Re: [R] ubuntu system refuses to update packages

From: Vincent Goulet <vincent.goulet_at_act.ulaval.ca>
Date: Mon, 10 Nov 2008 09:45:50 -0500

Le lun. 10 nov. à 00:45, Leon Yee a écrit :

> Dirk Eddelbuettel wrote:

>> On 9 November 2008 at 20:35, Alan Jackson wrote:
>> | There must be a simple answer to this.
>> | | I'm running ubuntu gutsy, currently have 2.7.2 loaded, but the  
>> update
>> | tools refuse to update it, and don't tell me why. With apt-get I  
>> get :
>> | | [668 ~]$ sudo apt-get -u -V --simulate dist-upgrade
>> | Reading package lists... Done
>> | Building dependency tree       | Reading state information... Done
>> | Calculating upgrade... Done
>> | The following packages have been kept back:
>> |    r-base (2.7.2-1gutsy0 => 2.8.0-1gutsy1)
>> |    r-base-core (2.7.2-1gutsy0 => 2.8.0-1gutsy1)
>> |    r-base-dev (2.7.2-1gutsy0 => 2.8.0-1gutsy1)
>> |    r-cran-rpart (3.1.41-1gutsy0 => 3.1.42-1gutsy0)
>> |    r-recommended (2.7.2-1gutsy0 => 2.8.0-1gutsy1)
>> | 0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
>> | | If I use a gui package manager, it tells me the update will break
>> | the installation and refuses to go forward, but doesn't show what  
>> the
>> | issue is.
>> In cases like this just take the set of packages and pass them  
>> directly to
>> 'sudo apt-get install' ie
>>   $ sudo apt-get install r-base r-base-core r-base-dev r-cran-rpart  
>> r-recommended
>> which will show which packages this will install (as new), upgrade,  
>> or
>> remove, if any.  It still allows you to pack out if you so choose.
>> In this case it is probably 'just' a fortran or c++ library  
>> transition.  If
>> you are still running gutsy you are also now two Ubuntu releases  
>> behind so
>> you may want to consider upgrading to hardy and/or intrepid.
>> By the way, this would have a good question for the r-sig-debian  
>> list.
>> Hth, Dirk
>

> Hi,
>

> I encountered similar problems:
>

> apt-get install r-base-core
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Some packages could not be installed. This may mean that you have
> requested an impossible situation or if you are using the unstable
> distribution that some required packages have not yet been created
> or been moved out of Incoming.
>

> Since you only requested a single operation it is extremely likely
> that
> the package is simply not installable and a bug report against
> that package should be filed.
> The following information may help to resolve the situation:
>

> The following packages have unmet dependencies:
> r-base-core: Depends: tcl8.5 (>= 8.5.0) but it is not installable
> Depends: tk8.5 (>= 8.5.0) but it is not installable
> E: Broken packages
>

> /etc/apt/sources.list
>

> deb http://mirror.optus.net/ubuntu/ gutsy-security main restricted
> universe multiverse
> deb-src http://mirror.optus.net/ubuntu/ gutsy-security restricted
> main multiverse universe
>

> deb http://mirror.optus.net/ubuntu/ gutsy universe main
> deb-src http://mirror.optus.net/ubuntu/ gutsy universe main
> deb http://mirror.optus.net/ubuntu/ gutsy-updates universe main
> deb-src http://mirror.optus.net/ubuntu/ gutsy-updates universe main
>

> deb http://cran.ms.unimelb.edu.au/bin/linux/ubuntu gutsy/
>

> deb http://security.ubuntu.com/ubuntu/ gutsy-security universe main
> deb-src http://security.ubuntu.com/ubuntu/ gutsy-security universe
> main
>
>

> It seems that R2.8.0 for gutsy is built on a system with tcl8.5 and
> tk8.5, which is not available in gutsy?

 From the CRAN Ubuntu README:

 >>>
Installation and compilation of R or some its packages may require Ubuntu packages from the "backports" repositories. In particular, this is the case for Tcl/Tk 8.5 on Gutsy and Hardy. Therefore, it is suggested to activate the backports repositories with an entry like

deb http://<my.favorite.ubuntu.mirror>/ hardy-backports main restricted universe

in your /etc/apt/sources.list file. See http://www.ubuntu.com/getubuntu/downloadmirrors   for the list of Ubuntu mirrors.
<<<

Vincent

>
>

> Best wishes,
> Leon
>

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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. Received on Mon 10 Nov 2008 - 14:49:40 GMT

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