installing R on Ubuntu

[Erin Hodgess]

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[Roland Rau-3]

I am not sure what the question is but maybe this provides a starting point?
http://cran.r-project.org/bin/linux/ubuntu/README

HTH,
Roland


On 4/16/07, Erin Hodgess <hodgess@...> wrote:
>
>
> ______________________________________________
> R-help@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Paul Heinrich Dietrich]

I've read some of R's literature on Linux, including the R Admin manual, and didn't find it very useful, which is probably my own limitation.  But I did finally manage to get it working well.  I'm posting this to help others.  The following worked when installing R 2.8.1 on Ubuntu 8.04 Hardy Heron.  Here are truly step-by-step instructions for those who don't know Linux (like me):

Installation and Initial Set-Up of R for Ubuntu Linux

1. Open the Bash terminal (Applications > Accessories > Terminal)
2. Type these lines to add the security key to access the latest version of the R Ubuntu package:
        user@computer:~$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
        user@computer:~$ gpg -a --export E2A11821 | sudo apt-key add -
3. Use the Bash terminal to open your sources.list file with gedit (text editor) for editing:
        user@computer:~$ sudo gedit /etc/apt/sources.list
4. Add this line to the bottom of the sources.list file:
        deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu hardy/
5. Save the file and go back to the Bash terminal.
6. Type this to update apt-get's database before you install R:
        user@computer:~$ sudo apt-get update
7. Install R with this command:
        user@computer:~$ sudo apt-get install r-base
8. Go to System > Administration > Synaptic Package Manager, and download the build-essential package.
9. To use R, simply enter R in the Bash terminal.  To quit, enter q().


Additional programs will be needed to install other packages or work with other programs:
1. Install compilers for C++ and Fortran
        user@computer:~$ sudo apt-get install g++ gfortran
2. Install the developer versions of Blas and Lapack (what are these?)
        user@computer:~$ apt-get install libblas-dev liblapack-dev


Updating Packages in R
1. Open the Bash terminal and start R with root permissions
        user@computer:~$ sudo R
2. Type > update.packages()


Installing the R Commander GUI
1. Open the Bash terminal and type:
       user@computer:~$ apt-get install r-cran-rcmdr


Using the R Commander GUI
library(Rcmdr)
...or once the library is open and Commander has been shut down, type: commander()


Notes
It looks like most of R has been put here:
/etc/R (Rprofile.site is here)
/usr/lib/R


Downloaded Packages seem to go here:
/usr/local/lib/R/site-library/

[Paul Heinrich Dietrich]

I've read some of R's literature on Linux, including the R Admin manual, and didn't find it very useful, which is probably my own limitation.  But I did finally manage to get it working well.  I'm posting this to help others.  The following worked when installing R 2.8.1 on Ubuntu 8.04 Hardy Heron.  Here are truly step-by-step instructions for those who don't know Linux (like me):

Installation and Initial Set-Up of R for Ubuntu Linux

1. Open the Bash terminal (Applications > Accessories > Terminal)
2. Type these lines to add the security key to access the latest version of the R Ubuntu package:
        user@computer:~$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
        user@computer:~$ gpg -a --export E2A11821 | sudo apt-key add -
3. Use the Bash terminal to open your sources.list file with gedit (text editor) for editing:
        user@computer:~$ sudo gedit /etc/apt/sources.list
4. Add this line to the bottom of the sources.list file:
        deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu hardy/
5. Save the file and go back to the Bash terminal.
6. Type this to update apt-get's database before you install R:
        user@computer:~$ sudo apt-get update
7. Install R with this command:
        user@computer:~$ sudo apt-get install r-base
8. Go to System > Administration > Synaptic Package Manager, and download the build-essential package.
9. To use R, simply enter R in the Bash terminal.  To quit, enter q().


Additional programs will be needed to install other packages or work with other programs:
1. Install compilers for C++ and Fortran
        user@computer:~$ sudo apt-get install g++ gfortran
2. Install the developer versions of Blas and Lapack (what are these?)
        user@computer:~$ apt-get install libblas-dev liblapack-dev


Updating Packages in R
1. Open the Bash terminal and start R with root permissions
        user@computer:~$ sudo R
2. Type > update.packages()


Installing the R Commander GUI
1. Open the Bash terminal and type:
       user@computer:~$ apt-get install r-cran-rcmdr


Using the R Commander GUI
library(Rcmdr)
...or once the library is open and Commander has been shut down, type: commander()


Notes
It looks like most of R has been put here:
/etc/R (Rprofile.site is here)
/usr/lib/R


Downloaded Packages seem to go here:
/usr/local/lib/R/site-library/

[Cruz Adam]

nice:)

The next step is to install Emacs, because we need a editor as we
code, we need to run the line as we go, so here is a very good guide
for the complete starter:

http://www.stat.rice.edu/~helpdesk/tutorial/ess.html

The official ESS manual does not bother to go into this brief, I can't
even start a R session in Emacs when I have read the ESS manual
several times, but it is getting clearer to me now as I have been
writing R codes by Emacs for a couple of weeks...

