Hi Lea, I have the same problem and I think its related to the latest Java 8 update. My workaround is to go back to java version 7 update 72
I have heard rumors that this something to do with the Java security settings but haven't figured out what yet. I would be interested if anyone works out how to fix this, Cheers, Mark -----Original Message----- From: mzmine-devel-requ...@lists.sourceforge.net [mailto:mzmine-devel-requ...@lists.sourceforge.net] Sent: 02 December 2014 10:48 To: mzmine-devel@lists.sourceforge.net Subject: Mzmine-devel Digest, Vol 79, Issue 2 Send Mzmine-devel mailing list submissions to mzmine-devel@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/mzmine-devel or, via email, send a message with subject or body 'help' to mzmine-devel-requ...@lists.sourceforge.net You can reach the person managing the list at mzmine-devel-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Mzmine-devel digest..." Today's Topics: 1. Fwd: Allocation of memory to MZmine and communication with R (Lea Gi?rtz Johnsen) ---------------------------------------------------------------------- Message: 1 Date: Tue, 02 Dec 2014 11:47:18 +0100 From: Lea Gi?rtz Johnsen <l...@ms-omics.com> Subject: [Mzmine-devel] Fwd: Allocation of memory to MZmine and communication with R To: mzmine-devel@lists.sourceforge.net Message-ID: <547d98b6.6040...@ms-omics.com> Content-Type: text/plain; charset="windows-1252" Hello, I have heard a lot about MZmine and find it very interesting. However I got stock with a few problems and I hope you will be able to help me solve them. My first problem is that I have problems allocating enough memory to MZmine. I can force MZmine to allocate 1 GB but (as in the attached .bat file), but if I try to allocate more I get the following error: And if I try to run the original script (where half the memory should be allocated to MZmine) I get this result: Do you have any idea on how I can get more memory allocated? 1 GB is not enough for my dataset and I get memory problems when I run the chromatogram builder. My second problem is that MZmine have problems communicating with R when I try to do baseline correction. The output you request in your manual from the command prompt are: .libPaths() ? ? ? [1] "C:/Users/Lea/Documents/R/win-library/3.1" ? ? ? [2] "C:/Programmer/R/R-3.1.2/library" When I try to run the packageDescriptions I get an error: " Could not find function "packageDescription" " - So I probably have a problem with my R installation, but I do not know how to fix this. I you could give me a hint I would very much appreciate it :-) Some system information: MZmine: is the newest version just downloaded a week ago. R (64 bit): version: 3.1.2 Location on computer: C:\Programmer\R\R-3.1.2 rJava location: C:\Users\Lea\Documents\R\win-library\3.1\rJava\jri\x64 My computer: 64-bit processor,? 32 GB RAM, Windows 8. Kind regards Lea Johnsen -------------- next part -------------- An HTML attachment was scrubbed... -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 9908 bytes Desc: not available -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 11691 bytes Desc: not available -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 9664 bytes Desc: not available -------------- next part -------------- @echo off rem Obtain the physical memory size rem for /f "skip=1" %%p in ('wmic os get totalvisiblememorysize') do if not rem 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. rem set /a HEAP_SIZE=%TOTAL_MEMORY% / 1024 / 2 set HEAP_SIZE=1024 rem Check if we are running on a 32-bit system. rem If yes, force the heap size to 1024 MB. rem for /f "skip=1" %%x in ('wmic cpu get addresswidth') do if not defined rem ADDRESS_WIDTH set ADDRESS_WIDTH=%%x rem if %ADDRESS_WIDTH%==32 ( rem set HEAP_SIZE=1024 rem ) 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 variamer 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 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-2.11.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 ------------------------------ ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! 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