[BioC] problems with bioconductor installation
Hervé Pagès
hpages at fhcrc.org
Wed Feb 24 07:20:56 CET 2010
Hi Pete,
Just putting this back on the list...
Pete Shepard wrote:
> OK,
>
> Thanks to Hervé and Wolfgang I have updated to R 2.10 and am now running
> Bioconductor 2.5. I am generally hesitant to install anything that is
> not available via Synaptic because it can lead to compatability issues
> and sometimes a serious detour. But, using the instructions below
> everything installed just fine.
Note that the list of .deb packages available via Synaptic is the
same as via apt-get. Furthermore, installing via one or the other
is equivalent, in particular they both update the local db of
installed packages. For example you can check that the .deb packages
that you installed with apt-get are now marked as installed in
Synaptic and vice versa. Not really surprising because Synaptic
uses apt-get/apt-cache in the background!
> I think the issue with the old R
> installation not talking to bioC 2.5 correctly was with Rcurl?
There are many reasons why versions of R < 2.10 won't work with
BioC 2.5. Glad things work for you now.
Cheers,
H.
>
> Thanks again.
>
> P
> 2010/2/22 Hervé Pagès <hpages at fhcrc.org <mailto:hpages at fhcrc.org>>
>
> Hi Pete,
>
> I'm joining Wolfgang and all the Bioconductor-on-Linux users out there
> to highly recommend that you compile/install R-2.10.1 from source.
> On Ubuntu it's particularly easy and that will allow you to run the
> current version of Bioconductor (2.5). We don't (and cannot) support
> older versions of BioC.
>
> On my 64bit Ubuntu 9.04 machine, I needed to install the following
> .deb packages before being able to compile/install R and BioC (some
> BioC packages require compilation too so it's really important that
> you manage to install those components):
>
> Required stuff:
> gcc
> gfortran
> g++
> gobjc
> libreadline5-dev
> libx11-dev
> libxt-dev
>
> Highly recommended stuff (TeX/LaTeX, tcltk, PNG, JPEG, cairo, Java):
> texlive
> texlive-latex-extra (for fullpage.sty)
> texi2html
> texinfo
> tk-dev
> libpng12-dev
> libjpeg62-dev
> libcairo2-dev
> manpages-dev (includes man pages for the C standard lib)
>
> Needed by some CRAN or BioC packages:
> libxml2-dev (for XML)
> libcurl4-openssl-dev (for RCurl)
> libnetcdf-dev (for xcms, RNetCDF, etc...)
> libgraphviz-dev (for RGraphviz)
> libmagick++9-dev (for EBImage)
>
> Each component can be installed with e.g. 'sudo apt-get install gcc'.
> Note that the 'sudo' command will prompt you for your regular password,
> not an admin password. Also note that, strictly speaking, the list above
> is for Ubuntu 9.04, but chances are high that it is very similar, if not
> the same, for Ubuntu 9.10.
>
> Cheers,
> H.
>
>
>
> Wolfgang Huber wrote:
>
> Dear Pete
>
>
> Thanks for all the suggestions. I am stuck running R version
> 2.9 due to my OS.
>
>
> Not true. I (and many others) are running Ubuntu 9.10, and on
> that R 2.10 (the latest release) as well as the current devel
> (what will be 2.11).
>
> Generic installation instructions are in the R FAQ, section 2.5.1:
> http://cran.r-project.org/doc/FAQ/R-FAQ.html
> You will need to install necessary compilers, latex, gnumake etc
> (which is anyway a good investment in the value of your computer.)
>
> For Ubuntu, you might also want to look at this:
> http://cran.r-project.org/bin/linux/ubuntu/
>
> Best wishes
> Wolfgang
>
> 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 at gmail.com <mailto:laxvid at gmail.com>
> <mailto:laxvid at gmail.com <mailto:laxvid at 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 at embl.de <mailto:whuber at embl.de>
> <mailto:whuber at embl.de <mailto: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 <mailto:mtmorgan at fhcrc.org>
> <mailto:mtmorgan at fhcrc.org <mailto: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
> <mailto:Bioconductor at stat.math.ethz.ch>
> <mailto:Bioconductor at stat.math.ethz.ch
> <mailto: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
> <mailto:Bioconductor at stat.math.ethz.ch>
> <mailto:Bioconductor at stat.math.ethz.ch
> <mailto: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
> <mailto:andreiaamaral at fm.ul.pt>
> <mailto:andreiaamaral at fm.ul.pt <mailto:andreiaamaral at fm.ul.pt>>
> > andreia.fonseca at gmail.com
> <mailto:andreia.fonseca at gmail.com>
> <mailto:andreia.fonseca at gmail.com
> <mailto:andreia.fonseca at gmail.com>>
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> <mailto:Bioconductor at stat.math.ethz.ch>
> <mailto:Bioconductor at stat.math.ethz.ch
> <mailto: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 <mailto:whuber at embl.de>
> <mailto:whuber at embl.de <mailto:whuber at embl.de>>
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> <mailto:Bioconductor at stat.math.ethz.ch>
> <mailto:Bioconductor at stat.math.ethz.ch
> <mailto: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
> >
>
> _______________________________________________
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> <mailto:Bioconductor at stat.math.ethz.ch>
> <mailto:Bioconductor at stat.math.ethz.ch
> <mailto: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
>
>
>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org <mailto:hpages at fhcrc.org>
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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