It is exactly the same as we code in Windows.

Thanks,
cruz

PS: The R gurus may find this thread annoying cause it is too trivial to them.


On Sun, Feb 8, 2009 at 9:13 AM, Paul Heinrich Dietrich
<paul.heinrich.dietrich@...> wrote:

>
> I've read some of R's literature on Linux, including the R Admin manual, and
> didn't find it very useful, which is probably my own limitation.  But I did
> finally manage to get it working well.  I'm posting this to help others.
> The following worked when installing R 2.8.1 on Ubuntu 8.04 Hardy Heron.
> Here are truly step-by-step instructions for those who don't know Linux
> (like me):
>
> Installation and Initial Set-Up of R for Ubuntu Linux
>
> 1. Open the Bash terminal (Applications > Accessories > Terminal)
> 2. Type these lines to add the security key to access the latest version of
> the R Ubuntu package:
>        user@computer:~$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
>        user@computer:~$ gpg -a --export E2A11821 | sudo apt-key add -
> 3. Use the Bash terminal to open your sources.list file with gedit (text
> editor) for editing:
>        user@computer:~$ sudo gedit /etc/apt/sources.list
> 4. Add this line to the bottom of the sources.list file:
>        deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu hardy/
> 5. Save the file and go back to the Bash terminal.
> 6. Type this to update apt-get's database before you install R:
>        user@computer:~$ sudo apt-get update
> 7. Install R with this command:
>        user@computer:~$ sudo apt-get install r-base
> 8. Go to System > Administration > Synaptic Package Manager, and download
> the build-essential package.
> 9. To use R, simply enter R in the Bash terminal.  To quit, enter q().
>
>
> Additional programs will be needed to install other packages or work with
> other programs:
> 1. Install compilers for C++ and Fortran
>        user@computer:~$ sudo apt-get install g++ gfortran
> 2. Install the developer versions of Blas and Lapack (what are these?)
>        user@computer:~$ apt-get install libblas-dev liblapack-dev
>
>
> Updating Packages in R
> 1. Open the Bash terminal and start R with root permissions
>        user@computer:~$ sudo R
> 2. Type > update.packages()
>
>
> Installing the R Commander GUI
> 1. Open the Bash terminal and type:
>       user@computer:~$ apt-get install r-cran-rcmdr
>
>
> Using the R Commander GUI
> library(Rcmdr)
> ...or once the library is open and Commander has been shut down, type:
> commander()
>
>
> Notes
> It looks like most of R has been put here:
> /etc/R (Rprofile.site is here)
> /usr/lib/R
>
>
> Downloaded Packages seem to go here:
> /usr/local/lib/R/site-library/
> --
> View this message in context: http://www.nabble.com/installing-R-on-Ubuntu-tp10025949p21894865.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Paul Heinrich Dietrich]

I would really like to see a good introduction to Emacs, and will check out that link.  I know that Emacs and ESS are supposed to be the best, and are the most customizable.  The reason I put the R Commander GUI instead of Emacs/ESS is because in my first attempt to get R on Ubuntu Linux, I did successfully get Emacs/ESS working (sadly, I don't remember how exactly), but found it too frustrating.  Again, I'm sure it's the best in the end, but here's what was driving me nuts:

Copy/Paste is not Ctrl-c and Ctrl-v...I figured it out, but don't remember what it is.
Entering a _ automatically creates a <-, and you must enter __ to get _.
There is no "stop" button (hopefully there is one in R Commander, haven't explored yet).
It kept trying to establish a working directory, and was inconsistent in when it would accept what directory.

I was also looking at the JGS GUI.  Online screenshots look incredible, but I didn't go with it because it depends on Java, which is not open-source, and I'm really liking that philosophy, but to each his own.

Thanks for the link, I'm anxious to try to figure out Emacs/ESS. I'll go look at it now.  Cheers.

[Paul Heinrich Dietrich]

Amendment/Question #1:

When I update.packages(), it tells me that rgl fails to update because it can't find X11.  Again, I'm pretty new to Ubuntu, but it looks like X comes with Ubuntu.  I see files under /etc/X11.  Does this mean I need to download x11-common (or x11-apps, or x11-utils, or one of the others?) with the Synaptic Package Manager?  I hesitate on this because it seems like X11 is not a simple add-on package, but something core to Ubuntu.  Any help is appreciated.  Thanks.

[Tom Backer Johnsen]

Dear me.  Is the installation of R under Ubuntu really that complex?  I
have a dual boot machine (Linux / Windows, where I use the latter the
most) and have plans to try R under Linux, but have not done so yet.  Is
it possible to simplify the Linux install procedure to make R more
accessible to novices?

Compare that to Windows.  (1) Download installation program (2) Run
installation program.  That is it.

Tom

Paul Heinrich Dietrich wrote:

> I've read some of R's literature on Linux, including the R Admin manual, and
> didn't find it very useful, which is probably my own limitation.  But I did
> finally manage to get it working well.  I'm posting this to help others.
> The following worked when installing R 2.8.1 on Ubuntu 8.04 Hardy Heron.
> Here are truly step-by-step instructions for those who don't know Linux
> (like me):
>
> Installation and Initial Set-Up of R for Ubuntu Linux
>
> 1. Open the Bash terminal (Applications > Accessories > Terminal)
> 2. Type these lines to add the security key to access the latest version of
> the R Ubuntu package:
> user@computer:~$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
> user@computer:~$ gpg -a --export E2A11821 | sudo apt-key add -
> 3. Use the Bash terminal to open your sources.list file with gedit (text
> editor) for editing:
> user@computer:~$ sudo gedit /etc/apt/sources.list
> 4. Add this line to the bottom of the sources.list file:
> deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu hardy/
> 5. Save the file and go back to the Bash terminal.
> 6. Type this to update apt-get's database before you install R:
> user@computer:~$ sudo apt-get update
> 7. Install R with this command:
> user@computer:~$ sudo apt-get install r-base
> 8. Go to System > Administration > Synaptic Package Manager, and download
> the build-essential package.
> 9. To use R, simply enter R in the Bash terminal.  To quit, enter q().
>
>
> Additional programs will be needed to install other packages or work with
> other programs:
> 1. Install compilers for C++ and Fortran
> user@computer:~$ sudo apt-get install g++ gfortran
> 2. Install the developer versions of Blas and Lapack (what are these?)
> user@computer:~$ apt-get install libblas-dev liblapack-dev
>
>
> Updating Packages in R
> 1. Open the Bash terminal and start R with root permissions
> user@computer:~$ sudo R
> 2. Type > update.packages()
>
>
> Installing the R Commander GUI
> 1. Open the Bash terminal and type:
>        user@computer:~$ apt-get install r-cran-rcmdr
>
>
> Using the R Commander GUI
> library(Rcmdr)
> ...or once the library is open and Commander has been shut down, type:
> commander()
>
>
> Notes
> It looks like most of R has been put here:
> /etc/R (Rprofile.site is here)
> /usr/lib/R
>
>
> Downloaded Packages seem to go here:
> /usr/local/lib/R/site-library/

--
+----------------------------------------------------------------+
| Tom Backer Johnsen, Psychometrics Unit,  Faculty of Psychology |
| University of Bergen, Christies gt. 12, N-5015 Bergen,  NORWAY |
| Tel : [phone]                        Fax : [phone] |
| Email : backer@...    URL : http://www.galton.uib.no/ |
+----------------------------------------------------------------+

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Joseph Magagnoli]

When I use ubuntu linux and R I use komodo edit with an R extension.   Seems
really similar to tinn-R.
http://www.sciviews.org/SciViews-K/index.html

joe

On Sun, Feb 8, 2009 at 8:56 AM, Paul Heinrich Dietrich <
paul.heinrich.dietrich@...> wrote:

>
> Amendment/Question #1:
>
> When I update.packages(), it tells me that rgl fails to update because it
> can't find X11.  Again, I'm pretty new to Ubuntu, but it looks like X comes
> with Ubuntu.  I see files under /etc/X11.  Does this mean I need to
> download
> x11-common (or x11-apps, or x11-utils, or one of the others?) with the
> Synaptic Package Manager?  I hesitate on this because it seems like X11 is
> not a simple add-on package, but something core to Ubuntu.  Any help is
> appreciated.  Thanks.
> --
> View this message in context:
> http://www.nabble.com/installing-R-on-Ubuntu-tp10025949p21899658.html
>  Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Prof Brian Ripley]

On Sun, 8 Feb 2009, Paul Heinrich Dietrich wrote:

>
> I would really like to see a good introduction to Emacs, and will check out
> that link.  I know that Emacs and ESS are supposed to be the best, and are
> the most customizable.  The reason I put the R Commander GUI instead of
> Emacs/ESS is because in my first attempt to get R on Ubuntu Linux, I did
> successfully get Emacs/ESS working (sadly, I don't remember how exactly),
> but found it too frustrating.  Again, I'm sure it's the best in the end, but
> here's what was driving me nuts:
>
> Copy/Paste is not Ctrl-c and Ctrl-v...I figured it out, but don't remember
> what it is.

That's optional -- you can set CUA if you like that (an item on the
Options menu, at least in the Emacs version I looked at).  But on an
X11 interface, selecting copies and right-click pastes. (Beware, your
Windows Manager may also have a separate clipboard.)

