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Updating R for Linux

5 messages · Dennis Fisher, Michael Rutter, Dirk Eddelbuettel +1 more

Original
Dennis Fisher
# 
Colleagues,

Please forgive my ignorance of this topic.  I am experienced with the  
installation/use of R in OSX and Windows, much less so with Linux.

I just created a virtual machine of Ubuntu 9.0.4.  Using the Synaptic  
Package Manager, I installed R 2.8.1.  I would like to obtain 2.9.x  
and I am having trouble doing so using the tools available within  
Ubuntu.

I tried
	apt-get install r-base
The system replied that the newest version was already installed and  
no changes were made.

I also added
	dev http://cran.cnr.berkeley.edu/bin/linux/debian etch-cran
to
	/etc/apt/sources.list
Running apt-get install r-base again yielded no response.

Can anyone advise on the simplest means to update to 2.9.x.  I need  
only the basic packages, nothing special.  Thanks in advance.

Dennis

Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
Michael Rutter
# 
Dennis,

Detailed instructions for adding the Ubuntu repositories can be found here:

http://cran.r-project.org/bin/linux/ubuntu/

I think you need to make this change:

dev http://cran.cnr.berkeley.edu/bin/linux/ubuntu jaunty/

You will also should install secure apt key as described in the 
instructions.

Michael
Dennis Fisher wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
On 23 September 2009 at 08:17, Dennis Fisher wrote:

        
| Colleagues,
| 
| Please forgive my ignorance of this topic.  I am experienced with the  
| installation/use of R in OSX and Windows, much less so with Linux.

Welcome!  We're here to help. 

| I just created a virtual machine of Ubuntu 9.0.4.  Using the Synaptic  
| Package Manager, I installed R 2.8.1.  I would like to obtain 2.9.x  
| and I am having trouble doing so using the tools available within  
| Ubuntu.
| 
| I tried
| 	apt-get install r-base
| The system replied that the newest version was already installed and  
| no changes were made.

Right.  But you want

	apt-get update			# to refresh information
	apt-get dist-upgrade		# to upgrade to newer versions
					# incl. possible dependencies

after you have done this:

| I also added
| 	dev http://cran.cnr.berkeley.edu/bin/linux/debian etch-cran

Wrong repo.  

You copied this from the _Debian_ README but there is also one for _Ubuntu_
in the neighboring directory (ie $CRAN/bin/linux/ubuntu/). Use that instead.

| to
| 	/etc/apt/sources.list
| Running apt-get install r-base again yielded no response.

Very close.  

| Can anyone advise on the simplest means to update to 2.9.x.  I need  
| only the basic packages, nothing special.  Thanks in advance.

The above will get you fresh and shiny R 2.9.2 packages courtesy of Vincent
and Michael (for the Ubuntu port).  Debian via CRAN works thanks to Johannes,
and yours truly looks after things in Debian itself which provides the basis
for these so-called 'ports'.

Keep posting with questions, you're very close.

Dirk

| 
| Dennis
| 
| Dennis Fisher MD
| P < (The "P Less Than" Company)
| Phone: 1-866-PLessThan (1-866-753-7784)
| Fax: 1-415-564-2220
| www.PLessThan.com
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Paul Leo
    

    

      
      #
    

  


  

      
I don't know if this will help you,  I run the current version of R
which is installed via Synaptic as described below.  I also install the
development version and run the two simultaneously. There is some
advantage to this is you want to do bioinformatics with R and
bioconductor...so I figure some may be interested

The most recent version of R can be obtained from the subversion
library . These are the command on the terminal window is you want to
install :

I will assume you want to make downloads to a directory
/media/Bioinform-D/Research/R_latest_install
and install R2.10 in 
/home/pleo/R_latest

###################as follows in a terminal window ###################
svn checkout https://svn.r-project.org/R/trunk/ /media/Bioinform-D/Research/R_latest_install

cd /media/Bioinform-D/Research/R_latest_install
## get recommed packages
./tools/rsync-recommended 

################ build it!

cd /home/pleo/R_latest
/media/Bioinform-D/Research/R_latest_install/configure --prefix=/home/pleo/R_latest
##### This is the only tricky bit; but you only need to do this once. The above command will get lots of info on required packages 
##### look for  "any no's"
##### you will probably need tcl8.5-dev , tk8.5.dev , tex , gfortran and gcc compilers redo the above command and see if you fixed
##### the configure error, note some "nos" are ok, use common sense , even with some "no"s it with make an excutable in most cases
make 
make check
### a very few tests may fail, don't worry about those !


