"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.UT
F-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
> _______________________
> http://kenjiria.blogspot.com
> http://gaitabh.blogspot.com
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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_U
S.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"
>
>
>
