Hello Lea,
Usually, under Windows (higher than XP), I would recommend, if you have
this possibility, to install everything "as administrator". That is to
say, launching R under admin privileges and reinstall "rJava" while
keeping the default libraries location. This should make things easier.
You also can get inspiration from here (I managed to get it work with
java 1.8_25):
https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/startMZmine_Windows_JUL_64.bat
Note: the start script (from trunk) had a recent bug, as well, so make
sure you've got the latest one...
Regards
Gauthier
On 12/02/2014 11:47 AM, Lea Giørtz Johnsen 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
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--
Gauthier BOAGLIO
CEFE - UMR 5175
1919 route de Mende
F-34293 Montpellier cedex 5
Tel: +33/0 4 67 61 32 15
Fax: +33/0 4 67 61 33 36
email: gauthier.boag...@cefe.cnrs.fr
www:
http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio
http://www.evolepid.org/people.php?name=boaglio
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