> Entering a _ automatically creates a <-, and you must enter __ to get _.

That's optional (and I realy think should be off by default now _ as
an addignment operator is ancient history).  Add

(ess-toggle-underscore nil)

to your .emacs.

> There is no "stop" button (hopefully there is one in R Commander, haven't
> explored yet).

You'll soon find that buttons are slow compared to keystrokes.

> It kept trying to establish a working directory, and was inconsistent in
> when it would accept what directory.

'It' being ESS, I guess,  There is an ess-help list on which to
discuss what you mean there.

> I was also looking at the JGS GUI.  Online screenshots look incredible, but
> I didn't go with it because it depends on Java, which is not open-source,
> and I'm really liking that philosophy, but to each his own.

I presume you mwan JGR.  Lots of Java is Open Source, and I beieve JGR
may run under OpenJDK.

> Thanks for the link, I'm anxious to try to figure out Emacs/ESS. I'll go
> look at it now.  Cheers.


--
Brian D. Ripley,                  ripley@...
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  [phone] (self)
1 South Parks Road,                     [phone] (PA)
Oxford OX1 3TG, UK                Fax:  [phone]

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Dirk Eddelbuettel]

Paul,

Very nice!  Comments below.

On 7 February 2009 at 17:12, Paul Heinrich Dietrich wrote:
|
| I've read some of R's literature on Linux, including the R Admin manual, and
| didn't find it very useful, which is probably my own limitation.  But I did
| finally manage to get it working well.  I'm posting this to help others.
| The following worked when installing R 2.8.1 on Ubuntu 8.04 Hardy Heron.
| Here are truly step-by-step instructions for those who don't know Linux
| (like me):
|
| Installation and Initial Set-Up of R for Ubuntu Linux
|
| 1. Open the Bash terminal (Applications > Accessories > Terminal)
| 2. Type these lines to add the security key to access the latest version of
| the R Ubuntu package:
| user@computer:~$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
| user@computer:~$ gpg -a --export E2A11821 | sudo apt-key add -
| 3. Use the Bash terminal to open your sources.list file with gedit (text
| editor) for editing:
| user@computer:~$ sudo gedit /etc/apt/sources.list
| 4. Add this line to the bottom of the sources.list file:
| deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu hardy/
| 5. Save the file and go back to the Bash terminal.
| 6. Type this to update apt-get's database before you install R:
| user@computer:~$ sudo apt-get update
| 7. Install R with this command:
| user@computer:~$ sudo apt-get install r-base
| 8. Go to System > Administration > Synaptic Package Manager, and download
| the build-essential package.

In 7. you use apt, in 8. you use Synaptic. Why not to both at once:

   $ sudo apt-get install r-base r-base-dev

as 'r-base-dev' depends on build-essential (and a few other things) and gets
you all this and more (see below).

| 9. To use R, simply enter R in the Bash terminal.  To quit, enter q().
|
|
| Additional programs will be needed to install other packages or work with
| other programs:
| 1. Install compilers for C++ and Fortran
| user@computer:~$ sudo apt-get install g++ gfortran
| 2. Install the developer versions of Blas and Lapack (what are these?)
| user@computer:~$ apt-get install libblas-dev liblapack-dev

The modified step 7 above would have done both for you.

| Updating Packages in R
| 1. Open the Bash terminal and start R with root permissions
| user@computer:~$ sudo R
| 2. Type > update.packages()

Yep. I also like 'sudo apt-get install littler' and I then copy or link
install.r to /usr/local/bin and just use

          $ sudo install.r foo far fie foo

which would then install the (hyopthetical) packages foo, far, fie and foo
from CRAN.

| Installing the R Commander GUI
| 1. Open the Bash terminal and type:
|        user@computer:~$ apt-get install r-cran-rcmdr
|
|
| Using the R Commander GUI
| library(Rcmdr)
| ...or once the library is open and Commander has been shut down, type:
| commander()
|
|
| Notes
| It looks like most of R has been put here:
| /etc/R (Rprofile.site is here)
| /usr/lib/R

Also /usr/share/R for architecture-independent files.

| Downloaded Packages seem to go here:
| /usr/local/lib/R/site-library/

Slightly more complex:  
 -- 'base R' and recommended packages are in /usr/lib/R/library/
 -- Debian-packaged R packages are in   /usr/lib/R/site-library/
 -- packages installed by you / R are in /usr/local/lib/R/site-library/


You did a great job documenting all things.  A 'fresh set of eyese' review
helps everybody. I suggest you get in touch with the Debian / Ubuntu
maintainers for CRAN (see the CRAN README in bin/linux/{ubuntu,debian} about
making this a more visible document.

Also, for your other emails:   'sudo apt-get install ess'  will just get you
a working ESS.

