[BioC] problems with bioconductor installation

[Lakshmanan Iyer]

Hi
In a terminal window, try:

sudo apt-get install curl
sudo apt-get install Rcurl

One of these should work. BTW, you would need the "admin" password for
this sudo.
-best
-Lax

On Mon, Feb 15, 2010 at 6:11 PM, Wolfgang Huber <whuber at embl.de> wrote:
>
> 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]]
>>>
>>>
>>>
>>>
>>> _______________________________________________
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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
>>
>> _______________________________________________
>> Bioconductor mailing list
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>> 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
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> 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
>
> _______________________________________________
> 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
>