[BioC] Problem with biomaRt update in R-2.15.1

[Wolfgang Huber]

Dear Eleni

you will need to install, at the linux level (e.g. through your distribution's package manager [1]) the xml2 system library. As a measure of success, who you type "xml2-config" on the unix shell, you should get a usage message from this program, rather "command not found". 

[1] AfaIk (others might know better) in Ubuntu, the relevant package name is "libxml2-dev".

	Best wishes
	Wolfgang



Il giorno Jan 8, 2013, alle ore 2:33 PM, Eleni Christodoulou [guest] <guest at bioconductor.org> ha scritto:

> 
> Dear Bioconductor experts,
> 
> I have been working with some Bioconductor packages in R14 which I was using in the past. I recently installed R15. I upgraded the Bioconductor installation using
> source("http://bioconductor.org/biocLite.R")  and
> biocLite("BiocUpgrade")
> 
> I got in my terminal:
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Old packages: 'biomaRt'
> Update all/some/none? [a/s/n]: 
> 
> I answered a (all packages) in the last question. However, biomaRt could not be installed. Here is the error message that I received:
> checking for xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package ‘XML’
> * removing ‘/home/cellnet/elenic/R15packages/XML’
> ERROR: dependency ‘XML’ is not available for package ‘biomaRt’
> * removing ‘/home/cellnet/elenic/R15packages/biomaRt’
> 
> I thus cannot update biomaRt which is essential for my analysis. Could you provide me with some help on this?
> 
> Thank you very much,
> E.C.
> 
> 
> 
> -- output of sessionInfo(): 
> 
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
> [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
> [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
> [7] LC_PAPER=C                LC_NAME=C                
> [9] LC_ADDRESS=C              LC_TELEPHONE=C           
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] plyr_1.8
> 
> loaded via a namespace (and not attached):
> [1] tools_2.15.1
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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