R SIG Debian - Apr 2012 - Error installing libraries (eg RODBC) on R-2.15.0 : cannot find 'config.log'

Dear list,

as I started installing R-2.15.0 on a Red Hat 4.5.1-4 as well a Ubuntu
10.04.3 systems.
While the basic installation went fine (like the previous R-2.14.2), now
I'm having trouble installing almost one third of the additional libraries
I want (which installed flawlessly with R-2.14.2), among them RODBC for
which I show the message below (obtained on Ubuntu) :

surf_forInstallation_> R  CMD INSTALL RODBC_1.3-5.tar.gz
* installing to library '/linux/biolo/R_surf/R-2.15.0/lib64/R/library'
* installing *source* package 'RODBC' ...
** package 'RODBC' successfully unpacked and MD5 sums checked
checking for gcc...
gcc -std=gnu99
checking for C compiler default output file name... configure: error: C
compiler cannot create executables
See `config.log' for more details.
ERROR: configuration failed for package 'RODBC'
* removing '/linux/biolo/R_surf/R-2.15.0/lib64/R/library/RODBC'


In fact, I get identical messages on our Red Hat 4.5.1-4 and the Ubuntu
10.04.3 systems mentioned above.
Obviously something with our C compiler(s) didn't work out.
In order to learn more about the problem I tried to look at config.log
mentioned in the installation-message above, however, I cannot find
the file, neither in my current path nor in
 /linux/biolo/R_surf/R-2.15.0/lib64/R/library .
Obviously the RODBC directory doesn't exist any more when the installation
attempt ends.

Any hints ?
I'm new to the Debian-list, but at least I haven't seen similar (recent)
posts on R-help or the bioconductor lists.

For completeness :
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


Many thanks in advance,
Wolfgang

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
IGBMC,
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
wolfgang.raffelsberger at igbmc.fr

	[[alternative HTML version deleted]]

On 04/18/2012 12:24 PM, Wolfgang Raffelsberger wrote:
> Dear list,
>
> as I started installing R-2.15.0 on a Red Hat 4.5.1-4 as well a Ubuntu
> 10.04.3 systems.
> While the basic installation went fine (like the previous R-2.14.2), now
> I'm having trouble installing almost one third of the additional
libraries
> I want (which installed flawlessly with R-2.14.2), among them RODBC for
> which I show the message below (obtained on Ubuntu) :
>
> surf_forInstallation_>  R  CMD INSTALL RODBC_1.3-5.tar.gz
> * installing to library
'/linux/biolo/R_surf/R-2.15.0/lib64/R/library'
> * installing *source* package 'RODBC' ...
> ** package 'RODBC' successfully unpacked and MD5 sums checked
> checking for gcc...
> gcc -std=gnu99
> checking for C compiler default output file name... configure: error: C
> compiler cannot create executables
> See `config.log' for more details.
> ERROR: configuration failed for package 'RODBC'
> * removing '/linux/biolo/R_surf/R-2.15.0/lib64/R/library/RODBC'
>
>
> In fact, I get identical messages on our Red Hat 4.5.1-4 and the Ubuntu
> 10.04.3 systems mentioned above.
> Obviously something with our C compiler(s) didn't work out.
> In order to learn more about the problem I tried to look at config.log
> mentioned in the installation-message above, however, I cannot find
> the file, neither in my current path nor in
>   /linux/biolo/R_surf/R-2.15.0/lib64/R/library .
> Obviously the RODBC directory doesn't exist any more when the
installation
> attempt ends.
>
> Any hints ?
> I'm new to the Debian-list, but at least I haven't seen similar
(recent)
> posts on R-help or the bioconductor lists.
Wolfgang,

For the Ubuntu box, I would start by using my R PPA found here:

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

I would also suggest using apt and/or synaptic to install as many 
packages as possible from the repositories (sudo apt-get install 
r-cran-rodbc, for example).

The error you received indicates to me you do not have any development 
packages or a c++ complier installed.  Have you installed
"r-base-dev"?
  That should install the needed compilers.

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