[BioC] problems with bioconductor installation

[Martin Morgan]

Hi Pete --

On 02/14/2010 01:53 PM, Pete Shepard wrote:
> Hello,
> 
> I am running Ubuntu 9.10, I used Synaptic to download R version 2.9.2. I am
> trying to download Bioconductor 2.5 using a R command using these

R 2.9.2 is compatible with Bioconductor 2.4. Use R 2.10.1 if you need
Bioconductor 2.5.

> instructions http://www.bioconductor.org/docs/install/. When I enter
> biocLite(), I get "argument 'lib' is missing: using
> '/home/pedro/R/i486-pc-linux-gnu-library/2.9" an error I never encountered
> in past ubuntu versions. After the packages finish installing, it says they
> are in a temp file ‘/tmp/RtmprtEjox/downloaded_packages’ and that there were

Both the warning about "argument 'lib' missing" and the statement that
the downloaded packages are in a temp file are standard output and are
meant to be informative rather than alarming; see ?install.packages for
what 'lib' is referring to.

> a couple of Warning messages:
> 
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, :
> installation of package 'RCurl' had non-zero exit status

likely further up in the installation RCurl fails to install with
additional detail, likely having to do with failure to find the
'libcurl' system dependencies. You'll want to use Synaptic to install
the version of libcurl suitable for 'development' (I don't know the
details for Synaptic, it is the version that contains the curl header
files).

> 2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, :
> installation of package 'biomaRt' had non-zero exit status

likely biomaRt fails because RCurl had failed; correct RCurl, and
biomaRt will work.

Hope this helps,

Martin

> I am wondering if anyone has has a similar issue? And if the two software
> packages are compatible or not?
> 
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> 
> 
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793