Hello Chris,
Thanks for your reply. I already wrote a long reply with screenshots,
R outputs and the startMZmine script, but still decided to try the
baseline correction before sending it - and magically, it worked :) No
idea why, since I don't remember changing anything after I sent you
the first email. I did close all programs after that and boot the
computer, so maybe that has something to do with it.
The path for R really is C:\Program Files\R\R-2.12.0 even though I
have version 2.15.2 installed. I had noticed the same thing myself. I
don't know the reason for this (maybe version 2.12.0 was installed
earlier and got updated?) but that is the path where R 2.15.2 can be
found.
Anyway, seems like the problem is solved. MZmine seems like a great
tool. Thank you for you time!
Best wishes,
Hilkka
Quoting Chris Pudney <ch...@focal-technologies.com>:
> G'day,
>
> Hilkka, you say you have R 2.15.2 installed. Looking at the start up script
> you included in your message there are two potential mistakes.
>
> This line should probably be changed from
>
> set R_HOME=C:\Program Files\R\R-2.12.0
>
> to
>
> set R_HOME=C:\Program Files\R\R-2.15.2
>
>
> And this line should probably be changed from
>
> set R_LIBS_USER=C:/Program Files/R/R-2.12.0/library
>
> to
>
> set R_LIBS_USER=C:/Program Files/R/R-2.15.2/library
>
> Could you also confirm whether you've installed the rJava and ptw
> packages in R.
>
> If not then run R and issue the following commands:
>
> install.packages(c("rJava", "ptw", "gplots"))
>
> See the instructions in the user manual:
> https://bit.ly/MZmineManual#h.1pys305nsw0o
>
> If you are still having problems after these changes then can you
> please send us the following:
>
> 1. Run R and send the output of the command: .libPaths()
> 2. Run R and send the output of the command: packageDescription("rJava")
> 3. Run R and send the output of the command: packageDescription("ptw")
> 4. The startMZmine script you use to run MZmine
>
> Thanks,
> Chris.
>
> -----
>
> 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
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