Hi Chris,
Thanks very much for your help. I think I've installed rJava correctly.
Here's the start script and the library paths.
Cheers,
Vincent
@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-2.15.2
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=%R_HOME%\library
rem Include R DLLs in PATH.
set PATH=%R_HOME%\bin\i386
rem The directory holding the JRI shared library (libjri.so).
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri\i386
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\jre6\bin\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-2.10.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
> .libPaths()
[1] "C:/Program Files/R/R-2.15.2/library"
> packageDescription("xcms")
Package: xcms
Version: 1.34.0
Date: 2012-08-30
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]>
Maintainer: Ralf Tautenhahn <[email protected]>
Depends: R (>= 1.9.0), methods, mzR (>= 1.1.6)
Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>= 1.5.2),
RANN,
snow, RUnit
Enhances: Rgraphviz, XML, KEGGSOAP
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)
URL: http://metlin.scripps.edu/download/
biocViews: MassSpectrometry, Metabolomics
Packaged: 2012-10-02 06:30:59 UTC; biocbuild
Built: R 2.15.1; i386-pc-mingw32; 2012-10-02 13:26:44 UTC; windows
-- File: C:/Program Files/R/R-2.15.2/library/xcms/Meta/package.rds
> packageDescription("ptw")
Package: ptw
Type: Package
Title: Parametric Time Warping
Version: 1.0-5
Date: 2013-01-09
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)
LazyLoad: yes
Repository: CRAN
Date/Publication: 2013-01-09 22:55:42
Packaged: 2013-01-09 19:43:53 UTC; tombloem
Built: R 2.15.2; x86_64-w64-mingw32; 2013-01-10 02:20:12 UTC; windows
-- File: C:/Program Files/R/R-2.15.2/library/ptw/Meta/package.rds
> packageDescription("rJava")
Package: rJava
Version: 0.9-3
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
Repository: CRAN
Date/Publication: 2011-12-11 10:41:33
Built: R 2.15.2; i386-w64-mingw32; 2013-01-04 12:44:01 UTC; windows
-- File: C:/Program Files/R/R-2.15.2/library/rJava/Meta/package.rds
>
On Wed, Jan 30, 2013 at 9:15 PM, Pudney Chris (ext) GBJH [via Mzmine-devel
-- Developer discussion] <[email protected]> wrote:
> G'day,
>
> > I changed the R user libraries setting and installed ptw but I'm
> still getting the task error.
>
> Did you also install the rJava package per the instructions in the manual?
> http://bit.ly/MZmineManual#h.1pys305nsw0o
>
> If so, and you're still getting the error then could you please share
> with us your full MZmine start script.
>
> If any messages are displayed in the command-line console then please
> share these also.
>
> And for good measure could you please repeat the following in R and let
> us know the output:
>
> .libPaths()
> packageDescription("xcms")
> packageDescription("ptw")
> packageDescription("rJava")
>
> Thanks,
> Chris.
>
> On 30/01/13 11:00, Pudney Chris (ext) GBJH wrote:
>
> > G'day,
> >
> > Vincent, I would suggest that you try changing the R_LIBS_USER setting
> in your start script to the following:
> >
> > set R_LIBS_USER=%R_HOME%\library
> >
> > This is because your .libPaths indicates that your R installation has
> only one directory in its path (the library sub-directory of %R_HOME%).
> It's where xcms is installed.
> >
> > This is unusual. Normally, when you run R you get the chance to install
> libraries in a personal folder. This is why the default setting of
> R_LIBS_USER is a sub-directory of %USER_PROFILE%.
> >
> > You'll also need to install the "ptw" package into R.
> >
> > There other R packages you might like to install in order to run other
> MZmine modules that depend on them, see
> >
> > http://bit.ly/MZmineManual#h.1pys305nsw0o
> >
> > Regards,
> > Chris.
> >
> > -----
> >
> > Hi! I'm having the same issue w heatmaps and baseline correction. Any
> help
> > would be greatly appreciated.
> >
> > Here are the R paths from the start script:
> >
> > rem Set R environment variables.
> > set R_HOME=C:\Program Files\R\R-2.15.2
> > 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=%USERPROFILE%\Documents\R\win-library\2.15.2
> >
> >> .libPaths()
> > [1] "C:/Program Files/R/R-2.15.2/library"
> >
> >> packageDescription("xcms")
> > Package: xcms
> > Version: 1.34.0
> > Date: 2012-08-30
> > Title: LC/MS and GC/MS Data Analysis
> > Author: Colin A. Smith <csmith@...>, Ralf Tautenhahn
> > <rtautenh@...>, Steffen Neumann
> > <sneumann@...>, Paul Benton
> > <hpaul.benton08@...>
> > Maintainer: Ralf Tautenhahn <rtautenh@...>
> > Depends: R (>= 1.9.0), methods, mzR (>= 1.1.6)
> > Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>=
> > 1.5.2), RANN, snow, RUnit
> > Enhances: Rgraphviz, XML, KEGGSOAP
> > 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)
> > URL:http://metlin.scripps.edu/download/
> > biocViews: MassSpectrometry, Metabolomics
> > Packaged: 2012-10-02 06:30:59 UTC; biocbuild
> > Built: R 2.15.1; i386-pc-mingw32; 2012-10-02 13:26:44 UTC; windows
> >
> > -- File: C:/Program Files/R/R-2.15.2/library/xcms/Meta/package.r
> >
>
>
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