[R-sig-Debian] Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)

[Johannes Ranke]

Am Montag, 30. März 2015, 12:30:37 schrieb Marius Hofert:
> Dear Johannes, Dear Dirk,
> 
> Thanks a lot for helping. Here is the missing information.
> 
> Here is how I installed R. This is basically how Martin Maechler
> showed me to install R under Ubuntu (in several versions so that they
> are also recognized by ESS). My goal is to adjust this to make it work
> for Debian:
> 
> 1) sudo emacs /etc/apt/sources.list # then add:
>    deb http://stat.ethz.ch/CRAN/bin/linux/debian jessie-cran3/
>    deb-src http://stat.ethz.ch/CRAN/bin/linux/debian jessie-cran3/
> 
> 2) sudo apt-get build-dep r-base

At this point you should simply do

    sudo apt-get install r-base r-base-dev

as per the Debian README on CRAN.

http://cran.r-project.org/bin/linux/debian/README.html

Then you do not have to build from sources as you did below! This will also 
give you /etc/R/Renviron.

Kind regards,

Johannes

> 
> 3) sudo mkdir /usr/local/R
>    sudo chown mhofert:mhofert /usr/local/R
> 
>    cd /usr/local/R
>    wget http://cran.r-project.org/src/base/R-3/R-3.1.3.tar.gz
>    tar -xzf R-3.1.3.tar.gz
>    mv R-3.1.3 R-3.1.3-source
> 
>    mkdir R-3.1.3-build
>    cd R-3.1.3-build
>    ../R-3.1.3-source/configure
> 
>    make
>    make check
>    make pdf
>    make info
> 
>    cd ..
>    ln -s /usr/local/R/R-3.1.3-build/bin/R /usr/local/R/R
> 
>    sudo emacs ~/etc/bash.bashrc # then add:
>    PATH=/usr/local/R:$PATH
> 
> .libPaths() shows:
> > .libPaths()
> 
> [1] "/usr/local/R/R-3.1.3-build/library"
> 
> and sessionInfo() is:
> > sessionInfo()
> 
> R version 3.1.3 (2015-03-09)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 8 (jessie)
> 
> locale:
>  [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
>  [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8
>  [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> Interestingly, under Ubuntu, I find /etc/R/Renviron, under Debian, it
> does not exist... hmmm... what's flawed in the above installation
> process (?)
> 
> Cheers,
> Marius
> 
> On Mon, Mar 30, 2015 at 7:39 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
> > Hi Marius,
> > 
> > On 30 March 2015 at 02:24, Marius Hofert wrote:
> > | I have Debian Testing running on a Lenovo Thinkpad X1
> > | Carbon (2015, 3rd gen.). I would like to have a package library
> > | independent of the installed R version. Under Ubuntu, I used to
> > | have the following line in ~/.Renviron:
> > | R_LIBS=/usr/local/R/library:/usr/lib/R/site-library This worked
> > | fine and /usr/local/R/library showed up in .libPaths().
> > 
> > Please look at
> > 
> >        /etc/R/Renviron
> >        /usr/lib/R/etc/Renviron
> > 
> > (which are the same file via softlinks) and how they set R_LIBS_SITE and
> > have been 2003 (!!).
> > 
> > | However, under Debian (with the same ~/.Renviron), my .libPaths()
> > | just shows "/usr/local/R/R-3.1.3-build/library" which is the
> > | version-dependent library (this used to come at 3rd position in
> > | .libPaths()). Does R on Debian not look for ~/.Renviron? I also
> > 
> > It should. See help(Startup).
> > 
> > And does:
> >   edd at max:~$ grep Hello .Renviron
> >   MARIUS="Hello, world from .Renviron"
> >   edd at max:~$ R -q -e 'Sys.getenv("MARIUS")'
> >   R> Sys.getenv("MARIUS")
> >   [1] "Hello, world from .Renviron"
> >   R>
> >   R>
> >   edd at max:~$
> > 
> > Small caveat: littler does not (yet). But you didn't say whether you used
> > R
> > or r.
> > 
> > Dirk
> > 
> > | tried R_LIBS_USER but no luck here either (although, as far as I
> > | understand Section 6.2 of "R Installation and Administration",
> > | R_LIBS or R_LIBS_USER should work (?))
> > | 
> > | Cheers, Marius
> > | 
> > | PS: I found two sites which seem to be related, but it was still
> > | not quite clear to me how to approach the problem:
> > | https://stat.ethz.ch/pipermail/r-sig-debian/2005-December/000050.html
> > | https://stat.ethz.ch/pipermail/r-sig-debian/2010-May/001146.html
> > | 
> > | _______________________________________________
> > | R-SIG-Debian mailing list
> > | R-SIG-Debian at r-project.org
> > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> > 
> > --
> > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
> 
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-- 
PD Dr. Johannes Ranke
Kronacher Str. 8
79639 Grenzach-Wyhlen