[BioC] Problem with biomaRt update in R-2.15.1

[James W. MacDonald]

Hi Eleni,

On 1/8/2013 8:33 AM, Eleni Christodoulou [guest] wrote:
> 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

This means that configure couldn't find the headers for libxml. How you 
do this is dependent on the distro you are using, and if you have sudo 
privileges. If you have sudo privileges, you can do something like

yum install libxml2-dev
or
apt-get install libxml2-dev

depending on your distro. Or if you don't have sudo privileges, you 
should ask the administrator to install them for you.

Best,

Jim


> 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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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099