Hi Tomas, No its definitely the 64 bit Java I have installed. I'll try to have a closer look shortly.
Cheers, Mark -----Original Message----- From: mzmine-devel-requ...@lists.sourceforge.net [mailto:mzmine-devel-requ...@lists.sourceforge.net] Sent: 02 December 2014 12:24 To: mzmine-devel@lists.sourceforge.net Subject: Mzmine-devel Digest, Vol 79, Issue 6 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. Re: Fwd: Allocation of memory to MZmine and communication with R (Tomas Pluskal) ---------------------------------------------------------------------- Message: 1 Date: Tue, 2 Dec 2014 21:24:09 +0900 From: Tomas Pluskal <plus...@oist.jp> Subject: Re: [Mzmine-devel] Fwd: Allocation of memory to MZmine and communication with R To: Developer discussion <mzmine-devel@lists.sourceforge.net> Cc: Lea Gi?rtz Johnsen <l...@ms-omics.com> Message-ID: <CAOH7_H=i5b2_00S-SQbeyXEzO=xHAT7543uo70S25BcLv=g=k...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Lea, [Note in the beginning: If you are not subscribed to the list, you can read the thread here: https://sourceforge.net/p/mzmine/mailman/mzmine-devel/] [Second note, to all: when responding to users' queries, please always cc the original sender. Most of them are not subscribed to the mailing list!] Regarding your memory problems, I think you installed the 32-bit version of Java (x86 version). Please uninstall it and then install the 64-bit (x64) version. The 32-bit version has a limit of ~1300 MB for heap size. As someone already commented, please download the just-released MZmine 2.12, as it has improved reporting of R-related problems. Best regards, Tomas On Tue, Dec 2, 2014 at 7:47 PM, Lea Gi?rtz Johnsen <l...@ms-omics.com> wrote: > > 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: ATT00001.png Type: image/png Size: 9908 bytes Desc: not available -------------- next part -------------- A non-text attachment was scrubbed... Name: ATT00003.png Type: image/png Size: 9664 bytes Desc: not available -------------- next part -------------- A non-text attachment was scrubbed... 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