[BioC] problems with bioconductor installation

[Wolfgang Huber]

Hi Pete

you will need to install libcurl-dev:
http://packages.ubuntu.com/karmic/libcurl-dev

This is a system dependency of the RCurl package, which in turn is required by the biomaRt package. The biocLite script cannot automatically deal with such system dependencies for all the various platforms that Bioconductor supports (Windows, Macs, Unices). I guess it would be technically possible, but would eat up so many resources (programmer time) that the project is better off investing in scientifically more rewarding functionalities.

               Best wishes 
                    Wolfgang


Il giorno Feb 15, 2010, alle ore 6:46 PM, Andreia Fonseca ha scritto:

Hi Pete,

you have to install the curl library in your ubuntu. Go to sinaptic and look
for the curls libs and then install. Then you'll see problem solved. The
other problem, is not a problem is just a warning message, like Martin said.
Cheers
Andreia
On Sun, Feb 14, 2010 at 11:12 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> 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 Œ/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?
>> 
>>      [[alternative HTML version deleted]]
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
> --
> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 



-- 
--------------------------------------------
Andreia J. Amaral
Unidade de Imunologia Clínica
Instituto de Medicina Molecular
Universidade de Lisboa
email: andreiaamaral at fm.ul.pt
        andreia.fonseca at gmail.com

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Wolfgang Huber
whuber at embl.de