R SIG Debian - Mar 2015 - Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)

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

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

Am Montag, 30. M?rz 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
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
-- 
PD Dr. Johannes Ranke
Kronacher Str. 8
79639 Grenzach-Wyhlen

Marius,

On 30 March 2015 at 12:30, Marius Hofert wrote:
| 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:

That's your beef.  We support reasonably feature complete packages built in
reasonably well-engineered and by now mostly debugged processes.  

You can of course build your own, but if you do and things break you get to
keep those pieces.

And how to build R(-devel) locally has been discussed in the past.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org