G'day,
I suspect that you've not set your R_LIBS_USER correctly in your
startMZmine_Windows.bat file.
Could you please tell us your settings for
R_HOME
R_LIBS_USER
Then could you please run R and tell us the output to the following
commands:
.libPaths()
.packageDescription("xcms")
Thanks,
Chris.
On 05/07/12 16:46, Geert Goeminne wrote:
> Dear,
>
> I tried your suggestion, and it works in R, i have the right version
> installed now, but when i run Mzmine it says it couldn't find XCMS -
> is XCMS installed in R?
>
> I installed everything as an administrator, and then i installed the
> packages in R not as an administrator but as a user because if you run
> this (install.packages(c("rJava", "ptw", "gplots")) ) as an
> adminsitrator i can not find where the win-library folder is put, and
> i need that for Mzmine, but when i run it as a user that folder is put
> in my userprofile.
>
> Why is this folder not created when you run it as an admin?
>
> This XCMS installing in Mzmine is really a big problem, is there no
> way to make this more easy?
>
> Cheers, Geert
>
>
>
> ------------------------------------------------------------------------
>
> *From: *"Pudney Chris (ext) GBJH" <chris.pud...@syngenta.com>
> *To: *mzmine-devel@lists.sourceforge.net, ge...@psb.ugent.be
> *Sent: *Thursday, July 5, 2012 5:20:36 AM
> *Subject: *Re: XCMS and Mzmine
>
> G'day,
>
> > I have managed to install XCMS and make it run in Mzmine after a
> lot of searching (on a windows
> > machine), now it runs but it says i need to upgrade XCMS to
> version 1.33.13, but if I go to the
> > XCMS page and download that version it actually downloads
> version 1.32.0, while it says this
> > should be version 1.33.13
>
> Unfortunately, there's a bug in version 1.32.0 that is fixed in
> version 1.33.2. The standard installation instructions for XCMS
> install 1.32.0 and I had hoped that by now the later version would
> have been released.
>
> Therefore, you need to install the latest development version of
> XCMS. To do so, run R and remove the current XCMS package:
>
> remove.packages("xcms")
>
> Then install the latest development version of XCMS:
>
> install.packages("xcms",
> repos="http://www.bioconductor.org/packages/2.11/bioc/";)
>
> Then check the installation
>
> packageDescription("xcms")
>
> And check the Version: and File: fields to ensure that the version
> is correct (>= 1.33.2) and is installed in a sub-directory of the
> value assigned to R_LIBS_USER in your startMZmine script.
>
> Regards,
> Chris.
>
>
> ------------------------------------------------------------------------
> /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./
>
>
>
>
> --
> ==================================================================
> Geert Goeminne, Ing.
>
> Tel:+32 (0)9 331 38 79 or (0)9 331 38 85
> fax:+32 (0)9 331 38 09
> VIB Department of Plant Systems Biology, Ghent University
> Technologiepark 927, 9052 Gent, BELGIUM
> ge...@psb.vib-ugent.be http://www.psb.vib-ugent.be
> ==================================================================
>
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