G'day,
I've been on leave so have only just come across the thread regarding
baseline-correction problems.
Yee-Soon did you manage to resolve this issue?
The error message you showed indicates that you haven't customised the
start-up script file correctly (startMZmine_Windows.bat).
Getting baseline correction working is fiddly. Here's what you need to do:
1. Install R
2. In R install the rJava package: install.packages("rJava")
3. In R install the ptw package: install.packages("ptw")
4. Configure your startMZmine_Windows.bat file. The one we use for
Windows 7 (64-bit) and R 2.15 is attached (rename the extension to .BAT)
You will need to customise the following:
set R_HOME=...
This is the R home directory. It should contain the bin, include, doc
and share sub-directories.
set PATH=%PATH%;..
This is the search path variable. Append (semi-colon separator) the
directory that contains the R executables (R.exe, Rcmd.exe, ...) and
libraries (R.dll, Rblas.dll, ...)
set R_LIBS_USER=...
This is the directory where R packages are installed. It should contain
the rJava and ptw sub-directories. It should be listed when you run the
.libPaths() command in R.
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri
This the the directory holding the JRI library (JRI.dll). It should be
a sub-directory of R_LIBS_USER. In some cases both an i386 and x64
sub-directory are present each containing a different JRI.dll. Choose
the sub-directory appropriate for your architecture, i.e. 32-bit choose
i386, 64-bit choose x64.
Regards,
Chris.
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@echo off
rem 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.
set HEAP_SIZE=4096
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-2.15.0\bin\x64
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%\My Documents\R\win64-library\2.15
rem Include R DLLs in PATH.
set PATH=%PATH%;%R_HOME%\bin
rem The directory holding the JRI shared library.
set JRI_LIB_PATH=%R_LIBS_USER%\rJava\jri
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 LOGGING_CONFIG_FILE=conf/logging.properties
set JAVA_PARAMETERS=-XX:+UseParallelGC -Djava.io.tmpdir=%TMP_FILE_DIRECTORY%
-Djava.util.logging.config.file=%LOGGING_CONFIG_FILE% -Xms%HEAP_SIZE%m
-Xmx%HEAP_SIZE%m -Djava.library.path="%JRI_LIB_PATH%"
set CLASS_PATH=lib\MZmine-2.8-SNAPSHOT.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
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