R SIG Debian - May 2010 - Non-zero exit status for survival package

I'm running R 2.11 on Karmic. I'm having difficulty installing quite a
few packages with the returned error message of "installation of package
"[whatever the packages happens to be]" had non-zero exit status. I
know
this message sometimes is caused by incorrect or missing java packages
and the like. I generally don't have issues with the installation of R
or R packages but I don't know where to start on this. I have looked to
ensure that I have fortran and C++ compilers installed. I want to (if I
can) avoid indiscriminately installing packages "until it starts
working". I'm not sure how to go about troubleshooting this. Could
anyone lend a hand, please?

Thanks,
Patrick
> sessionInfo()
R version 2.11.0 (2010-04-22) 
x86_64-pc-linux-gnu 

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

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

loaded via a namespace (and not attached):
[1] tools_2.11.0
> capabilities()
    jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
libxml     fifo   cledit 
    TRUE     TRUE     TRUE     TRUE     TRUE    FALSE     TRUE     TRUE
TRUE     TRUE     TRUE 
   iconv      NLS  profmem    cairo 
    TRUE     TRUE     TRUE     TRUE

Patrick,

Can you give an example of a package that you have tried to install?  Or 
you using 32 or 64-bit Karmic?

Thanks,
Michael

On 05/09/2010 10:35 AM, Patrick Richardson wrote:
> I'm running R 2.11 on Karmic. I'm having difficulty installing
quite a
> few packages with the returned error message of "installation of
package
> "[whatever the packages happens to be]" had non-zero exit status.
I know
> this message sometimes is caused by incorrect or missing java packages
> and the like. I generally don't have issues with the installation of R
> or R packages but I don't know where to start on this. I have looked to
> ensure that I have fortran and C++ compilers installed. I want to (if I
> can) avoid indiscriminately installing packages "until it starts
> working". I'm not sure how to go about troubleshooting this. Could
> anyone lend a hand, please?
>
> Thanks,
> Patrick
>
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-pc-linux-gnu
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
>   [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
> LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
>> capabilities()
>      jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
> libxml     fifo   cledit
>      TRUE     TRUE     TRUE     TRUE     TRUE    FALSE     TRUE     TRUE
> TRUE     TRUE     TRUE
>     iconv      NLS  profmem    cairo
>      TRUE     TRUE     TRUE     TRUE
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
-- 
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

Patrick,

Perhaps it's not the problem you're having, but just in case. Did you
follow this step of the CRAN Ubuntu README file:

Users who need to compile R packages from source [e.g. package maintainers, or
anyone installing packages with install.packages()] should also install the
r-base-dev package:

   sudo apt-get install r-base-dev

Cheers,

Vincent

Le dim. 9 mai ? 10:35, Patrick Richardson a ?crit :
> I'm running R 2.11 on Karmic. I'm having difficulty installing
quite a
> few packages with the returned error message of "installation of
package
> "[whatever the packages happens to be]" had non-zero exit status.
I know
> this message sometimes is caused by incorrect or missing java packages
> and the like. I generally don't have issues with the installation of R
> or R packages but I don't know where to start on this. I have looked to
> ensure that I have fortran and C++ compilers installed. I want to (if I
> can) avoid indiscriminately installing packages "until it starts
> working". I'm not sure how to go about troubleshooting this. Could
> anyone lend a hand, please?
> 
> Thanks,
> Patrick
> 
>> sessionInfo()
> R version 2.11.0 (2010-04-22) 
> x86_64-pc-linux-gnu 
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8       
> [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
> LC_MESSAGES=en_US.UTF-8   
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> LC_ADDRESS=C              
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base     
> 
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
> 
>> capabilities()
>    jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
> libxml     fifo   cledit 
>    TRUE     TRUE     TRUE     TRUE     TRUE    FALSE     TRUE     TRUE
> TRUE     TRUE     TRUE 
>   iconv      NLS  profmem    cairo 
>    TRUE     TRUE     TRUE     TRUE
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian