[R-sig-Debian] R hangs on the stats.so library

[Michael Rutter]

On 12/20/2010 09:53 AM, ottorino wrote:
> Dear all,
> I having this problem on my laptop.
> It was caused by my clumsy attempts to upgrade the system.
> As I wrote here,
> (http://www.mail-archive.com/r-sig-debian@r-project.org/msg01364.html)
> I was trying to solve the same problem with JAGS/rjags on my laptop.
>
> After typing R in a terminal I'm currently get the following:
>
>> R version 2.9.0 (2009-04-17)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> ......some unrelevant lines
>>
>> Loading required package: graphics
>> Loading required package: stats
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>    impossibile caricare libreria condivisa '/usr/local/lib/R/library/stats/libs/stats.so':
>>    /usr/local/lib/R/library/stats/libs/stats.so: undefined symbol: _gfortran_pow_r8_i4
>> Errore: package 'stats' could not be loaded
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>    impossibile caricare libreria condivisa '/usr/local/lib/R/library/stats/libs/stats.so':
>>    /usr/local/lib/R/library/stats/libs/stats.so: undefined symbol: _gfortran_pow_r8_i4
>> Durante l'avvio - Warning message:
>> package stats in options("defaultPackages") was not found
>>>
>
> What I did before:
>
> sudo nano /etc/apt/sources.list
>
> The file sources.list contains the following lines
> ######################################################
> deb http://it.archive.ubuntu.com/ubuntu/ lucid main restricted
> deb-src http://it.archive.ubuntu.com/ubuntu/ lucid main restricted
>
> deb http://it.archive.ubuntu.com/ubuntu/ lucid-updates main restricted
> deb-src http://it.archive.ubuntu.com/ubuntu/ lucid-updates main
> restricted
>
> deb http://it.archive.ubuntu.com/ubuntu/ lucid universe
> deb-src http://it.archive.ubuntu.com/ubuntu/ lucid universe
> deb http://it.archive.ubuntu.com/ubuntu/ lucid-updates universe
> deb-src http://it.archive.ubuntu.com/ubuntu/ lucid-updates universe
>
> deb http://it.archive.ubuntu.com/ubuntu/ lucid multiverse
> deb-src http://it.archive.ubuntu.com/ubuntu/ lucid multiverse
> deb http://it.archive.ubuntu.com/ubuntu/ lucid-updates multiverse
> deb-src http://it.archive.ubuntu.com/ubuntu/ lucid-updates multiverse
>
> deb http://security.ubuntu.com/ubuntu lucid-security main restricted
> deb-src http://security.ubuntu.com/ubuntu lucid-security main restricted
> deb http://security.ubuntu.com/ubuntu lucid-security universe
> deb-src http://security.ubuntu.com/ubuntu lucid-security universe
> deb http://security.ubuntu.com/ubuntu lucid-security multiverse
> deb-src http://security.ubuntu.com/ubuntu lucid-security multiverse
> deb http://cran.stat.unipd.it/bin/linux/ubuntu lucid/
> deb http://it.archive.ubuntu.com/ubuntu/ lucid-backports main restricted
> universe
> ######################################################
> Then I did:
>
> sudo apt-get update
> sudo apt-get upgrade
>
> and then a lot of clumsy commands to try to recover from the situation.
> I can post them all if necessary, but basically they were:
>
> sudo apt-get remove r-base
> sudo apt-get remove r-base-core
>
> sudo apt-get install r-base-core
> sudo apt-get remove r-base-core r-dev
> sudo apt-get install  r-base-core r-dev r-recommended
>
> and similar attempts.
>
> Since I was getting some error from R I probaly worsen th situation
> typing:
>
> sudo apt-get install libmpc
> sudo apt-get install r-devel
> whereis libgfortran
> whereis libgfortran.so.2
> sudo apt-get install libgfortran3
> sudo apt-get install libgfortran3-dev
> sudo apt-get install libgfortran2
> sudo apt-get install libgfortran3-dbg
> R
> sudo apt-get remove  libgfortran3-dbg
> sudo apt-get install build-essential
> sudo apt-get install r-base-core r-doc-info r-mathlib r-recommended
> R
> sudo apt-get install r-base-dev
> sudo apt-get install f2c
> R
> sudo apt-get install r-base-core r-doc-info r-mathlib r-recommended
> sudo apt-get remove  r-base-core r-doc-info r-mathlib r-recommended
> r-base-dev
> sudo apt-get install r-base-core r-doc-info r-mathlib r-recommended
> r-base-dev
> R
> sudo apt-get remove f2c
> sudo apt-get install g++ gfortran
> sudo apt-get autoremove
>
> I do not exactly remember why I gave the above commands, since all the
> above happened about one month ago, but I remember that the problem was
> caused by libgfortran.so.2
>
> Could please someone help me to escape from this situation ?
> Thanks
>

The first thing to diagnose is why you have this this line in your 
sources.list:

 > deb http://cran.stat.unipd.it/bin/linux/ubuntu lucid/

Yet, the version of R you are using is old, 2.9.0.  It appears that the 
line is correct.  I would suggest launching Synaptic and seeing which 
versions of r-base are available.  If you search for 'r-base' within 
Synaptic, right click on the package for 'Properties'.  Click the 
versions tab, and there should be two listed.  See if you can install 
2.12 from there.

If you are using JAGS, check out my Launchpad PPA:

https://launchpad.net/~marutter/+archive/rrutter

It has a package for JAGS available for lucid.  That might help.

Hope this helps,
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