About R-Project

satimis · 08-07-2010, 07:39 AM

Just finished installing R on Ubuntu 10.04, running on a VM, download following packages on repo;

r-base
littler
r-cran-plotrix
r-cran-qtl
r-cran-rggobi

But I could not get R started. r is on /usr/bin/r

On console evoking it just hanging there. Any additional packages I need to install? Thanks

B.R.
satimis

amani · 08-07-2010, 09:38 AM

Install more of R (via synaptic)

#sudo apt-get check

#R

>library(Rcmdr)

'>' is the R prompt

amani · 08-07-2010, 09:41 AM

Also what do you get from

#sudo R --verbose

satimis · 08-07-2010, 10:33 AM

Quote:

Originally Posted by amani

Also what do you get from

#sudo R --verbose

Hi amani,

I got it. I should use R (capital letter) NOT r

$ R

Code:

R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Which command shall I run to exit R rather than closing the terminal? exit/quit didn't work. Thanks

Edit:

I found it on the printout

> q()
Save workspace image? [y/n/c]: n

B.R.
satimis

knudfl · 08-07-2010, 10:41 AM

Ubuntu 10.04 Lucid : ls -tl /var/lib/dpkg/info/ | grep r-base
→ → r-base r-base-core

which R
The reply is /usr/bin/R

May be you did the command 'r' insted of 'R' ?
( I have no errors. R displays the usual text and the prompt ( > ))
.....

satimis · 08-07-2010, 10:45 AM

Quote:

Originally Posted by amani

Install more of R (via synaptic)

#sudo apt-get check

#R

>library(Rcmdr)

'>' is the R prompt

Hi amani,

$ sudo apt-get check

$ R
....
....

> library(Rcmdr)

Code:

Error in library(Rcmdr) : there is no package called 'Rcmdr'

What is the name of the package?

B.R.
satimis

satimis · 08-07-2010, 11:01 AM

Quote:

Originally Posted by knudfl

Ubuntu 10.04 Lucid : ls -tl /var/lib/dpkg/info/ | grep r-base
→ → r-base r-base-core

Hi,

$ ls -tl /var/lib/dpkg/info/ | grep r-base

Code:

-rw-r--r-- 1 root root   1399 2010-08-07 18:47 r-base-html.list
-rw-r--r-- 1 root root    166 2010-08-07 18:47 r-base.list
-rw-r--r-- 1 root root    123 2010-08-07 18:32 r-base-dev.list
-rw-r--r-- 1 root root  42701 2010-08-07 18:32 r-base-core.list
-rw-r--r-- 1 root root  53339 2010-01-19 05:38 r-base-core.md5sums
-rw-r--r-- 1 root root    118 2010-01-19 05:38 r-base-core.conffiles
-rwxr-xr-x 1 root root   2453 2010-01-19 05:38 r-base-core.postinst
-rwxr-xr-x 1 root root    160 2010-01-19 05:38 r-base-core.postrm
-rwxr-xr-x 1 root root    667 2010-01-19 05:38 r-base-core.preinst
-rwxr-xr-x 1 root root    689 2010-01-19 05:38 r-base-core.prerm
-rw-r--r-- 1 root root     30 2010-01-19 05:27 r-base-core.shlibs
-rw-r--r-- 1 root root     63 2010-01-18 23:31 r-base-dev.md5sums
-rw-r--r-- 1 root root   1075 2010-01-18 23:31 r-base-html.md5sums
-rw-r--r-- 1 root root    209 2010-01-18 23:31 r-base.md5sums
-rwxr-xr-x 1 root root    425 2010-01-18 23:31 r-base-dev.preinst

Whether I have to install all of them?

Quote:

which R
The reply is /usr/bin/R

May be you did the command 'r' insted of 'R' ?
( I have no errors. R displays the usual text and the prompt ( > ))
.....

Yes I ran

$ which r
/usr/bin/r

because all packages start with r NOT R. Later I found it.

