Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)

Hi Marius,

thanks for your reply.

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.

That sounds good. I just modified the instructions to R-devel and used
a more "Kurt-like" naming convention:

1) sudo nano /etc/apt/sources.list
   deb http://stat.ethz.ch/CRAN/bin/linux/debian jessie-cran3/
   deb-src http://stat.ethz.ch/CRAN/bin/linux/debian jessie-cran3/

...

9) Create a (symbolic) link (don't use 'make install'):
   cd ..
   ln -s /usr/local/R/R-devel_build/bin/R /usr/local/R/R-devel

Why not put a link into /usr/local/bin which is already in the path?

10) mkdir /usr/local/R/library
11) Add /usr/local/R to PATH:
    sudo nano /etc/bash.bashrc # then put in:
    PATH=/usr/local/R:$PATH # R installation
12) Reboot

Reboot??? It is sufficient to source your bash config file to get the new path.

Kind regards,

Johannes

Clearly, some words (of warning) are in order ..., e.g., to use $USER
in 4) instead of <user>, to adapt the right path in 5), to have tools
like tar available or also to maybe choose some other file than
/etc/bash.bashrc for adjusting PATH (see
http://forums.debian.net/viewtopic.php?f=5&t=121169 for why I chose
this file).

I very much like Dirk's message here: "That's your beef" (good word of
warning), but someone who needs to go that way should be able to
follow along the above lines.

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.

... there was a problem for me initially (some kind of
host-resolve-thingy -- can't remember anymore). After googling, I then
found the other key server and it was also suggested to use the actual
key the error message mentions (see step 2)) instead of the fixed
381BA480. I understand too little about the involved risk of changing
that but the above worked for me.

Many cheers (and sorry for the late reply -- it's end-of-term),
Marius

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-v
ers 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

--
PD Dr. Johannes Ranke
Kronacher Str. 8
79639 Grenzach-Wyhlen

--
PD Dr. Johannes Ranke
Kronacher Str. 8
79639 Grenzach-Wyhlen