##### optional:
make vignettes
## now modify /home/pleo/.emacs to set exec path i.e add line: (setq inferior-R-program-name "/home/pleo/R_latest/bin/R") 
          
make dvi
make pdf
make info

your done , you can use the R2.9.2 AND R.10 at the same time if needed.
All this is from the R admin pdf avaliable from CRAN
############################## 
Note if you want to stick to the current version of R- use as Dirk suggested as it will make updates easier. 
PS I do this on ubuntu 8.1 not that that sound make a difference ..

Cheers
PAul

-----Original Message-----
From: Dirk Eddelbuettel <edd at debian.org>
To: Dennis Fisher <fisher at plessthan.com>
Cc: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] Updating R for Linux
Date: Wed, 23 Sep 2009 10:39:08 -0500

        
On 23 September 2009 at 08:17, Dennis Fisher wrote:

        
| Colleagues,
| 
| Please forgive my ignorance of this topic.  I am experienced with the  
| installation/use of R in OSX and Windows, much less so with Linux.

Welcome!  We're here to help. 

| I just created a virtual machine of Ubuntu 9.0.4.  Using the Synaptic  
| Package Manager, I installed R 2.8.1.  I would like to obtain 2.9.x  
| and I am having trouble doing so using the tools available within  
| Ubuntu.
| 
| I tried
| 	apt-get install r-base
| The system replied that the newest version was already installed and  
| no changes were made.

Right.  But you want

	apt-get update			# to refresh information
	apt-get dist-upgrade		# to upgrade to newer versions
					# incl. possible dependencies

after you have done this:

| I also added
| 	dev http://cran.cnr.berkeley.edu/bin/linux/debian etch-cran

Wrong repo.  

You copied this from the _Debian_ README but there is also one for _Ubuntu_
in the neighboring directory (ie $CRAN/bin/linux/ubuntu/). Use that instead.

| to
| 	/etc/apt/sources.list
| Running apt-get install r-base again yielded no response.

Very close.  

| Can anyone advise on the simplest means to update to 2.9.x.  I need  
| only the basic packages, nothing special.  Thanks in advance.

The above will get you fresh and shiny R 2.9.2 packages courtesy of Vincent
and Michael (for the Ubuntu port).  Debian via CRAN works thanks to Johannes,
and yours truly looks after things in Debian itself which provides the basis
for these so-called 'ports'.

Keep posting with questions, you're very close.

Dirk

| 
| Dennis
| 
| Dennis Fisher MD
| P < (The "P Less Than" Company)
| Phone: 1-866-PLessThan (1-866-753-7784)
| Fax: 1-415-564-2220
| www.PLessThan.com
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

  
  


  


      

    

    

      
      

        


  

        

      Paul Leo
    

    

      
      #
    

  


  

      
Hi Dennis,

Just to clarify; I took your post as an opportunity to answer a
(related) question I have seen one or twice - about running the current
AND development versions of R on the same machine.

You should NOT do this unless you really need  R2.10 (and BioC 2.5).

 The HIGHLY prefered method of installing ANY  software on linux is  via
a packet manager like apt or synaptic so all the dependencies can be
taken care easily and updates are then easy to do.


