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

[Michael Rutter]

On 03/28/2011 05:36 PM, Edin Villalobos Mora wrote:
> Good evenings, Michael. You were right, 'sudo apt-get autoremove' didn't
> solve the problem. In fact, didn't find any package to remove.
> Then I tried removing compilers, reboot, and reinstalling r-base-dev,
> but the problem persist.
> But, strangely it appears 30 packages are without upgrades, and tried
> the upgrade because it's about r-cran packages, most of them.
> The upgrade was succesful and installed most of the R packages that I
> failed to install (like nlme) inside R.
> Then tested my luck in R: 'sudo R', 'update.packages()'... only packages
> 'MASS' and 'class' need updates and failed again with 'buffer overflow'.
> Also, the problem persists with 'pwr', 'agricolae' and 'mvoutlier'
> packages...
> Now I have the weird idea to change to my windows partition to use R...
> or a virtual machine?

Edin,

Given your description of the problem, this appears to be an Ubuntu
problem.  R appears to be functioning fine based on what you have
described.  It appears something wrong with the current state of your
Ubuntu system, and that is beyond the scope of this sig email list.  I
have been unable to recreate the errors you describe on any of my Ubuntu
boxes, so I think the issues are specific to your machine.

If you send me the exact transcript of your session when you try to
update the packages, I can take another look.  Please send this
information directly to me and we will see if we can solve the problem
off the email list.

Michael

> ------------------------------------------------------------------------
> *De:* Michael Rutter <mar36 at psu.edu>
> *Para:* Edin Villalobos Mora <edivimo at yahoo.es>
> *CC:* r-sig-debian at r-project.org
> *Enviado:* lun,28 marzo, 2011 13:07
> *Asunto:* Re: [R-sig-Debian] "Buffer overflow" updating and installing
> packages...
> 
> 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
> 

-- 
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