B.R.
satimis

knudfl · 08-07-2010, 11:21 AM

Quote:

What is the name of the package ? ..... ( library(Rcmdr) )

The package providing : /usr/lib/R/site-library/Rcmdr/R/Rcmdr
.. is : r-cran-rcmdr
http://packages.ubuntu.com/search?se...keywords=Rcmdr

P.S. : Sorry , 'dpkg --get-selections | grep r-base' is a more correct
command, to show 'r-base'.
About 'ls -tl /var/lib/dpkg/info/ ' : Mostly used this way ...
ls -tl /var/lib/dpkg/info/ | grep list > last-packages.txt
> 1) to save a text file, 2) to avoid all the pre and post install information.
.....
This is the spectacular one :
dpkg-query -W -f 'section:${section}\t${package}\t${version}\t-\t${architecture}\t-\t${description}\n' | grep r-base

knudfl · 08-07-2010, 11:56 AM

PPS : the command '/usr/bin/r' is from package 'littler'

http://packages.ubuntu.com/search?se...Fusr%2Fbin%2Fr

Description : http://packages.ubuntu.com/karmic/littler

..

satimis · 08-07-2010, 11:37 PM

Quote:

Originally Posted by knudfl

The package providing : /usr/lib/R/site-library/Rcmdr/R/Rcmdr
.. is : r-cran-rcmdr
http://packages.ubuntu.com/search?se...keywords=Rcmdr

- snip -

Hi,

I can't install r-cran-rcmdr on R;

> install.packages("r-cran-rcmdr", dependencies=TRUE)

Code:

Warning in install.packages("r-cran-rcmdr", dependencies = TRUE) :
  argument 'lib' is missing: using '/home/satimisub04dk01/R/x86_64-pc-linux-gnu-library/2.10'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning: unable to access index for repository http://mirrors.geoexpat.com/cran/src/contrib
Warning messages:
1: In open.connection(con, "r") : unable to resolve 'cran.r-project.org'
2: In getDependencies(pkgs, dependencies, available, lib) :
  package ‘r-cran-rcmdr’ is not available

I can install it on Ubuntu repo;

$ sudo aptitude install r-cran-rcmdr

Code:

.....
Processing triggers for python-support ...
Setting up r-cran-abind (1.1.0-4) ...
Setting up r-cran-car (1.2-16-2) ...
Setting up r-cran-colorspace (1.0.1-1) ...
Setting up r-cran-vr (7.3-0-1) ...
Setting up r-cran-effects (2.0.10-1) ...
Setting up r-cran-zoo (1.6-2-1) ...
Setting up r-cran-lmtest (0.9.26-1) ...
Setting up r-cran-mvtnorm (0.9-8-1) ...
Setting up r-cran-multcomp (1.1-4-1) ...
Setting up r-cran-relimp (1.0-1-2) ...
Setting up r-cran-rgl (0.89-1) ...
Setting up r-cran-sm (2.2-3-2) ...
Setting up r-cran-sandwich (2.2-5-1) ...
Setting up r-cran-strucchange (1.3-7-2) ...
Setting up r-cran-rcmdr (1.5-4-1ubuntu0.1) ...
Reading package lists... Done             
Building dependency tree       
Reading state information... Done
Reading extended state information      
Initializing package states... Done
Writing extended state information... Done

Above packages installed as well.

Others noted and thanks

B.R.
satimis

satimis · 08-07-2010, 11:41 PM

Quote:

Originally Posted by knudfl

PPS : the command '/usr/bin/r' is from package 'littler'

http://packages.ubuntu.com/search?se...Fusr%2Fbin%2Fr

Description : http://packages.ubuntu.com/karmic/littler

..

I can't start r

On terminal
$ r

There is no response just hanging there. Whether it is waiting for input? What shall I do?

TIA

B.R.
satimis

knudfl · 08-08-2010, 02:39 AM

Lots of commands are not "starting" or doing anything without an argument.
( 'r' is not 'R' , and works different.)

Dirk Eddelbuettel littler: http://dirk.eddelbuettel.com/code/littler.html

The r manual : man r

And you can type : r --help
.. and read that the command : 'r --usage' will display more information :
Quote: "More documentation is provided in the 'r' manual page and via
the tests directory in the sources" → → littler_0.1.3.orig.tar.gz
..

amani · 08-09-2010, 10:32 AM

To install packages use synaptic or

from within R

#sudo R

>install.packages()

After this everything will be on GUIs

knudfl · 08-11-2010, 07:56 AM

Thank you, @ amani. ( There is no "Thanks" button in this forum.)

1) 'sudo R' , 2) install.packages()
.. and the tcl-tk GUI will open and show all available packages.

@ satimis, suggest :
Report this thread to be moved to e.g. the 'Software Forum'.
( The 'General Forum' is for things not related to Linux, *nix.)
..

satimis · 08-11-2010, 09:15 AM

Quote:

Originally Posted by knudfl

PPS : the command '/usr/bin/r' is from package 'littler'

http://packages.ubuntu.com/search?se...Fusr%2Fbin%2Fr

Description : http://packages.ubuntu.com/karmic/littler

..

Hi knudfl,

Thanks for your advice and links

B.R.
satimis