Issues installing mzmatch.R package

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soph

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Sep 17, 2013, 7:03:14 PM9/17/13
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Hi there,

I've recently downloaded the new v19 of IDEOM and I've also upgrated R into the latest version v3.0.1.

I had no problem in installing any packages, but mzmatch.R.
Below I've copied the Error message I am getting.

Is there any way to fix it?

Thanks

Sophia


> a
Error: object 'a' not found
> source ("http://puma.ibls.gla.ac.uk/mzmatch.R/install_mzmatch.R")
trying URL 'http://puma.ibls.gla.ac.uk/mzmatch.R/mzmatch.R.tar.gz'
Content type 'application/x-gzip' length 111312 bytes (108 Kb)
opened URL
downloaded 108 Kb

ERROR: dependency 'XML' is not available for package 'mzmatch.R'
* removing 'C:/Users/Martin/Documents/R/win-library/R-3.0.1/library/mzmatch.R'
Warning messages:
1: running command '"C:/Users/Martin/Documents/R/win-library/R-3.0.1/bin/x64/R" CMD INSTALL -l "C:\Users\Martin\Documents\R\win-library\R-3.0.1\library" "mzmatch.R.tar.gz"' had status 1
2: In install.packages(pkgs = "mzmatch.R.tar.gz", repos = NULL, type = "source") :
  installation of package ‘mzmatch.R.tar.gz’ had non-zero exit status
> library (rJava)
> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386') {print('Loading XP 32bit startup')
+ .jinit ()}
> library (mzmatch.R)
Error in library(mzmatch.R) : there is no package called ‘mzmatch.R’
> mzmatch.init (4000)
Error: could not find function "mzmatch.init"

Gavin Blackburn

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Sep 18, 2013, 7:02:54 AM9/18/13
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Hi Sophia,

 

It’s telling you the XML package isn’t installed so it won’t install mzmatch.R.

 

Try running the following lines below in R separately, this should include everything you need.

 

 

install.packages(c("rJava","XML","snow","caTools","bitops","ptw","gplots","rcdk"))

 

source("http://bioconductor.org/biocLite.R")
 
biocLite(c("pcaMethods","lima","mzR","metabolomics","rankProd","xcms"))

Let me know if you have any more error messages after that, I can always come across and give you a hand.

 

Cheers,

 

Gavin

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soph

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Sep 18, 2013, 4:47:19 PM9/18/13
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Thanks for the replies guys!

The problem was solved once I run the 32-bit version of R 3.1.0 on my 64-bit system, after Gavin's suggestion.

Apparently there is an incompatibility issue with the 64-bit version of R 3.1.0 and RankProd yet to be solved ?

Your help has been much appreciated.

Cheers

Soph

Gavin Blackburn

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Sep 19, 2013, 5:05:46 AM9/19/13
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Hi Sophia,

 

I think RankProd is ok, although I don’t use it at the moment.

 

Let me know if you want me to come over and have a look.

 

Cheers,

 

Gavin.

 

 

From: id...@googlegroups.com [mailto:id...@googlegroups.com] On Behalf Of soph


Sent: 18 September 2013 21:47
To: id...@googlegroups.com

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