[BioC] problems in installing biomart

[Steve Lianoglou]

Hi Andreia,

Inspect the error your getting a bit more closely, see inline:

On Nov 11, 2009, at 11:19 AM, Andreia Fonseca wrote:

> Dear Forum
>
> my machine runs Ubuntu 9.04. I am trying to install Biomart, what I  
> realize
> is that something is missing and it can't install XML, RCurl but I  
> don't
> know what more to do, I looked in previous posts but I did not find
> infoprmation that helped.
> Thanks
> Andreia
> biocLite("biomaRt")
> Running biocinstall version 2.3.14 with R version 2.8.1
> Your version of R requires version 2.3 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>  argument 'lib' is missing: using '/home/user/R/x86_64-pc-linux-
> gnu-library/2.8'
> also installing the dependencies ŒXML‚, ŒRCurl‚
>
> trying URL 'http://cran.fhcrc.org/src/contrib/XML_2.6-0.tar.gz'
> Content type 'application/x-gzip' length 680366 bytes (664 Kb)
> opened URL
> ==================================================
> downloaded 664 Kb
>
> trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.3-0.tar.gz'
> Content type 'application/x-gzip' length 799689 bytes (780 Kb)
> opened URL
> ==================================================
> downloaded 780 Kb
>
> trying URL '
> http://bioconductor.org/packages/2.3/bioc/src/contrib/biomaRt_1.16.0.tar.gz'
> Content type 'application/x-gzip' length 278561 bytes (272 Kb)
> opened URL
> ==================================================
> downloaded 272 Kb
>
> * Installing *source* package 'XML' ...
> 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 ANSI C... none needed
> checking how to run the C preprocessor... gcc -E
> checking for sed... /bin/sed
> checking for pkg-config... /usr/bin/pkg-config
> checking for xml2-config... no
> Cannot find xml2-config

Some googling will show you that xml2-config is part of libxml2. My  
guess is that libxml2 is not installed in your system, and is probably  
just an apt-get install away.

> ERROR: configuration failed for package 'XML'
> ** Removing '/home/user/R/x86_64-pc-linux-gnu-library/2.8/XML'
> * Installing *source* package 'RCurl' ...
> checking for curl-config... no
> Cannot find curl-config

Likewise for curl.

Simply try to install libxml2 and curl via apt-get (or is it  
synaptic?) and try the biocLite install again.

HTH,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact