[R-sig-Debian] "Buffer overflow" updating and installing packages...

[Michael Rutter]

On 03/28/2011 02:43 PM, Edin Villalobos Mora wrote:
> Good morning. First, thanks for your help Michael. I typed what you
> suggest me:
>
> kagamin at kagamin-laptop:~$ sudo apt-get -f install
> [sudo] password for kagamin:
> Leyendo lista de paquetes... Hecho
> Creando árbol de dependencias
> Leyendo la información de estado... Hecho
> Los siguientes paquetes se instalaron automáticamente y no son necesarios:
> liblash2 libktnef4 libboost-regex1.40.0 libdebconf-kde0 libqt4-assistant
> libpackagekit-glib2-14 libkpimtextedit4 libkimproxy4 kpackagekit libjpeg8
> libboost-program-options1.40.0 kdelibs5 libkxmlrpcclient4 libdvbpsi5
> libgeos-3.1.0 kdesudo libavutil-extra-49 libpackagekit-qt-14 libx264-85
> install-package libqgpgme1 libqt4-webkit libboost-signals1.40.0 cvs
> libqtassistantclient4 libkpimidentities4 libaudid3tag2 libgirepository1.0-0
> libao2 packagekit-backend-aptcc libkblog4 python-packagekit libmowgli1
> libxml++1.0c2a packagekit gdebi-kde software-properties-kde kdepimlibs5
> libkholidays4 update-manager-kde libmodplug0c2 packagekit-backend-apt
> libsox1a libjpeg-progs virtuoso-nepomuk libsyndication4 libebml0 libmpcdec3
> libmatroska0 libgpgme++2 libnetcdf4
> Utilice «apt-get autoremove» para eliminarlos.
> 0 actualizados, 0 se instalarán, 0 para eliminar y 30 no actualizados.
>
> My Ubuntu is in spanish, by the way, a 32-bit version ('uname -m'
> returns 'i686'). Looking to the .deb packages mentioned it appears none
> is related to R or CRAN, and the list is about packages no longer
> necessary. I did 'sudo apt-get remove' and tried again. The problem is
> still there, and it occurs after the mirrors-window pop up, even I tried
> different mirrors, just in case.
> The download of the packages is ok, and immediatly appears the "buffer
> overflow" message. I tried with the update of the packages 'nlme',
> 'boot' and 'cluster' and the installation of 'agricolae' and 'ggplot2'
> with the same result: 'non-zero exit status'.
> Another suggestion?

OK, I would run 'sudo apt-get autoremove' and remove the unneeded 
packages.  That may fix the problem, but my guess is that it would not. 
  The issue seems to occur when you go to compile the packages you are 
downloading, so I am not even sure if it is related to R.

I would start by removing the compilers.  Try:

sudo apt-get remove r-base-dev gcc g++ gfortran

Reboot, then reinstall r-base-dev and see if that fixes the problem.

Michael





> --
> Dr. Michael A. Rutter
> School of Science
> Penn State Erie, The Behrend College
> Station Road
> Erie, PA 16563
> http://math.bd.psu.edu/faculty/rutter
>


-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter