Dear,
I am trying to run MzMine on a windows 7 (64-bit) machine.
Running: MZmine-2.13.1
Using R 3.1.2
Location: C:\Program Files\R\R-3.1.2
32bit version: "C:\Program Files\R\R-3.1.2\bin\i386\Rgui.exe"
64bit version: "C:\Program Files\R\R-3.1.2\bin\x64\Rgui.exe"
.libPaths()
Output:
[1] "C:/Users/cremersg/Documents/R/win-library/3.1"
[2] "C:/Program Files/R/R-3.1.2/library"
packageDescription("xcms")
output:
[1] NA Warning message: In packageDescription("xcms") : no package 'xcms' was
found
packageDescription("ptw ")
output:
[1] NA Warning message: In packageDescription("ptw") : no package 'ptw' was
found
packageDescription("rJava ")
output:
[1] NA Warning message: In packageDescription("rJava") : no package 'rJava'
was found
Java 8 update 40
The steps I took to overcome this problem:
Started project R to check if it works,
Read the manual, to see if this error was reported earlier,
Tried to run the program NOT in administration mode - this does not work -
need admin mode.
In the attached files you can find:
[1] The error message screenshot
[2] The startMZmine batch file (converted to TEXT)
Hope you can help me resolve the problem,
Kind regards, Geert
Geert Cremers
Scheidings- en conversietechnologie (building: 12 - MAN - Milieuanalyses)
VITO NV | Boeretang 200 | 2400 Mol
Tel. +32 14 33 50 20 | geert.crem...@vito.be
[cid:image001.jpg@01CDCE3A.4E197A50]<http://www.vito.be/>[cid:image001.jpg@01CD3F0D.B57AA190]<http://www.linkedin.com/company/17947>[cid:image003.jpg@01CD3F0D.B57AA190]<http://twitter.com/#!/vitobelgium>[cid:image002.jpg@01CD3F0D.B57AA190]<https://www.facebook.com/VITObelgium>
[https://vito.be/files/achema2015.jpg]<http://www.achema.de/>
VITO Disclaimer: http://www.vito.be/e-maildisclaimer
@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-3.1.2
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 COMMENT: the set folder does niet exist in project-R 3.1.2 --> how ever NO
error is generated during start up
rem OLD 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=java
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 I've tryed to replace above code line by: set MAIN_CLASS=MZmine-2.13.1
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
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
