Hi Joern

after upgrading to 2.6.1, it worked like a charm :-)

thanks!

Kenji

On Jan 17, 2008 11:41 AM, Joern Toedling <toedling@ebi.ac.uk> wrote:

> Hello,
>
> "xtable" is not a Bioconductor package, so you can get it from your
> local CRAN mirror as well, try
> install.packages("xtable")
> In theory, biocLite can also be used to download CRAN packages, so I
> don't really know what went wrong in your case.
> Two suggestions:
> 1. please consider updating your R to the current release version 2.6.1
> and Bioconductor to the current release version 2.1. When you call the
> "biocLite" function from within R2.6.1, it will automatically retreive
> BioC 2.1 package versions.
> 2. since you are on Linux, it may be a good idea to create a separate
> directory for your R add-on packages. You can set an environment
> variable R_LIBS which tells R where to look for packages (besides the R
> installation directory) and also where to install add-on packages into,
> for example I have the following line in my "~/.cshrc" shell setup file:
> setenv R_LIBS "${HOME}/rpackages"
> telling R that it is the directory ~/rpackages  in my case. That works
> if you are using c-shell and derivatives. If you are using bash, there's
> another syntax for setting environment variables and the file is
> "~/.bashrc".
> One main advantage of setting this variable is that you won't have to
> reinstall add-on packages every time you update your R version.
>
> Regards,
> Joern
>
> Leonardo Kenji Shikida wrote:
> > I am having problems installing xtable. May anybody help me, please?
> >
> > thanks in advance
> >
> > Kenji
> >
> >
> >>  biocLite("xtable")
> >>
> > Running biocinstall version 2.0.8 with R version 2.5.1
> > Your version of R requires version 2.0 of Bioconductor.
> > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> > dependencies,  :
> >          argument 'lib' is missing: using
> > '/home/kenji/R/i486-pc-linux-gnu-library/2.5'
> > Warning message:
> > package 'xtable' is not available in: install.packages(pkgs = pkgs,
> repos =
> > repos, dependencies = dependencies,
> >
> >> sessionInfo()
> >>
> > R version 2.5.1 (2007-06-27)
> > i486-pc-linux-gnu
> >
> > locale:
> >
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] "tools"     "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> > [7] "methods"   "base"
> >
> > other attached packages:
> >     affy   affyio  Biobase
> > "1.14.2"  "1.4.1" "1.14.1"
> >
> >
> >
>
>


-- 

[]

Kenji
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