Dirk

| --
| View this message in context: http://www.nabble.com/installing-R-on-Ubuntu-tp10025949p21894862.html
| Sent from the R help mailing list archive at Nabble.com.
|
| ______________________________________________
| R-help@... mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| and provide commented, minimal, self-contained, reproducible code.

--
Three out of two people have difficulties with fractions.

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Dirk Eddelbuettel]

On 8 February 2009 at 20:36, Tom Backer Johnsen wrote:
| Dear me.  Is the installation of R under Ubuntu really that complex?  I
| have a dual boot machine (Linux / Windows, where I use the latter the
| most) and have plans to try R under Linux, but have not done so yet.  Is
| it possible to simplify the Linux install procedure to make R more
| accessible to novices?

Yes. 'sudo apt-get install r-base ess ggobi' and you have working R, ESS and
Ggobi.  Start Emacs, type 'M-x R' and you have an R session inside Emacs.

Is that really easier to accomplish in Windows?

Dirk

|
| Compare that to Windows.  (1) Download installation program (2) Run
| installation program.  That is it.
|
| Tom
|
| Paul Heinrich Dietrich wrote:
| > I've read some of R's literature on Linux, including the R Admin manual, and
| > didn't find it very useful, which is probably my own limitation.  But I did
| > finally manage to get it working well.  I'm posting this to help others.
| > The following worked when installing R 2.8.1 on Ubuntu 8.04 Hardy Heron.
| > Here are truly step-by-step instructions for those who don't know Linux
| > (like me):
| >
| > Installation and Initial Set-Up of R for Ubuntu Linux
| >
| > 1. Open the Bash terminal (Applications > Accessories > Terminal)
| > 2. Type these lines to add the security key to access the latest version of
| > the R Ubuntu package:
| > user@computer:~$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
| > user@computer:~$ gpg -a --export E2A11821 | sudo apt-key add -
| > 3. Use the Bash terminal to open your sources.list file with gedit (text
| > editor) for editing:
| > user@computer:~$ sudo gedit /etc/apt/sources.list
| > 4. Add this line to the bottom of the sources.list file:
| > deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu hardy/
| > 5. Save the file and go back to the Bash terminal.
| > 6. Type this to update apt-get's database before you install R:
| > user@computer:~$ sudo apt-get update
| > 7. Install R with this command:
| > user@computer:~$ sudo apt-get install r-base
| > 8. Go to System > Administration > Synaptic Package Manager, and download
| > the build-essential package.
| > 9. To use R, simply enter R in the Bash terminal.  To quit, enter q().
| >
| >
| > Additional programs will be needed to install other packages or work with
| > other programs:
| > 1. Install compilers for C++ and Fortran
| > user@computer:~$ sudo apt-get install g++ gfortran
| > 2. Install the developer versions of Blas and Lapack (what are these?)
| > user@computer:~$ apt-get install libblas-dev liblapack-dev
| >
| >
| > Updating Packages in R
| > 1. Open the Bash terminal and start R with root permissions
| > user@computer:~$ sudo R
| > 2. Type > update.packages()
| >
| >
| > Installing the R Commander GUI
| > 1. Open the Bash terminal and type:
| >        user@computer:~$ apt-get install r-cran-rcmdr
| >
| >
| > Using the R Commander GUI
| > library(Rcmdr)
| > ...or once the library is open and Commander has been shut down, type:
| > commander()
| >
| >
| > Notes
| > It looks like most of R has been put here:
| > /etc/R (Rprofile.site is here)
| > /usr/lib/R
| >
| >
| > Downloaded Packages seem to go here:
| > /usr/local/lib/R/site-library/
|
|
| --
| +----------------------------------------------------------------+
| | Tom Backer Johnsen, Psychometrics Unit,  Faculty of Psychology |
| | University of Bergen, Christies gt. 12, N-5015 Bergen,  NORWAY |
| | Tel : [phone]                        Fax : [phone] |
| | Email : backer@...    URL : http://www.galton.uib.no/ |
| +----------------------------------------------------------------+
|
| ______________________________________________
| R-help@... mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| and provide commented, minimal, self-contained, reproducible code.

--
Three out of two people have difficulties with fractions.

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Dirk Eddelbuettel]

On 8 February 2009 at 06:56, Paul Heinrich Dietrich wrote:
|
| Amendment/Question #1:
|
| When I update.packages(), it tells me that rgl fails to update because it
| can't find X11.  Again, I'm pretty new to Ubuntu, but it looks like X comes
| with Ubuntu.  I see files under /etc/X11.  Does this mean I need to download
| x11-common (or x11-apps, or x11-utils, or one of the others?) with the
| Synaptic Package Manager?  I hesitate on this because it seems like X11 is
| not a simple add-on package, but something core to Ubuntu.  Any help is
| appreciated.  Thanks.

What is wrong with

     $ sudo apt-get install r-cran-rgl

By the way, you may want to subscribe to the r-sig-finance list and continue
the discussion there.

Dirk

--
Three out of two people have difficulties with fractions.

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[John Fox-6]

Dear Paul,

I haven't read everything in this thread, but have a couple of comments
relative to using the R Commander:

> -----Original Message-----
> From: r-help-bounces@... [mailto:r-help-bounces@...]
On
> Behalf Of Paul Heinrich Dietrich
> Sent: February-08-09 9:08 AM
> To: r-help@...
> Subject: Re: [R] installing R on Ubuntu
>
>
> I would really like to see a good introduction to Emacs, and will check
out
> that link.  I know that Emacs and ESS are supposed to be the best, and are
> the most customizable.  The reason I put the R Commander GUI instead of
> Emacs/ESS is because in my first attempt to get R on Ubuntu Linux, I did
> successfully get Emacs/ESS working (sadly, I don't remember how exactly),
> but found it too frustrating.  Again, I'm sure it's the best in the end,
but
> here's what was driving me nuts:

The R Commander isn't meant to be a serious programming editor, but rather a
basic-statistics GUI. I think that you'll find it disappointing as an
editor.

>
> Copy/Paste is not Ctrl-c and Ctrl-v...I figured it out, but don't remember
> what it is.
> Entering a _ automatically creates a <-, and you must enter __ to get _.
> There is no "stop" button (hopefully there is one in R Commander, haven't
> explored yet).

There is no "stop" button in the Rcmdr; having one isn't be a bad idea, but
I'm not sure how I could implement it in a platform-independent manner (or
even, frankly, in a platform-dependent manner). Perhaps someone has a
suggestion for doing that.

Regards,
 John

> It kept trying to establish a working directory, and was inconsistent in
> when it would accept what directory.
>
> I was also looking at the JGS GUI.  Online screenshots look incredible,
but
> I didn't go with it because it depends on Java, which is not open-source,
> and I'm really liking that philosophy, but to each his own.
>
> Thanks for the link, I'm anxious to try to figure out Emacs/ESS. I'll go
> look at it now.  Cheers.
> --
> View this message in context:
http://www.nabble.com/installing-R-on-Ubuntu-
> tp10025949p21899227.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Paul Heinrich Dietrich]

Hi Dirk,
Sorry, I'm not trying to drag out the installation process here, but just trying to get it to work right in Linux.

Dirk Eddelbuettel wrote:

What is wrong with

     $ sudo apt-get install r-cran-rgl

 I tried this suggestion, and here was the terminal output:

r-cran-rgl is already the newest version.
r-cran-rgl set to manually installed.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

So, just to double-check, I went into R as sudo, entered update.packages(), and got this:

rgl :
 Version 0.76 installed in /usr/lib/R/site-library
 Version 0.82 available at http://streaming.stat.iastate.edu/CRAN

...and later this...

* Installing *source* package 'rgl' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed
checking for libpng-config... no
checking libpng... checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking png.h usability... no
checking png.h presence... no
checking for png.h... no
checking for png_read_update_info in -lpng... no
configure: libpng header and lib found
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package 'rgl'
** Removing '/usr/lib/R/site-library/rgl'
** Restoring previous '/usr/lib/R/site-library/rgl'

The downloaded packages are in
        /tmp/RtmpIW4d37/downloaded_packages
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package 'rgl' had non-zero exit status

[Paul Heinrich Dietrich]

I'm definitely out of my league here, but I think that if someone only enters that code in an Ubuntu system, then they will have only the latest version of R in Ubuntu, which at this time I think is 2.6.2, instead of 2.8.1, and Ubuntu only "maintains" a handful of packages, instead of 1600+ right now on CRAN.  If you want to get the latest R in Ubuntu and download any current package, it seems like you have to follow a method like I've tried to piece together.  I hope I'm wrong here.  Cheers.

Dirk Eddelbuettel wrote:

On 8 February 2009 at 20:36, Tom Backer Johnsen wrote:
| Dear me.  Is the installation of R under Ubuntu really that complex?  I
| have a dual boot machine (Linux / Windows, where I use the latter the
| most) and have plans to try R under Linux, but have not done so yet.  Is
| it possible to simplify the Linux install procedure to make R more
| accessible to novices?

Yes. 'sudo apt-get install r-base ess ggobi' and you have working R, ESS and
Ggobi.  Start Emacs, type 'M-x R' and you have an R session inside Emacs.

Is that really easier to accomplish in Windows?

[Paul Heinrich Dietrich]

Thanks John, I appreciate it.  It sounds like Emacs is the way to go for an editor.

John Fox-6 wrote:

Dear Paul,

I haven't read everything in this thread, but have a couple of comments
relative to using the R Commander:

...

