[BioC] Problem with biomaRt update in R-2.15.1

[Eleni Christodoulou]

Thank you very much for your replies. It worked with libxml2-dev package.

Best,
E.C.

On 01/08/2013 03:41 PM, Wolfgang Huber wrote:
> 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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-- 
Eleni Christodoulou
PhD student
Cellular Networks Group

BIOTEC TU Dresden
Tatzberg 47/49
01307 Dresden, Germany
phone: +49-351-463-40076
e-mail: eleni.christodoulou at biotec.tu-dresden.de