R SIG Debian - Oct 2010 - How to get write permissions for (lib="~/.R/library") ??

Hi

I am trying to install R-igraph, but when I issue the command :

install.packages("igraph", lib="~/.R/library")

in the R session, I get the following error:

Warning in install.packages("igraph", lib = "~/.R/library")
:
  'lib = "~/.R/library"' is not writable
Error in install.packages("igraph", lib = "~/.R/library") :
  unable to install packages

I have tried the command by logging in as the root user, but that also
didn't work.

Can anyone please help me??

Thanks,
Pragya

	[[alternative HTML version deleted]]

Dear Pragya,

Did you first create the folder '.R/library' in your home? It sounds 
weird that it is not writable... Next, if you log as root, it is likely 
that '~' refers to the home of the root user. Thus, you might need to 
explicitly give the complete name. But really, I wouldn't advise to 
install packages *in your home* while logged as root: every file will be 
owned by root...

Once you manage to use '~/.R/library' as a regular user, my advice is to
tell it in a .Renviron file (directly in '~/'), so that you don't
need
to explicitly tell while installing packages.

### Packages in the home directory:
R_LIBS="~/.R/library:${R_LIBS}"

With this, R will try first in '~/.R/library', and next in the usual 
folders if it didn't succeed.

Hope this helps,
Mathieu.


Le 30/10/2010 02:34, pragya agarwal a ?crit :
> Hi
>
> I am trying to install R-igraph, but when I issue the command :
>
> install.packages("igraph", lib="~/.R/library")
>
> in the R session, I get the following error:
>
> Warning in install.packages("igraph", lib =
"~/.R/library") :
>    'lib = "~/.R/library"' is not writable
> Error in install.packages("igraph", lib =
"~/.R/library") :
>    unable to install packages
>
> I have tried the command by logging in as the root user, but that also
> didn't work.
>
> Can anyone please help me??
>
> Thanks,
> Pragya
>
> 	[[alternative HTML version deleted]]
>
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Mathieu Basille, Post-Doc

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On Sat, Oct 30, 2010 at 1:34 AM, pragya agarwal <pragya015 at gmail.com>
wrote:
> Hi
>
> I am trying to install R-igraph, but when I issue the command :
>
> install.packages("igraph", lib="~/.R/library")
>
> in the R session, I get the following error:
>
> Warning in install.packages("igraph", lib =
"~/.R/library") :
> ?'lib = "~/.R/library"' is not writable
> Error in install.packages("igraph", lib =
"~/.R/library") :
> ?unable to install packages
I believe this means something went wrong, and in the past you may
have run something as root or another user.  Or that you have the
library in .R, but the default in Ubuntu deb packaging is not a dot
file, it is R/x86_64-pc-linux-gnu-library.  That's a setting in
/etc/R/Renviron. I have:

R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/2.12'}
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}

Assuming that .R/library is what you really want to use, just give
yourself permission there.

Below, suppose "username" is you user login name, the one you want to
own the files.

You can re-set the permissions.  This isn't an R thing, it is just a
linux thing.  Open a terminal

# cd
# ls -la .R

That should let you see.

# cd .R
# chown -R username library

"username" will now own library and everything below in it.

PJ

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas