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

Dear Dirk, Dear Johannes,

Thanks for helping, I could solve the problem.

By reading your posts, I got a bit of the impression that questions
beyond the 'standard installation' process are not really welcome on
R-SIG-Debian. If this is the case, I'm sorry for my post. I wasn't
aware of this, but Dirk makes it clear why on
https://stat.ethz.ch/pipermail/r-sig-debian/2013-March/002062.html.

As Dirk also mentioned on
http://stackoverflow.com/questions/8343686/how-to-install-2-different-r-versions-on-debian
installing from source is the only practical way in case one needs
several R versions. I now went back to Chapter 2 of
http://cran.r-project.org/doc/manuals/r-release/R-admin.html to read
more about it and to see whether I have done something substantially
wrong. This seemed not to be the case.

Next, Dirk's wonderful little example helped... I could check that
.Renviron is indeed found. Then it was easy: my local
version-independent library was not found simply because .libPaths()
only contains those folders which physically exist (also mentioned on
?.libPaths). And indeed, I had not checked that.

Here is thus the final solution that worked (in case useful for others
or being improved upon [slightly expanded in comparison to the
original one, e.g., also addressing how to obtain a key -- the server
is different than keys.gnupg.net mentioned on CRAN.]):

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/ # => then run sudo
   apt-get update. It fails due to a missing key => note the missing key
number
   # and use sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-key
   <NUMBER> where # <NUMBER> = number of the missing public key

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 # if old versions exist (./R-devel, ./R-devel-build,
   ./R-devel.tar.gz etc.), # delete them first, then do: 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 # we do
   ./configure *outside* the source directory (=> keep sources)

   make make check make pdf make info

   cd ..  ln -s /usr/local/R/R-3.1.3-build/bin/R /usr/local/R/R

   mkdir /usr/local/R/library # create version-independent library

   sudo emacs ~/etc/bash.bashrc # then add: PATH=/usr/local/R:$PATH

4) ~/.Renviron should contain R_LIBS=/usr/local/R/library


Thanks & cheers,
Marius


On Mon, Mar 30, 2015 at 1:09 PM, Dirk Eddelbuettel <edd at debian.org>
wrote:
>
> 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

Dear Marius,

thanks for sharing your thoughts on this. I am not very happy that you provide 
instructions to install R 3.1.3 from sources when binaries are already 
provided on CRAN. The installation instructions you share bring more work and 
a more non-standard setup, unless you want two different copies of R. But your 
instructions do not cover that case!
>From my point of view it could be interesting if it were modified for
keeping
an up to date copy of R-devel in addition to the released version, but in the 
way you are giving it here I think it may lead people to be distracted from 
the easy and clean way to do it. I say clean, because when you use the .deb 
packages it is much easier to remove or revert what you have done.

So maybe you could modify your instructions to the case where someone wants to 
have R-devel in addition to the released R version, if that is what you are 
aiming at? I could then add it to the README for Debian on CRAN.

And then, regarding your comment on the keyserver listed in the README,
what's
wrong with keys.gnupg.net? I just tested it (again) and it worked fine.

Kind regards, 

Johannes

Am Montag, 30. M?rz 2015, 20:42:47 schrieb Marius
Hofert:
> Dear Dirk, Dear Johannes,
> 
> Thanks for helping, I could solve the problem.
> 
> By reading your posts, I got a bit of the impression that questions
> beyond the 'standard installation' process are not really welcome
on
> R-SIG-Debian. If this is the case, I'm sorry for my post. I wasn't
> aware of this, but Dirk makes it clear why on
> https://stat.ethz.ch/pipermail/r-sig-debian/2013-March/002062.html.
> 
> As Dirk also mentioned on
>
http://stackoverflow.com/questions/8343686/how-to-install-2-different-r-vers
> ions-on-debian installing from source is the only practical way in case one
> needs several R versions. I now went back to Chapter 2 of
> http://cran.r-project.org/doc/manuals/r-release/R-admin.html to read
> more about it and to see whether I have done something substantially
> wrong. This seemed not to be the case.
> 
> Next, Dirk's wonderful little example helped... I could check that
> .Renviron is indeed found. Then it was easy: my local
> version-independent library was not found simply because .libPaths()
> only contains those folders which physically exist (also mentioned on
> ?.libPaths). And indeed, I had not checked that.
> 
> Here is thus the final solution that worked (in case useful for others
> or being improved upon [slightly expanded in comparison to the
> original one, e.g., also addressing how to obtain a key -- the server
> is different than keys.gnupg.net mentioned on CRAN.]):
> 
> 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/ # => then run
> sudo apt-get update. It fails due to a missing key => note the missing
key
> number # and use sudo apt-key adv --keyserver keyserver.ubuntu.com
> --recv-key <NUMBER> where # <NUMBER> = number of the missing
public key
> 
> 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 # if old versions exist (./R-devel, ./R-devel-build,
>    ./R-devel.tar.gz etc.), # delete them first, then do: 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 # we do
>    ./configure *outside* the source directory (=> keep sources)
> 
>    make make check make pdf make info
> 
>    cd ..  ln -s /usr/local/R/R-3.1.3-build/bin/R /usr/local/R/R
> 
>    mkdir /usr/local/R/library # create version-independent library
> 
>    sudo emacs ~/etc/bash.bashrc # then add: PATH=/usr/local/R:$PATH
> 
> 4) ~/.Renviron should contain R_LIBS=/usr/local/R/library
> 
> 
> Thanks & cheers,
> Marius
> 
> On Mon, Mar 30, 2015 at 1:09 PM, Dirk Eddelbuettel <edd at
debian.org> wrote:
> > 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
> 
> _______________________________________________
> 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