[R-sig-Debian] Ubuntu 13.10 - not able to upgrade R

Alex Mandel tech_dev at wildintellect.com
Mon Apr 21 21:39:30 CEST 2014 

Looks like you will need to update packages in a specific order. Since
spatial depends on date, date needs to updated first.

update.packages("date")

Then try again and see what it tells you next.
It's a bit of a pain but will eventually work. The other option is to
dump the list of current packages. Uninstall the old and try to install
from the list.

Thanks,
Alex

On 04/21/2014 12:23 PM, claude krzisch wrote:
> Hi,
> Thank you for your response. It was one of the first things I did.
> However, it doesn't work. The error messages are (in french)
> 
> /Les packages source téléchargés sont dans//
> //    '/tmp/Rtmp4IaeBv/downloaded_packages'//
> //essai de l'URL 'http://cran.irsn.fr/src/contrib/spatial_7.3-8.tar.gz'//
> //Content type 'application/x-gzip' length 43593 bytes (42 Kb)//
> //URL ouverte//
> //==================================================//
> //downloaded 42 Kb//
> //
> //Erreur : package 'date' was built before R 3.0.0: please re-install it//
> //Exécution arrêtée//
> //
> //Les packages source téléchargés sont dans//
> //    '/tmp/Rtmp4IaeBv/downloaded_packages'//
> //mise à jour de la liste HTML des packages dans '.Library'//
> //Making 'packages.html' ... Terminé.//
> //Il y a eu 50 avis ou plus (utilisez warnings() pour voir les 50
> premiers)//
> //> warnings()//
> //Messages d'avis ://
> //1: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'Ecfun' a eu un statut de sortie non nul//
> //2: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'BH' a eu un statut de sortie non nul//
> //3: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'FNN' a eu un statut de sortie non nul//
> //4: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'lava' a eu un statut de sortie non nul//
> //5: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'ape' a eu un statut de sortie non nul//
> //6: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'clue' a eu un statut de sortie non nul//
> //7: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'date' a eu un statut de sortie non nul//
> //8: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'deldir' a eu un statut de sortie non nul//
> //9: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'e1071' a eu un statut de sortie non nul//
> //10: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'effects' a eu un statut de sortie non nul//
> //11: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'energy' a eu un statut de sortie non nul//
> //12: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'evaluate' a eu un statut de sortie non nul//
> //13: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'expm' a eu un statut de sortie non nul//
> //14: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'gam' a eu un statut de sortie non nul//
> //15: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'geoRglm' a eu un statut de sortie non nul//
> //16: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'gridBase' a eu un statut de sortie non nul//
> //17: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'gss' a eu un statut de sortie non nul//
> //18: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'gtools' a eu un statut de sortie non nul//
> //19: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'gvlma' a eu un statut de sortie non nul//
> //20: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'hexbin' a eu un statut de sortie non nul//
> //21: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'HH' a eu un statut de sortie non nul//
> //22: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'igraph' a eu un statut de sortie non nul//
> //23: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'igraphdata' a eu un statut de sortie non
> nul//
> //24: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'iterators' a eu un statut de sortie non
> nul//
> //25: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'longitudinalData' a eu un statut de
> sortie non nul//
> //26: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'mapproj' a eu un statut de sortie non nul//
> //27: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'markdown' a eu un statut de sortie non nul//
> //28: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'MatrixModels' a eu un statut de sortie
> non nul//
> //29: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'mice' a eu un statut de sortie non nul//
> //30: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'oz' a eu un statut de sortie non nul//
> //31: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'pastecs' a eu un statut de sortie non nul//
> //32: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'permute' a eu un statut de sortie non nul//
> //33: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'plotrix' a eu un statut de sortie non nul//
> //34: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'plyr' a eu un statut de sortie non nul//
> //35: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'polynom' a eu un statut de sortie non nul//
> //36: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'proxy' a eu un statut de sortie non nul//
> //37: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'psych' a eu un statut de sortie non nul//
> //38: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'qcc' a eu un statut de sortie non nul//
> //39: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'rbounds' a eu un statut de sortie non nul//
> //40: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'Rcsdp' a eu un statut de sortie non nul//
> //41: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'scatterplot3d' a eu un statut de sortie
> non nul//
> //42: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'seriation' a eu un statut de sortie non
> nul//
> //43: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'sfsmisc' a eu un statut de sortie non nul//
> //44: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'shape' a eu un statut de sortie non nul//
> //45: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'slam' a eu un statut de sortie non nul//
> //46: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'sm' a eu un statut de sortie non nul//
> //47: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'sp' a eu un statut de sortie non nul//
> //48: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'statmod' a eu un statut de sortie non nul//
> //49: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'survival' a eu un statut de sortie non nul//
> //50: In install.packages(update[instlib == l, "Package"], l, ... ://
> //  l'installation du package 'svGUI' a eu un statut de sortie non nul/
> ...
> 
> Another idea
> Thank you so much
> 
> CK
> 
> 
> Le 21/04/2014 02:14, Alex Mandel a écrit :
>> 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:
>>> 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 écrit :
>>>> 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
>>>>
>>> _______________________________________________
>>> R-SIG-Debian mailing list
>>> R-SIG-Debian at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>>
> 
>

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