Hi Lea,
With regards to your R problem then your start script looks like this:
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
Please try changing it to:
rem Set R environment variables.
set R_HOME= C:\Programmer\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
Also, MZmine 2.12 was just released today which provides a more detailed error
when communicating with R. This might help you if you still have problems with
R.
Best,
Thomas
From: Gauthier Boaglio [mailto:gauthier.boag...@gmail.com]
Sent: 2. december 2014 12:27
To: mzmine-devel@lists.sourceforge.net
Subject: Re: [Mzmine-devel] Fwd: Allocation of memory to MZmine and
communication with R
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:
[cid:image001.jpg@01D00E2C.6706E780]
And if I try to run the original script (where half the memory should be
allocated to MZmine) I get this result:
[cid:image002.jpg@01D00E2C.6706E780]
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.
[cid:image003.jpg@01D00E2C.6706E780]
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
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net<mailto:Mzmine-devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
--
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<mailto: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
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
