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

On Tue, Mar 31, 2015 at 2:05 AM, Johannes Ranke <jranke at uni-bremen.de>
wrote:
> 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.
Dear Johannes,

... no one in his/her clear mind would go that way unless necessary. I
have given reasons for when and why it is necessary.
> 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!
... because it is trivial from the procedure I described. Replace the
version number by 'devel' or 'rc' (for patched) and the rest
remains
pretty much the same (obviously adapting the download link).

>
> 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,
yes, that's a use case. Or if you need >= 2 R versions to check back
with older versions or if a user with a different R version reports a
bug and you can not reproduce it with the version you have etc...
>  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.
>
I frequently install new R-devel versions... simply removing
/usr/local/R/R-devel* first. There might be side-effects I don't know,
but that never gave me problems.
> 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/
2) sudo apt-get update # => fails, but note the number of the missing
public key; then do:
   sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-key
<NUMBER> # <NUMBER> = number after NO_PUBKEY
3) Build dependencies (compilers etc.):
   sudo apt-get build-dep r-base
4) Install path:
   sudo mkdir /usr/local/R
   sudo chown <user>:<user> /usr/local/R
5) Get and unpack R:
   cd /usr/local/R
   # if it exists, delete the old ./R-devel, ./R-devel-build,
./R-devel.tar.gz etc. then do:
   wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz # see
CRAN -> R Sources for the link
   tar -xzf R-devel.tar.gz
   mv R-devel R-devel_source
6) Set up build directory (don't use ./configure within source
directory; sources would be lost)
   mkdir R-devel_build
7) Configure:
   cd R-devel_build
   ../R-devel_source/configure # ~2min
8) Build:
   make # 10min (desktop); much longer on Android (seems to hang but
just let it run!)
   make check # ~3min
   make pdf # ~2min
   make info # ~1min
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
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

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-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

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
> >> 
> >> _______________________________________________
> >> 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