The R Commander isn't meant to be a serious programming editor, but rather a
basic-statistics GUI. I think that you'll find it disappointing as an
editor.

...

There is no "stop" button in the Rcmdr; having one isn't be a bad idea, but
I'm not sure how I could implement it in a platform-independent manner (or
even, frankly, in a platform-dependent manner). Perhaps someone has a
suggestion for doing that.

[Paul Heinrich Dietrich]

Hi Brian,
I'm sure buttons are slow compared to keystrokes, but how do you stop R with a keystroke, similar to the R interface in Windows?  Thanks.

Sorry about the JGS-JGR goof...just coming across too many new things right now.  JGR it is.

[Paul Heinrich Dietrich]

Hi Dirk,
Many thanks for your insight.

Dirk Eddelbuettel wrote:

Paul,

Very nice!  Comments below.

On 7 February 2009 at 17:12, Paul Heinrich Dietrich wrote:
|
| I've read some of R's literature on Linux, including the R Admin manual, and
| didn't find it very useful, which is probably my own limitation.  But I did
| finally manage to get it working well.  I'm posting this to help others.
| The following worked when installing R 2.8.1 on Ubuntu 8.04 Hardy Heron.
| Here are truly step-by-step instructions for those who don't know Linux
| (like me):
|
| Installation and Initial Set-Up of R for Ubuntu Linux
|
| 1. Open the Bash terminal (Applications > Accessories > Terminal)
| 2. Type these lines to add the security key to access the latest version of
| the R Ubuntu package:
| user@computer:~$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
| user@computer:~$ gpg -a --export E2A11821 | sudo apt-key add -
| 3. Use the Bash terminal to open your sources.list file with gedit (text
| editor) for editing:
| user@computer:~$ sudo gedit /etc/apt/sources.list
| 4. Add this line to the bottom of the sources.list file:
| deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu hardy/
| 5. Save the file and go back to the Bash terminal.
| 6. Type this to update apt-get's database before you install R:
| user@computer:~$ sudo apt-get update
| 7. Install R with this command:
| user@computer:~$ sudo apt-get install r-base
| 8. Go to System > Administration > Synaptic Package Manager, and download
| the build-essential package.

In 7. you use apt, in 8. you use Synaptic. Why not to both at once:

   $ sudo apt-get install r-base r-base-dev

as 'r-base-dev' depends on build-essential (and a few other things) and gets
you all this and more (see below).

| 9. To use R, simply enter R in the Bash terminal.  To quit, enter q().
|
|
| Additional programs will be needed to install other packages or work with
| other programs:
| 1. Install compilers for C++ and Fortran
| user@computer:~$ sudo apt-get install g++ gfortran
| 2. Install the developer versions of Blas and Lapack (what are these?)
| user@computer:~$ apt-get install libblas-dev liblapack-dev

The modified step 7 above would have done both for you.

| Updating Packages in R
| 1. Open the Bash terminal and start R with root permissions
| user@computer:~$ sudo R
| 2. Type > update.packages()

Yep. I also like 'sudo apt-get install littler' and I then copy or link
install.r to /usr/local/bin and just use

          $ sudo install.r foo far fie foo

which would then install the (hyopthetical) packages foo, far, fie and foo
from CRAN.

| Installing the R Commander GUI
| 1. Open the Bash terminal and type:
|        user@computer:~$ apt-get install r-cran-rcmdr
|
|
| Using the R Commander GUI
| library(Rcmdr)
| ...or once the library is open and Commander has been shut down, type:
| commander()
|
|
| Notes
| It looks like most of R has been put here:
| /etc/R (Rprofile.site is here)
| /usr/lib/R

Also /usr/share/R for architecture-independent files.

| Downloaded Packages seem to go here:
| /usr/local/lib/R/site-library/

Slightly more complex:  
 -- 'base R' and recommended packages are in /usr/lib/R/library/
 -- Debian-packaged R packages are in   /usr/lib/R/site-library/
 -- packages installed by you / R are in /usr/local/lib/R/site-library/


You did a great job documenting all things.  A 'fresh set of eyese' review
helps everybody. I suggest you get in touch with the Debian / Ubuntu
maintainers for CRAN (see the CRAN README in bin/linux/{ubuntu,debian} about
making this a more visible document.

Also, for your other emails:   'sudo apt-get install ess'  will just get you
a working ESS.

Dirk

| --
| View this message in context: http://www.nabble.com/installing-R-on-Ubuntu-tp10025949p21894862.html
| Sent from the R help mailing list archive at Nabble.com.
|
| ______________________________________________
| [e-mail] mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| and provide commented, minimal, self-contained, reproducible code.

--
Three out of two people have difficulties with fractions.

