[BioC] installing xtable

Joern Toedling toedling at ebi.ac.uk
Thu Jan 17 14:41:47 CET 2008


"xtable" is not a Bioconductor package, so you can get it from your
local CRAN mirror as well, try
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
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.


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:
> 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"

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