G'day,
Thanks Hattan - well-spotted.
The default PATH variable was the issue. I've CC'd the mzmine-devel list.
Regards
Chris Pudney<mailto:chris.pud...@syngenta.com> | Data Visualization Specialist
| Information Exploitation Team
From: Hattan Alharbi [mailto:hattanalha...@cmail.carleton.ca] On Behalf Of
Hattan
Sent: Thursday, 18 July 2013 12:52 PM
To: Pudney Chris (ext) GBJH
Subject: RE: R baseline correction issue
The solution
in windows 7
Go to computer >>right click on properties
advanced system setting
advanced
environmental variables
User variables or HP (or the name of your computer)
New
Variable name PATH
Variable value C:\Program Files\Java\jre6\bin;C:\Program
Files\R\R-2.15.3;C:\Documents\R\win-library\2.15
consider the version of R and Java
The new version of R 3.0 has nothing to do with the problem
Good Luck
________________________________
From: chris.pud...@syngenta.com<mailto:chris.pud...@syngenta.com>
[chris.pud...@syngenta.com]
Sent: June 26, 2013 9:00 PM
To: haa...@mail.usask.ca<mailto:haa...@mail.usask.ca>
Subject: RE: R baseline correction issue
G'day,
You might be right about R v3.0 being the cause of the problem.
If you still have R 2.15.2 installed then you could please try it. You will
first need to run R 2.15.2 and install the necessary packages (rJava, ptw,
xcms, CAMERA etc) as installing them in R 3.0 will not result in them being
installed in R 2.15.2 and vice-versa.
I've attached a start-up script configured to use R 2.15.2 (you might need to
double check it; strip the .txt extension).
If it still doesn't work then please provide the information you did in your
first message but for R 2.15.2 (see this
guide<http://mzmine-devel-developer-discussion.970458.n3.nabble.com/Mzmine-devel-Configuring-MZmine-to-use-R-Baseline-correction-requires-R-but-it-couldn-t-be-loaded-Co-td4024242.html>)
Regards
Chris Pudney<mailto:chris.pud...@syngenta.com> | Data Visualization Specialist
| Information Exploitation Team
-----Original Message-----
From: Hattan Alharbi [mailto:hattanalha...@cmail.carleton.ca] On Behalf Of
Hattan
Sent: Thursday, 27 June 2013 4:10 AM
To: Pudney Chris (ext) GBJH
Subject: RE: R baseline correction issue
Thanks
I have considered your comments but does not work. Attach file that contains
your request about the output.
I am not good in visual basic and software developing but I think the problem
might be due to the new version of R is not compatible with something else. Or
the java is not also fully effective.
I am using the program to support my data analysis from Xcalibur (RAW) and it
works excellent, but I have some questions but I do not to take from your time.
The reason for baseline correction is that I am looking for compounds that have
intensity more than 2% (only >2%) however, I do not know how to narrow the
number of the compounds based on the intensity). I hope the best for the
program developers and I do have some suggestions
wish you the best
p.s. I am not using it for metabolomic but for water samples
________________________________________
From: Pudney Chris (ext) GBJH [chris.pud...@syngenta.com]
Sent: June 25, 2013 10:00 PM
To:
mzmine-devel@lists.sourceforge.net<mailto:mzmine-devel@lists.sourceforge.net>;
haa...@mail.usask.ca<mailto:haa...@mail.usask.ca>
Subject: Re: R baseline correction issue
G'day,
> I am attaching word file containing the details of the problem (R baseline
> correction issue).
> I am doing well so far with the program but could not perform the baseline
> correction via R > for both 2.15.2 and 3.0.1 .
Thanks for the detailed information you provided.
I think you are fairly close with your start up script.
I've made a couple of minor changes:
1. changed
set R_LIBS_USER=C:/Program Files/R/R-3.0.1/library
to
set R_LIBS_USER=C:\Users\HP\Documents\R\win-library\3.0
2. deleted
set %USERPROFILE%\Documents\R\win-library\3.0
Please try the attached script and let us know how you get on.
If you still have problems could you please send us the output of the following
commands:
dir "C:\Program Files\R\R-3.0.1\bin\x64"
dir "C:\Users\HP\Documents\R\win-library\3.0\rJava\jri\x64"
and any other diagnostic messages.
Regards,
Chris.
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Registered Office : Syngenta Limited, European Regional Centre, Priestley Road,
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________________________________
This message may contain confidential information. If you are not the
designated recipient, please notify the sender immediately, and delete the
original and any copies. Any use of the message by you is prohibited.
________________________________
Syngenta Limited, Registered in England No 2710846
Registered Office : Syngenta Limited, European Regional Centre, Priestley Road,
Surrey Research Park, Guildford, Surrey, GU2 7YH, United Kingdom
This message may contain confidential information. If you are not the
designated recipient, please notify the sender immediately, and delete the
original and any copies. Any use of the message by you is prohibited.
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