Hello All,


Thanks for all the suggestions. I am stuck running R version 2.9 due to my
OS. I was able to get Bioconductor to work with this version of R by  doing
a "old.packages(repos=biocinstallRepos())" and
"update.packages(repos=biocinstallRepos(), ask=FALSE)" now  I am running
Bioconductor 2.4 and it works fine.

Thanks,

peter

On Tue, Feb 16, 2010 at 3:56 AM, Lakshmanan Iyer <laxvid@gmail.com> wrote:

> 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@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@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 Ś/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@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@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@fm.ul.pt
> >        andreia.fonseca@gmail.com
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@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@embl.de
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
> _______________________________________________
> Bioconductor mailing list
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
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>

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