R SIG Debian - Feb 2016 - Change Rscript and `/usr/lib/R/bin/R` relation

Dear all,

I am trying to use multiple version of R unpacked from CRAN deb files.

It does work successfully, except for some packages installation, whether 
Rscript has been used. I have configured alternatives and switch R 
environments without any problem and can install most of the packages.

'=====================================================$ update-alternatives
--display R
R - auto mode
  link currently points to /opt/R/3.2.3/usr/lib/R/bin/R
/opt/R/3.2.3/usr/lib/R/bin/R - priority 200
/usr/lib/R/bin/R - priority 100
Current 'best' version is '/opt/R/3.2.3/usr/lib/R/bin/R'.


$ update-alternatives --display Rscript
Rscript - auto mode
  link currently points to /opt/R/3.2.3/usr/lib/R/bin/Rscript
/opt/R/3.2.3/usr/lib/R/bin/Rscript - priority 200
/usr/lib/R/bin/Rscript - priority 100
Current 'best' version is '/opt/R/3.2.3/usr/lib/R/bin/Rscript'.
'=====================================================
Rscript always invokes `/usr/lib/R/bin/R`, but my alternatives are 
configured against `/usr/bin/R`

'=====================================================$ Rscript --verbose -e
'Sys.getenv("R_HOME")'
running
  '/usr/lib/R/bin/R --slave --no-restore -e
Sys.getenv("R_HOME")'

[1] "/usr/lib/R"
'=====================================================
As have been mentioned by Dirk Eddelbuettel, in order to make Rscript 
invoke correct R, I can adjust `PATH` environment variable.

Which was done, but in my case didn't work out. Rscript still calls `/usr/
lib/R/bin/R`

'=====================================================$ env | grep PATH
PATH=/opt/R/3.2.3/usr/lib/R/bin:/opt/python/conda/bin::/usr/local/sbin:/
usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games


$ Rscript --version && Rscript --verbose -e
'print("Hello")'
    R scripting front-end version 3.2.3 (2015-12-10)
    running
      '/usr/lib/R/bin/R --slave --no-restore -e
print("Hello")'

    [1] "Hello"
'=====================================================

Could you please advise where I should dig further in order to force 
Rscript to use `/usr/bin/R` or `/opt/R/3.2.3/usr/lib/R/bin/R`?


Regards, Cron Acronis.

Thanks for bringing the question over from StackOverflow [1].  I am not very
impressed that you STILL hide behind a pseudonym and I am starting to
question my sanity as to why I take time out to help someone like
that. Anyway, read on ...

[1] http://stackoverflow.com/questions/35313704/rscript-launch-custom-r/

On 10 February 2016 at 15:50, Cron Acronis wrote:
| Dear all,
| 
| I am trying to use multiple version of R unpacked from CRAN deb files.

That will not work "as is". They have their path baked in.

You could expand them into a Docker container each, and invoke those.

You _could_ try re-setting RHOME, R_HOME, ...   But rest assured that you
attempt to deploy R in a way NOT foreseen or designed by the authors.

| It does work successfully, except for some packages installation, whether 
| Rscript has been used. I have configured alternatives and switch R 
| environments without any problem and can install most of the packages.
| 
| '=====================================================| $
update-alternatives --display R
| R - auto mode
|   link currently points to /opt/R/3.2.3/usr/lib/R/bin/R
| /opt/R/3.2.3/usr/lib/R/bin/R - priority 200
| /usr/lib/R/bin/R - priority 100
| Current 'best' version is '/opt/R/3.2.3/usr/lib/R/bin/R'.
| 
| 
| $ update-alternatives --display Rscript
| Rscript - auto mode
|   link currently points to /opt/R/3.2.3/usr/lib/R/bin/Rscript
| /opt/R/3.2.3/usr/lib/R/bin/Rscript - priority 200
| /usr/lib/R/bin/Rscript - priority 100
| Current 'best' version is
'/opt/R/3.2.3/usr/lib/R/bin/Rscript'.
| '=====================================================| 
| Rscript always invokes `/usr/lib/R/bin/R`, but my alternatives are 
| configured against `/usr/bin/R`
| 
| '=====================================================| $ Rscript
--verbose -e 'Sys.getenv("R_HOME")'
| running
|   '/usr/lib/R/bin/R --slave --no-restore -e
Sys.getenv("R_HOME")'
| 
| [1] "/usr/lib/R"
| '=====================================================| 
| As have been mentioned by Dirk Eddelbuettel, in order to make Rscript 
| invoke correct R, I can adjust `PATH` environment variable.

That presumed a local build into the location where PATH finds it. That is
how some R Core members use different versions, and that approach 'was good
enough for me' too.   You are overcomplicating things here and get to pick
up
the pieces.

| Which was done, but in my case didn't work out. Rscript still calls `/usr/
| lib/R/bin/R`
| 
| '=====================================================| $ env | grep PATH
| PATH=/opt/R/3.2.3/usr/lib/R/bin:/opt/python/conda/bin::/usr/local/sbin:/
| usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
| 
| 
| $ Rscript --version && Rscript --verbose -e
'print("Hello")'
|     R scripting front-end version 3.2.3 (2015-12-10)
|     running
|       '/usr/lib/R/bin/R --slave --no-restore -e
print("Hello")'
| 
|     [1] "Hello"
| '=====================================================| 
| 
| Could you please advise where I should dig further in order to force 
| Rscript to use `/usr/bin/R` or `/opt/R/3.2.3/usr/lib/R/bin/R`?