Cheers 
Paul

Email: p.leo at uq.edu.au   Web: http://www.di.uq.edu.au


-----Original Message-----
From: Paul Leo <p.leo at uq.edu.au>
To: Dirk Eddelbuettel <edd at debian.org>
Cc: Dennis Fisher <fisher at plessthan.com>, r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] Updating R for Linux
Date: Thu, 24 Sep 2009 10:12:33 +1000

I don't know if this will help you,  I run the current version of R
which is installed via Synaptic as described below.  I also install the
development version and run the two simultaneously. There is some
advantage to this is you want to do bioinformatics with R and
bioconductor...so I figure some may be interested

The most recent version of R can be obtained from the subversion
library . These are the command on the terminal window is you want to
install :

I will assume you want to make downloads to a directory
/media/Bioinform-D/Research/R_latest_install
and install R2.10 in 
/home/pleo/R_latest

###################as follows in a terminal window ###################
svn checkout https://svn.r-project.org/R/trunk/ /media/Bioinform-D/Research/R_latest_install

cd /media/Bioinform-D/Research/R_latest_install
## get recommed packages
./tools/rsync-recommended 

################ build it!

cd /home/pleo/R_latest
/media/Bioinform-D/Research/R_latest_install/configure --prefix=/home/pleo/R_latest
##### This is the only tricky bit; but you only need to do this once. The above command will get lots of info on required packages 
##### look for  "any no's"
##### you will probably need tcl8.5-dev , tk8.5.dev , tex , gfortran and gcc compilers redo the above command and see if you fixed
##### the configure error, note some "nos" are ok, use common sense , even with some "no"s it with make an excutable in most cases
make 
make check
### a very few tests may fail, don't worry about those !


##### optional:
make vignettes
## now modify /home/pleo/.emacs to set exec path i.e add line: (setq inferior-R-program-name "/home/pleo/R_latest/bin/R") 
          
make dvi
make pdf
make info

your done , you can use the R2.9.2 AND R.10 at the same time if needed.
All this is from the R admin pdf avaliable from CRAN
############################## 
Note if you want to stick to the current version of R- use as Dirk suggested as it will make updates easier. 
PS I do this on ubuntu 8.1 not that that sound make a difference ..

Cheers
PAul

-----Original Message-----
From: Dirk Eddelbuettel <edd at debian.org>
To: Dennis Fisher <fisher at plessthan.com>
Cc: r-sig-debian at r-project.org
Subject: Re: [R-sig-Debian] Updating R for Linux
Date: Wed, 23 Sep 2009 10:39:08 -0500

        
On 23 September 2009 at 08:17, Dennis Fisher wrote:

        
| Colleagues,
| 
| Please forgive my ignorance of this topic.  I am experienced with the  
| installation/use of R in OSX and Windows, much less so with Linux.

Welcome!  We're here to help. 

| I just created a virtual machine of Ubuntu 9.0.4.  Using the Synaptic  
| Package Manager, I installed R 2.8.1.  I would like to obtain 2.9.x  
| and I am having trouble doing so using the tools available within  
| Ubuntu.
| 
| I tried
| 	apt-get install r-base
| The system replied that the newest version was already installed and  
| no changes were made.

Right.  But you want

	apt-get update			# to refresh information
	apt-get dist-upgrade		# to upgrade to newer versions
					# incl. possible dependencies

after you have done this:

| I also added
| 	dev http://cran.cnr.berkeley.edu/bin/linux/debian etch-cran

Wrong repo.  

You copied this from the _Debian_ README but there is also one for _Ubuntu_
in the neighboring directory (ie $CRAN/bin/linux/ubuntu/). Use that instead.

| to
| 	/etc/apt/sources.list
| Running apt-get install r-base again yielded no response.

Very close.  

| Can anyone advise on the simplest means to update to 2.9.x.  I need  
| only the basic packages, nothing special.  Thanks in advance.

The above will get you fresh and shiny R 2.9.2 packages courtesy of Vincent
and Michael (for the Ubuntu port).  Debian via CRAN works thanks to Johannes,
and yours truly looks after things in Debian itself which provides the basis
for these so-called 'ports'.

Keep posting with questions, you're very close.

Dirk

| 
| Dennis
| 
| Dennis Fisher MD
| P < (The "P Less Than" Company)
| Phone: 1-866-PLessThan (1-866-753-7784)
| Fax: 1-415-564-2220
| www.PLessThan.com
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian