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Ubuntu 13.10 - not able to upgrade R

9 messages · Martin Bel, Dirk Eddelbuettel, claude krzisch +1 more

Original
Dirk Eddelbuettel
#
On 18 April 2014 at 05:49, Martin Bel wrote:
| Hi,
| I'm having some issues upgrading R. I'm using ubuntu linux 13.10, saucy and would like to upgrade R to the new version.I'm currently using 3.0.1
| I've been following the instructions given in:1. http://stackoverflow.com/questions/10476713/how-to-upgrade-r-in-ubuntuand2. http://cran.r-project.org/bin/linux/ubuntu/
| 
| Here is exactly what i did, following mostly the stackoverflow description:
| 1) Added the cran mirror link to the sources list(I've actually tryed with 3 different mirrors just in case)sudo gedit /etc/apt/sources.listdeb http://cran.cnr.berkeley.edu/bin/linux/ubuntu/ saucy/
| 2) Getting the key step gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9gpg -a --export E084DAB9 | sudo apt-key add -
| 3) Run the updates/upgradessudo apt-get update && sudo apt-get upgrade
| After a large list of succesful updates i get the following result in the terminal:
| 
| W: Failed to fetch http://cran.cnr.berkeley.edu/bin/linux/ubuntu/saucy/InRelease  
| W: Failed to fetch http://cran.cnr.berkeley.edu/bin/linux/ubuntu/saucy/Release.gpg  Cannot initiate the connection to cran.cnr.berkeley.edu:80 (2607:f140:0:8000::201). - connect (101: Network is unreachable) [IP: 2607:f140:0:8000::201 80]
| W: Some index files failed to download. They have been ignored, or old ones used instead.Reading package lists... DoneBuilding dependency tree       Reading state information... Done0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

You have a network error with the host, so use a different mirror.  I use

    deb http://cran.rstudio.com.org/bin/linux/ubuntu saucy/
 
as I found the RStudio CDN to be reliably fast.

Dirk

| I've done this a few times. At this point there are no more updates and the R error is isolated.
| Is there a solution to this or should i just re-install R.
| Thanks for your time,
| Martin
|  		 	   		   		 	   		  
| 	[[alternative HTML version deleted]]
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Dirk Eddelbuettel
#
On 18 April 2014 at 06:01, Dirk Eddelbuettel wrote:
| You have a network error with the host, so use a different mirror.  I use
| 
|     deb http://cran.rstudio.com.org/bin/linux/ubuntu saucy/
|  
| as I found the RStudio CDN to be reliably fast.

That's what I get for editing on the fly.  URL should be 

     deb http://cran.rstudio.com/bin/linux/ubuntu saucy/

I am trying to switch more machines from using r-project.org to rstudio.com
which serves faster...

Dirk
 
| Dirk
| 
| | I've done this a few times. At this point there are no more updates and the R error is isolated.
| | Is there a solution to this or should i just re-install R.
| | Thanks for your time,
| | Martin
| |  		 	   		   		 	   		  
| | 	[[alternative HTML version deleted]]
| | 
| | _______________________________________________
| | R-SIG-Debian mailing list
| | R-SIG-Debian at r-project.org
| | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| 
| -- 
| Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Dirk Eddelbuettel
#
On 18 April 2014 at 16:39, Martin Bel wrote:
| I've tried a few different mirrors before, including the rstudio one. 
| To be sure i've tried again with the one you provided, but didn't work.

We can't really help you at the granularity of "didn't work": What did you
try?  How did it fail? What were the errors?

Maybe read some of the HOWTOs on the web about 'how to ask a good question'
as eg this classic variant: http://www.catb.org/esr/faqs/smart-questions.html
 
| I've found this other method, that worked. I guess it's not the official one,
| right?
| 
| 
| sudo add-apt-repository ppa:marutter/rrutter

Yes that is a different repository from the CRAN repository. They are related though.

I honestly do not know what your question is.  Thousands of people _use_ the
CRAN Ubuntu repo happily.  Maybe you just need to re-read the README...

Good luck,  Dirk
Dirk Eddelbuettel
#
On 18 April 2014 at 17:06, Martin Bel wrote:
| Dirk,
| 
| Below is my original mail, a question i sent yesterday. 
| I wanted to upgrade R but for some reason this didn't work.
| Your response to this e-mail was: try the rstudio mirror or some other. This
| didn't work, meaning i couldn't upgrade R. 
| 
| As you probably didn't have this first question in your mail history, it didn't
| make sense. Sorry for this.

