R SIG Debian - May 2010 - Changing R_LIB_USER variable in ubuntu...

Hi,

I'm an experienced R user on windows, but new to linux.  This may be an 
issue with how R (or Ubuntu) was install on my computer, but maybe not. 
   I just installed Ubuntu 10.04, I have administrator privileges and 
am using R 2.11.  Here goes:

I'd like to change the location where R installs packages not included
in the base installation (using install.packages()).  Right now it is
saving them to
"/home/ken/R/i486-pc-linux-gnu-library/2.11" like it should based on
the default R_LIB_USER setting in /etc/R/Renviron.

I think that this is quite a bulky filepath and would prefer to shorten 
it (ie. "~/R/2.11/library").  Unfortunately, /etc/R/ is read only for 
me (as is /usr/R/).  Therefore I can't change the R_LIB_USER variable.  
I understand the rationale behind protecting /etc/ and /usr/, but is 
there any way to customize this variable once and not worry about it 
when I install future packages?

Thank a lot!

Ken

On 05/29/2010 11:44 PM, Kenneth Takagi wrote:
> Hi,
>
> I'm an experienced R user on windows, but new to linux. This may be an
> issue with how R (or Ubuntu) was install on my computer, but maybe not.
> I just installed Ubuntu 10.04, I have administrator privileges and am
> using R 2.11. Here goes:
>
> I'd like to change the location where R installs packages not included
> in the base installation (using install.packages()). Right now it is
> saving them to
> "/home/ken/R/i486-pc-linux-gnu-library/2.11" like it should based
on
> the default R_LIB_USER setting in /etc/R/Renviron.
>
> I think that this is quite a bulky filepath and would prefer to shorten
> it (ie. "~/R/2.11/library"). Unfortunately, /etc/R/ is read only
for me
> (as is /usr/R/). Therefore I can't change the R_LIB_USER variable. I
> understand the rationale behind protecting /etc/ and /usr/, but is there
> any way to customize this variable once and not worry about it when I
> install future packages?
Ken,

When I install packages in R using Ubunutu, I always use 'sudo'.

[command line]sudo R

...R launches...
 >install.packages("foo")

That will install the packages in a /usr directory and all users on the 
machine will have access to them.

If that is not what you are looking for, let us know.

Michael

thank a lot for you answer.  Since I'm new to linux, I still have a 
couple questions based on your response:

1) do I create a file named .Renvirons or just Renvirons in my home directory?

@) In the following lines of the script:
> ### Packages in the home directory:
> R_LIBS="~/.R-site/site-library:${R_LIBS}"
how exactly would I change the file path to"~/R/2.11/library") for
example?

Thanks for putting up with my limited knowledge, I'm slowly learning!

Best,
Ken





Quoting Christophe Bonenfant <bonenfan at biomserv.univ-lyon1.fr>:
> Dear Ken,
>
> I changed the lib path as you would like on my Debian system. The only
> thing you have to do is to create a .Renviron file in your home directory.
>
> Mine looks like:
>
> ### xpdf as the default pdf viewer
> R_PDFVIEWER='/usr/bin/xpdf'
>
> ### To get R in English:
> LANGUAGE=en
>
> ### Packages in the home directory:
> R_LIBS="~/.R-site/site-library:${R_LIBS}"
>
> Change the path to your convenience. R will read this file when
> launched. You will not need root privileges to intall packages anymore.
>
> Hope this helps.
>
> Christophe
>
> Le 30/05/2010 05:44, Kenneth Takagi a ?crit :
>> Hi,
>>
>> I'm an experienced R user on windows, but new to linux.  This may
be an
>> issue with how R (or Ubuntu) was install on my computer, but maybe not.
>>   I just installed Ubuntu 10.04, I have administrator privileges and am
>> using R 2.11.  Here goes:
>>
>> I'd like to change the location where R installs packages not
included
>> in the base installation (using install.packages()).  Right now it is
>> saving them to
>> "/home/ken/R/i486-pc-linux-gnu-library/2.11" like it should
based on
>> the default R_LIB_USER setting in /etc/R/Renviron.
>>
>> I think that this is quite a bulky filepath and would prefer to shorten
>> it (ie. "~/R/2.11/library").  Unfortunately, /etc/R/ is read
only for me
>> (as is /usr/R/).  Therefore I can't change the R_LIB_USER variable.
I
>> understand the rationale behind protecting /etc/ and /usr/, but is
there
>> any way to customize this variable once and not worry about it when I
>> install future packages?
>>
>> Thank a lot!
>>
>> Ken
>>
>> _______________________________________________
>> R-SIG-Debian mailing list
>> R-SIG-Debian at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>>
>>
>
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>
>

Thanks, I will give this a try and see how it goes!

Best,
Ken




Quoting Christophe Bonenfant <bonenfan at biomserv.univ-lyon1.fr>:
> Hi Ken,
>
>> thank a lot for you answer.  Since I'm new to linux, I still have a
>> couple questions based on your response:
>
> You're welcome, no problem!
>
>> 1) do I create a file named .Renvirons or just Renvirons in my home
>> directory?
>
> Create a ".Renviron" file with a dot, meaning this file is
hidden. And
> as far as I know R will be looking for a .Renviron but not Renviron file
> by default.
>
> Try "ls -a" in a shell to see all the hidden files of your home
directory.
>
>> @) In the following lines of the script:
>>> ### Packages in the home directory:
>>> R_LIBS="~/.R-site/site-library:${R_LIBS}"
>>
>> how exactly would I change the file path
to"~/R/2.11/library") for example?
>
> Well, I would try this:
>
> R_LIBS="~/R/2.11/library:${R_LIBS}"
>
> then you will have the following structure:
>
> /home/ken/
> ----------/R/2.11/library/
> --------------------------package1/
> --------------------------package2/
> ...
>
> in your home directory.
>
> The point is that you now have a /R folder in you home when browsing
> files with Nautilus. Once again, add a dot before to make it hidden
> (ctrl+H to see it in Nautilus then) and keep things tidy in your home.
>
> As Mickael rightly  pointed out, this way of managing libraries is
> local, it means that another user of you computer will not see and nor
> access the libraries you installed as "ken" user. To do so, you
need to
> install package as a root as Mickael suggests.
>
>> Thanks for putting up with my limited knowledge, I'm slowly
learning!
>
> It is a matter of weeks, then you'll feel comfortable with the
> configuration file in GNU/Linux.
>
> Good luck!
>
> Christophe
>
>
>

Hi Ken,

you can override R_LIBS_USER in ~/.Rprofile (in your case this expands to 
/home/ken/.Rprofile). For example, I have 

	R_LIBS_USER="~/lib/R/library"

in my file. Details can be found from within R with 

	> ?Startup

Note that R CMD does not seem to respect the settings in ~/.Rprofile. If I 
recall correctly, it used to in earlier R versions.

Kind regards,

Johannes



Am Sonntag, 30. Mai 2010, um 05:44:24 schrieb Kenneth
Takagi:
> Hi,
> 
> I'm an experienced R user on windows, but new to linux.  This may be an
> issue with how R (or Ubuntu) was install on my computer, but maybe not.
>    I just installed Ubuntu 10.04, I have administrator privileges and
> am using R 2.11.  Here goes:
> 
> I'd like to change the location where R installs packages not included
> in the base installation (using install.packages()).  Right now it is
> saving them to
> "/home/ken/R/i486-pc-linux-gnu-library/2.11" like it should based
on
> the default R_LIB_USER setting in /etc/R/Renviron.
> 
> I think that this is quite a bulky filepath and would prefer to shorten
> it (ie. "~/R/2.11/library").  Unfortunately, /etc/R/ is read only
for
> me (as is /usr/R/).  Therefore I can't change the R_LIB_USER variable.
> I understand the rationale behind protecting /etc/ and /usr/, but is
> there any way to customize this variable once and not worry about it
> when I install future packages?
> 
> Thank a lot!
> 
> Ken
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian