[BioC] problems installing lumi

[Martin Morgan]

Hi Hermann -- nice to see you here.

On 09/06/2012 01:02 AM, Hermann Norpois wrote:
> Dear list,
>
> I had and still have trouble installing lumi. After an R update and the
> installation of the hdrcde package it still does not work with the lumi
> package via biocLite("lumi"). This is the answer (R version 2.15): And I
> was not able to install the packages with dependencies neither.
>
> I would be happy for some help.
> Thanks
> Hermann Norpois
>
> * installing *source* package ‘XML’ ...
> ** Paket ‘XML’ erfolgreich entpackt und MD5 Summen überprüft
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> No ability to remove finalizers on externalptr objects in this verison of R
> checking for sed... /bin/sed
> checking for pkg-config... /usr/bin/pkg-config
> checking for xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package ‘XML’

XML on non-Windows requires that the system XML library needs to be 
available. Likely you need to use your package manager to install 
libxml2-devel; for me on Ubuntu I would say

   sudo apt-get install libxml2-dev
> * removing ‘/usr/local/lib/R/site-library/XML’
> * installing *source* package ‘RCurl’ ...
> ** Paket ‘RCurl’ erfolgreich entpackt und MD5 Summen überprüft
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package ‘RCurl’

curl is also a system dependency,

   sudo apt-get install libcurl3-dbg

> * removing ‘/usr/local/lib/R/site-library/RCurl’
> ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package
> ‘rtracklayer’

the rest of the errors look like they will be corrected by libxml and 
libcurl installation.

Martin

> * removing ‘/usr/local/lib/R/site-library/rtracklayer’
> ERROR: dependency ‘XML’ is not available for package ‘annotate’
> * removing ‘/usr/local/lib/R/site-library/annotate’
> ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
> * removing ‘/usr/local/lib/R/site-library/genefilter’
> ERROR: dependencies ‘annotate’, ‘genefilter’ are not available for package
> ‘methylumi’
> * removing ‘/usr/local/lib/R/site-library/methylumi’
> ERROR: dependencies ‘methylumi’, ‘rtracklayer’, ‘annotate’ are not
> available for package ‘lumi’
> * removing ‘/usr/local/lib/R/site-library/lumi’
>
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>
>
>
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