Build from source into the chosen location.
 
| Regards, Cron Acronis.

In the future, use a real name if you want real help from real people.

Dirk
 
| _______________________________________________
| 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

On Wed, 10 Feb 2016 10:18:51 -0600, Dirk Eddelbuettel wrote:
> Thanks for bringing the question over from StackOverflow [1].  I am not
> very impressed that you STILL hide behind a pseudonym and I am starting
> to question my sanity as to why I take time out to help someone like
> that. Anyway, read on ...
> 
> [1] http://stackoverflow.com/questions/35313704/rscript-launch-custom-r/
> 
> On 10 February 2016 at 15:50, Cron Acronis wrote:
> | Dear all,
> |
> | I am trying to use multiple version of R unpacked from CRAN deb files.
> 
> That will not work "as is". They have their path baked in.
> 
> You could expand them into a Docker container each, and invoke those.
> 
> You _could_ try re-setting RHOME, R_HOME, ...   But rest assured that
> you attempt to deploy R in a way NOT foreseen or designed by the
> authors.
> 
> | It does work successfully, except for some packages installation,
> whether | Rscript has been used. I have configured alternatives and
> switch R | environments without any problem and can install most of the
> packages.
> |
> | '=====================================================> | $
update-alternatives --display R | R - auto mode |   link currently
> points to /opt/R/3.2.3/usr/lib/R/bin/R | /opt/R/3.2.3/usr/lib/R/bin/R -
> priority 200 | /usr/lib/R/bin/R - priority 100 | Current 'best'
version
> is '/opt/R/3.2.3/usr/lib/R/bin/R'.
> |
> |
> | $ update-alternatives --display Rscript | Rscript - auto mode |   link
> currently points to /opt/R/3.2.3/usr/lib/R/bin/Rscript |
> /opt/R/3.2.3/usr/lib/R/bin/Rscript - priority 200 |
> /usr/lib/R/bin/Rscript - priority 100 | Current 'best' version is
> '/opt/R/3.2.3/usr/lib/R/bin/Rscript'.
> | '=====================================================> |
> | Rscript always invokes `/usr/lib/R/bin/R`, but my alternatives are |
> configured against `/usr/bin/R`
> |
> | '=====================================================> | $
Rscript --verbose -e 'Sys.getenv("R_HOME")'
> | running |   '/usr/lib/R/bin/R --slave --no-restore -e
> Sys.getenv("R_HOME")'
> |
> | [1] "/usr/lib/R"
> | '=====================================================> |
> | As have been mentioned by Dirk Eddelbuettel, in order to make Rscript
> | invoke correct R, I can adjust `PATH` environment variable.
> 
> That presumed a local build into the location where PATH finds it. That
> is how some R Core members use different versions, and that approach
> 'was good enough for me' too.   You are overcomplicating things
here and
> get to pick up the pieces.
> 
> | Which was done, but in my case didn't work out. Rscript still calls
> `/usr/ | lib/R/bin/R`
> |
> | '=====================================================> | $ env |
grep PATH |
> PATH=/opt/R/3.2.3/usr/lib/R/bin:/opt/python/conda/bin::/usr/local/sbin:/
> |
> usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
> |
> |
> | $ Rscript --version && Rscript --verbose -e
'print("Hello")'
> |     R scripting front-end version 3.2.3 (2015-12-10)
> |     running |       '/usr/lib/R/bin/R --slave --no-restore -e
> print("Hello")'
> |
> |     [1] "Hello"
> | '=====================================================> |
> |
> | Could you please advise where I should dig further in order to force |
> Rscript to use `/usr/bin/R` or `/opt/R/3.2.3/usr/lib/R/bin/R`?
> 
> Build from source into the chosen location.
>  
> | Regards, Cron Acronis.
> 
> In the future, use a real name if you want real help from real people.
> 
> Dirk
>  
Dear Dirk,

Probably you would like to know, that I have managed to solve the problem 
by using `schroot`.

It can attach current user `home` folder to `rootfs` from `chroot` where.

After I have configured the `trusty64`, I have just created a clone.
Inside the clone I have installed another version of R from CRAN repo.
<--------------------------------START------------->
root at chroot-test:/# schroot -l
chroot:trusty64
chroot:trusty64_clone


$ cat /etc/schroot/chroot.d/trusty64.conf 
[trusty64]
description=Ubuntu 14.04 Trusty Tahr
directory=/test/schroot/trusty64
users=quant
type=directory
profile=desktop
#personality=linux
preserve-environment=true
root-groups=root

$ cat /etc/schroot/chroot.d/trusty64_clone.conf 
[trusty64_clone]
description=Ubuntu 14.04 Trusty Tahr
directory=/test/schroot/trusty64
users=quant
type=directory
profile=desktop
#personality=linux
preserve-environment=true
root-groups=root

root at chroot-test:/etc# debootstrap --variant=minbase --arch amd64 trusty /
test/schroot/trusty64/ http://archive.ubuntu.com/ubuntu/


root at chroot-test:/etc# schroot -c trusty64 -u quant
root at chroot-test:/etc# schroot -c trusty64_clone -u quant
<--------------------------------END--------------->

-- 
Regards. Alexey.