______________________________________________
[e-mail] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Tom Backer Johnsen]

Dirk Eddelbuettel wrote:

> On 8 February 2009 at 20:36, Tom Backer Johnsen wrote:
> | Dear me.  Is the installation of R under Ubuntu really that complex?  I
> | have a dual boot machine (Linux / Windows, where I use the latter the
> | most) and have plans to try R under Linux, but have not done so yet.  Is
> | it possible to simplify the Linux install procedure to make R more
> | accessible to novices?
>
> Yes. 'sudo apt-get install r-base ess ggobi' and you have working R, ESS and
> Ggobi.  Start Emacs, type 'M-x R' and you have an R session inside Emacs.
>
> Is that really easier to accomplish in Windows?

No.  If it is that simple to install R under a Debian vaiant of Linux,
it definitely is easier.  On the other hand, using Emacs is not (as far
as I know) the thing for novices.  What I would prefer is something that
is as simple to use as the Windows (or even better, the Mac interface)
for R.

Tom

>
> Dirk
>
> |
> | Compare that to Windows.  (1) Download installation program (2) Run
> | installation program.  That is it.
> |
> | Tom
> |
> | Paul Heinrich Dietrich wrote:
> | > I've read some of R's literature on Linux, including the R Admin manual, and
> | > didn't find it very useful, which is probably my own limitation.  But I did
> | > finally manage to get it working well.  I'm posting this to help others.
> | > The following worked when installing R 2.8.1 on Ubuntu 8.04 Hardy Heron.
> | > Here are truly step-by-step instructions for those who don't know Linux
> | > (like me):
> | >
> | > Installation and Initial Set-Up of R for Ubuntu Linux
> | >
> | > 1. Open the Bash terminal (Applications > Accessories > Terminal)
> | > 2. Type these lines to add the security key to access the latest version of
> | > the R Ubuntu package:
> | > user@computer:~$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
> | > user@computer:~$ gpg -a --export E2A11821 | sudo apt-key add -
> | > 3. Use the Bash terminal to open your sources.list file with gedit (text
> | > editor) for editing:
> | > user@computer:~$ sudo gedit /etc/apt/sources.list
> | > 4. Add this line to the bottom of the sources.list file:
> | > deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu hardy/
> | > 5. Save the file and go back to the Bash terminal.
> | > 6. Type this to update apt-get's database before you install R:
> | > user@computer:~$ sudo apt-get update
> | > 7. Install R with this command:
> | > user@computer:~$ sudo apt-get install r-base
> | > 8. Go to System > Administration > Synaptic Package Manager, and download
> | > the build-essential package.
> | > 9. To use R, simply enter R in the Bash terminal.  To quit, enter q().
> | >
> | >
> | > Additional programs will be needed to install other packages or work with
> | > other programs:
> | > 1. Install compilers for C++ and Fortran
> | > user@computer:~$ sudo apt-get install g++ gfortran
> | > 2. Install the developer versions of Blas and Lapack (what are these?)
> | > user@computer:~$ apt-get install libblas-dev liblapack-dev
> | >
> | >
> | > Updating Packages in R
> | > 1. Open the Bash terminal and start R with root permissions
> | > user@computer:~$ sudo R
> | > 2. Type > update.packages()
> | >
> | >
> | > Installing the R Commander GUI
> | > 1. Open the Bash terminal and type:
> | >        user@computer:~$ apt-get install r-cran-rcmdr
> | >
> | >
> | > Using the R Commander GUI
> | > library(Rcmdr)
> | > ...or once the library is open and Commander has been shut down, type:
> | > commander()
> | >
> | >
> | > Notes
> | > It looks like most of R has been put here:
> | > /etc/R (Rprofile.site is here)
> | > /usr/lib/R
> | >
> | >
> | > Downloaded Packages seem to go here:
> | > /usr/local/lib/R/site-library/
> |
> |
> | --
> | +----------------------------------------------------------------+
> | | Tom Backer Johnsen, Psychometrics Unit,  Faculty of Psychology |
> | | University of Bergen, Christies gt. 12, N-5015 Bergen,  NORWAY |
> | | Tel : [phone]                        Fax : [phone] |
> | | Email : backer@...    URL : http://www.galton.uib.no/ |
> | +----------------------------------------------------------------+
> |
> | ______________________________________________
> | R-help@... mailing list
> | https://stat.ethz.ch/mailman/listinfo/r-help
> | PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> | and provide commented, minimal, self-contained, reproducible code.
>

--
+----------------------------------------------------------------+
| Tom Backer Johnsen, Psychometrics Unit,  Faculty of Psychology |
| University of Bergen, Christies gt. 12, N-5015 Bergen,  NORWAY |
| Tel : [phone]                        Fax : [phone] |
| Email : backer@...    URL : http://www.galton.uib.no/ |
+----------------------------------------------------------------+

______________________________________________
R-help@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.