Dear MZmine developer team,
I'm trying to perform baseline correction in MZmine, but keep getting
the error message "Could not start R. Please check if R is installed
and path to the libraries is set properly in the startMmine script." I
have tried to edit the startMmine script according to the
instructions, and the library path should now be fine after I changed
it (checked it in R with .libPaths() ). I also changed i386 to x64 in
these rows:
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
I have Windows 7 and version 2.15.2 of R. All the required R packages
are installed. Any idea what could cause the error? Here's the
complete script I now have:
@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-2.12.0
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=C:/Program Files/R/R-2.12.0/library
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=-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
Best regards,
Hilkka Kontro
University of Helsinki
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