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

[Marius Hofert]

On Thu, Apr 2, 2015 at 5:49 AM, Johannes Ranke <jranke at uni-bremen.de> wrote:
> 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?

... I think the reason was that ESS auto-recognizes everything in
/usr/local/R if your main R version in use is installed there, see C-h
k ess-rterm-version-paths...

>
>> 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.

oh yes, sure.

Cheers,
M

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