Hi Lea,
I am glad it works for you know, although I doubt that the problem really was
in using / vs \ characters. In my startMZmine.bat, I use \ everywhere and it
works fine:
set R_HOME=C:\Program Files\R\R-3.1.2
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
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri\i386
Cheers,
Tomas
On Dec 8, 2014, at 21:20, Lea Giørtz Johnsen
<l...@ms-omics.com<mailto:l...@ms-omics.com>> wrote:
Hi again,
Just wanted to let you now that I found the error when I realized that what I
would normally write as: C:\Programmer\R\R-3.1.2\library in R should be written
as: C:/Programmer/R/R-3.1.2/library. So after changing \ to / in the MZmine
start script it seems that everything now works :-)
Best regards Lea
Den 05-12-2014 kl. 03:19 skrev Tomas Pluskal:
Hi Lea,
The error messages you get (access denied, package "methods" in
options("defaultPackages") was not found etc.) suggest that there is something
wrong with your R installation.
Perhaps the access rights to the C:/Programmer/R/R-3.1.2/library folder are not
correctly set? (just guessing)
I recommend to try to re-install R into a different folder.
Anyway, I think this problem is not in MZmine..
Best regards,
Tomas
On Dec 4, 2014, at 22:34, Lea Giørtz Johnsen
<l...@ms-omics.com<mailto:l...@ms-omics.com>> wrote:
Hi all,
Thanks a lot for your quick (and very useful) responses.
I have downloaded the latest (2.12) version of MZmine and installed the
64 bit version of Java and that fixed the problems I had with the memory
allocation.
However I am unfortunately still not able to get MZmine to communicate
properly with R.
I have tried to uninstall R and then reinstall R and the required
packages as administrator.
When I then try to do baseline correction I get a window with the
following error:
The "RubberBand baseline corrector" requires the "rJava" R package which
couldn't be loaded - is it installed in R?
The same error appears if I install the packages without administrator
properties and change the R_LIBS_USER setting from: %R_HOME%\library to:
%USERPROFILE%\Documents\R\win-library\3.1
I then tried to run MZmine as administrator, but that resulted in the
following message in cmd:
Checking physical memory size...
Found 32586 MB memory, 64-bit system
Java heap size set to 16293 MB
java version "1.7.0_71"
Java(TM) SE Runtime Environment (build 1.7.0_71-b14)
Java HotSpot(TM) 64-Bit Server VM (build 24.71-b01, mixed mode)
Error: Could not find or load main class net.sf.mzmine.main.MZmineCore
Press any key to continue . . .
And then I ran out of ideas of what to do next. So if you have any ideas
I would really appreciate it.
Best regards,
Lea
Some additional info:
When I run: Programmer\R\R-3.1.2\bin\x64\R.exe in cmd I get the
following output with some warnings (which probably is trying to tell me
what is wrong..):
Advarselsbesked:(sorry for the danish... It says: warning message)
In normalizePath(path.expand(path), winslash, mustWork) :
path[2]="C:/Programmer/R/R-3.1.2/library": Adgang nægtet (Danish again... It
says: access denied)
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
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.
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.
Advarselsbesked: (again: warning message)
package "methods" in options("defaultPackages") was not found
During startup - Advarselsbeskeder:
1: package 'datasets' in options("defaultPackages") was not found
2: package 'utils' in options("defaultPackages") was not found
3: package 'grDevices' in options("defaultPackages") was not found
4: package 'graphics' in options("defaultPackages") was not found
5: package 'stats' in options("defaultPackages") was not found
6: package 'methods' in options("defaultPackages") was not found
package "methods" in options("defaultPackages") was not found
During startup - Advarselsbeskeder:
1: package 'datasets' in options("defaultPackages") was not found
2: package 'utils' in options("defaultPackages") was not found
3: package 'grDevices' in options("defaultPackages") was not found
4: package 'graphics' in options("defaultPackages") was not found
5: package 'stats' in options("defaultPackages") was not found
6: package 'methods' in options("defaultPackages") was not found
.libPaths()
[1] "C:/Users/Lea/Documents/R/win-library/3.1"
[2] "C:/Programmer/R/R-3.1.2/library"
packageDescription("xcms")
Fejl: could not find function "packageDescription"
My startMZmine_Windows.bat script:
@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:\Programmer\R\R-3.1.2
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\3.1
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=-showversion -classpath lib\* -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
------------------------------------------------------------------------------
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===============================================
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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------------------------------------------------------------------------------
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Mzmine-devel mailing list
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===============================================
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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