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 Giørtz 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()
> Â Â Â [1] "C:/Users/Lea/Documents/R/win-library/3.1"
> Â Â Â [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
>
>
>
>
>
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