I saw your email and replied to it. I keep mailing list emails so
re-resending the post is not necessary.

All we have below are three __warning__ messages ("W" -> warning; "E" ->
errors).  No errors here. I suggested switching mirrors. 

| Finally, i could upgrade R with this line:
| sudo add-apt-repository ppa:marutter/rrutter

Very good. I won't try any longer to waste everybody's time then.

Dirk
 
| Best,
| Martin
| 
| 
| 
| 
| Hi,
| I'm having some issues upgrading R. I'm using ubuntu linux 13.10, saucy and would like to upgrade R to the new version.I'm currently using 3.0.1
| I've been following the instructions given in:1. http://stackoverflow.com/questions/10476713/how-to-upgrade-r-in-ubuntuand2. http://cran.r-project.org/bin/linux/ubuntu/
| 
| Here is exactly what i did, following mostly the stackoverflow description:
| 1) Added the cran mirror link to the sources list(I've actually tryed with 3 different mirrors just in case)sudo gedit /etc/apt/sources.listdeb http://cran.cnr.berkeley.edu/bin/linux/ubuntu/ saucy/
| 2) Getting the key step gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9gpg -a --export E084DAB9 | sudo apt-key add -
| 3) Run the updates/upgradessudo apt-get update && sudo apt-get upgrade
| After a large list of succesful updates i get the following result in the terminal:
| 
| W: Failed to fetch http://cran.cnr.berkeley.edu/bin/linux/ubuntu/saucy/InRelease 
| W: Failed to fetch http://cran.cnr.berkeley.edu/bin/linux/ubuntu/saucy/Release.gpg Cannot initiate the connection to cran.cnr.berkeley.edu:80 (2607:f140:0:8000::201). - connect (101: Network is unreachable) [IP: 2607:f140:0:8000::201 80]
| W: Some index files failed to download. They have been ignored, or old ones used instead.Reading package lists... DoneBuilding dependency tree Reading state information... Done0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
| 
| I've done this a few times. At this point there are no more updates and the R error is isolated.
| Is there a solution to this or should i just re-install R.
| Thanks for your time,
| Martin
| 
| 
| > Date: Fri, 18 Apr 2014 14:54:56 -0500
| > To: belmartin at outlook.com
| > CC: edd at debian.org; r-sig-debian at r-project.org
| > Subject: RE: [R-sig-Debian] Ubuntu 13.10 - not able to upgrade R
| > From: edd at debian.org
| >
| >
| > On 18 April 2014 at 16:39, Martin Bel wrote:
| > | I've tried a few different mirrors before, including the rstudio one.
| > | To be sure i've tried again with the one you provided, but didn't work.
| >
| > We can't really help you at the granularity of "didn't work": What did you
| > try? How did it fail? What were the errors?
| >
| > Maybe read some of the HOWTOs on the web about 'how to ask a good question'
| > as eg this classic variant: http://www.catb.org/esr/faqs/smart-questions.html
| >
| > | I've found this other method, that worked. I guess it's not the official
| one,
| > | right?
| > |
| > |
| > | sudo add-apt-repository ppa:marutter/rrutter
| >
| > Yes that is a different repository from the CRAN repository. They are related
| though.
| >
| > I honestly do not know what your question is. Thousands of people _use_ the
| > CRAN Ubuntu repo happily. Maybe you just need to re-read the README...
| >
| > Good luck, Dirk
| >
| > --
| > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
2 days later
claude krzisch
# 
Hi
I work with Ubuntu (now trusty) and I have a problem related, I presume, 
to the upgrade of R : I am unable to download some packages I relied 
heavily on previously as "date","survival" ... I tried to upgrade my 
packages without any success always with the same message : the package 
has been compiled before R 3.0.3, please recompile it. It is the first 
time that I have this type of problem and I don't know how to respond to 
it. Must I download the source package and compile it ? And how may I do 
it ?

Thank you for your help

CK


Le 18/04/2014 21:54, Dirk Eddelbuettel a ?crit :
Alex Mandel
# 
Open an R session and run update.packages()
It will pull down and recompile whatever packages you have installed.

Thanks,
Alex
On 04/20/2014 02:50 PM, claude krzisch wrote: