I choose
I get the same error.
There is no report in the cmd window which runs with MZ mine.
I'm running Windows 7 (64 bit)
my Java is Version 8 update 45
R --version gave me the following information in Rstudio...
R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
Thank you for your help,
Brandi West
@echo off
rem ***********************************************************************
rem * 1. Set R environment variables. Choose appropriate version numbers.
rem ***********************************************************************
set R_HOME=C:\Program Files\R\R-3.2.0
set R_LIBS_USER=C:\Users\bwes419\Documents\R\win-library\3.2
rem ***********************************************************************
rem ***********************************************************************
rem * 2. Set remaining R environment variables.
rem ***********************************************************************
set R_LIBS=C:\Program Files\R\R-3.2.0\library
set R_SHARE_DIR=C:\Program Files\R\R-3.2.0\share
set R_INCLUDE_DIR=C:\Program Files\R\R-3.2.0\include
set R_DOC_DIR=C:\Program Files\R\R-3.2.0\doc
rem ***********************************************************************
rem ***********************************************************************
rem * 3. Include R DLLs in PATH, and set directory holding the shared
rem * library (libjri.dll).
rem ***********************************************************************
set PATH=%PATH%;C:\Program Files\R\R-3.2.0\bin\x64
set JRI_LIB_PATH=C:\Users\bwes419\rJava\jri\x64;C:\Program
Files\R\R-3.2.0\library\rJava\jri\x64
rem ***********************************************************************
rem ***********************************************************************
rem * 4. It is usually not necessary to modify the JAVA_COMMAND parameter,
rem * but if you like to run a specific Java Virtual Machine, you may
rem * set the path to the java command of that JVM.
rem ***********************************************************************
set JAVA_COMMAND=java
rem ***********************************************************************
rem ***********************************************************************
rem * 5. The HEAP_SIZE variable line defines the Java heap size in MB.
rem * That is the total amount of memory available to MZmine 2.
rem * Please adjust according to the amount of memory of your computer.
rem * Maximum value on a 32-bit Windows system is about 1300.
rem ***********************************************************************
set HEAP_SIZE=1024
rem ***********************************************************************
rem ***********************************************************************
rem * 6. The TMP_FILE_DIRECTORY parameter defines the location where
rem * temporary files (parsed raw data) will be placed. Default is
rem * %TEMP%, which represents the system temporary directory.
rem ***********************************************************************
set TMP_FILE_DIRECTORY=%TEMP%
rem ***********************************************************************
rem ***********************************************************************
rem * It is not necessary to modify the following section.
rem ***********************************************************************
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=MZminePI.jar
set MAIN_CLASS=net.sf.mzmine.main.MZmineCore
rem Show java version, in case a problem occurs
%JAVA_COMMAND% -version > MZminePI.log 2>&1
echo. >> MZminePI.log
rem This command starts the Java Virtual Machine
echo Running MZminePI...
echo %JAVA_COMMAND% %JAVA_PARAMETERS% -classpath %CLASS_PATH% %MAIN_CLASS% %*
>> MZminePI.log
echo. >> MZminePI.log
%JAVA_COMMAND% %JAVA_PARAMETERS% -classpath %CLASS_PATH% %MAIN_CLASS% %* >>
MZminePI.log 2>&1
rem If there was an error, give the user chance to see it
IF ERRORLEVEL 1 (
echo See MZminePI.log for errors
pause
)
rem ***********************************************************************
Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation. All rights reserved.
C:\Users\bwes419>cd..
C:\Users>cd..
C:\>cd "Program Files"
C:\Program Files>cd R
C:\Program Files\R>cd R-3.2.0
C:\Program Files\R\R-3.2.0>cd bin
C:\Program Files\R\R-3.2.0\bin>cd x64
C:\Program Files\R\R-3.2.0\bin\x64>dir
Volume in drive C is Windows
Volume Serial Number is 1C94-CFF9
Directory of C:\Program Files\R\R-3.2.0\bin\x64
25/05/2015 10:42 a.m. <DIR> .
25/05/2015 10:42 a.m. <DIR> ..
17/04/2015 01:40 p.m. 16,384 open.exe
17/04/2015 01:40 p.m. 25,815,552 R.dll
17/04/2015 01:40 p.m. 39,936 R.exe
17/04/2015 01:40 p.m. 343,623 Rblas.dll
17/04/2015 01:40 p.m. 39,936 Rcmd.exe
17/04/2015 01:40 p.m. 23,040 Rfe.exe
17/04/2015 01:40 p.m. 377,527 Rgraphapp.dll
17/04/2015 01:40 p.m. 22,016 Rgui.exe
17/04/2015 01:40 p.m. 131,391 Riconv.dll
17/04/2015 01:41 p.m. 2,186,240 Rlapack.dll
17/04/2015 01:40 p.m. 26,112 Rscript.exe
17/04/2015 01:40 p.m. 24,064 RSetReg.exe
17/04/2015 01:40 p.m. 22,528 Rterm.exe
13 File(s) 29,068,349 bytes
2 Dir(s) 375,690,522,624 bytes free
C:\Program Files\R\R-3.2.0\bin\x64>R.exe
R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 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/bwes419/Documents/R/win-library/3.2"
[2] "C:/Program Files/R/R-3.2.0/library"
> 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/bwes419/Documents/R/win-library/3.2/xcms/Meta/package.rds
> packageDescription("ptw")
Package: ptw
Type: Package
Title: Parametric Time Warping
Version: 1.9-10
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...@gmail.com>
Maintainer: Ron Wehrens <ron.wehr...@gmail.com>
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). Both
warping of peak profiles and of peak lists are supported.
License: GPL (>= 2)
Imports: nloptr, graphics, grDevices, stats
NeedsCompilation: yes
Packaged: 2015-06-30 13:39:55 UTC; ron
Repository: CRAN
Date/Publication: 2015-07-01 06:11:39
Built: R 3.2.1; x86_64-w64-mingw32; 2015-07-09 02:50:16 UTC; windows
-- File: C:/Users/bwes419/Documents/R/win-library/3.2/ptw/Meta/package.rds
> 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 3.2.1; i386-w64-mingw32; 2015-06-30 15:10:04 UTC; windows
-- File: C:/Users/bwes419/Documents/R/win-library/3.2/rJava/Meta/package.rds
>------------------------------------------------------------------------------
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