[BioC] installing xtable

[Martin Morgan]

"Leonardo Kenji Shikida" <shikida at gmail.com> writes:

> 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 at 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.

xtable on CRAN requires R>=2.6.0, so when biocLite went looking for a
version that would work with your old version of R, it did not find
one. Updating to R 2.6.1 allows biocLite to find a correct version of
xtable.

Martin


>> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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