[R] installation problems from an Rstudio server

[Prof Brian Ripley]

On 20/06/2013 09:53, Erin Hodgess wrote:
> Dear R People:
>
> I'm not sure if this is an R problem or a Centos 5 problem, but here it
> goes:


It is not an R problem.  Your message is garbled (don't send HTML?), but 
the essence is

gcc: error trying to exec 'as': execvp: Permission denied

That is a problem with your compiler installation: it cannot execute its 
assembler pass.

>
> I'm running Rstudio from a Centos 5 server.  When I try to install packages
> from a non-root account, I get the following:
>
>> Sys.umask()[1] "22"> install.packages("maps")Installing package into ‘/home/erin1/R/x86_64-unknown-linux-gnu-library/3.0’
> (as ‘lib’ is unspecified)trying URL
> 'http://cran.rstudio.com/src/contrib/maps_2.3-2.tar.gz'Content type
> 'application/x-gzip' length 1426362 bytes (1.4 Mb)opened
> URL==================================================downloaded 1.4 Mb
> * installing *source* package ‘maps’ ...** package ‘maps’ successfully
> unpacked and MD5 sums checked** libs** arch - gcc -std=gnu99 -g -O2
> -I/usr/local/include -L/usr/local/lib64  Gmake.c   -o GmakeGmake.c: In
> function ‘get_lh’:
> Gmake.c:111: warning: cast from pointer to integer of different
> sizeGmake.c:113: warning: cast from pointer to integer of different
> sizeGmake.c: In function ‘main’:Gmake.c:211: warning: cast from
> pointer to integer of different sizeGmake.c:214: warning: cast from
> pointer to integer of different sizeGmake.c:217: warning: cast from
> pointer to integer of different sizeGmake.c:219: warning: cast from
> pointer to integer of different sizeGmake.c:221: warning: cast from
> pointer to integer of different sizeGmake.c:224: warning: cast from
> pointer to integer of different sizeGmake.c:227: warning: cast from
> pointer to integer of different sizegcc: error trying to exec 'as':
> execvp: Permission deniedmake: *** [Gmake] Error 1ERROR: compilation
> failed for package ‘maps’* removing
> ‘/home/erin1/R/x86_64-unknown-linux-gnu-library/3.0/maps’Warning in
> install.packages :
>    installation of package ‘maps’ had non-zero exit status
>
> The downloaded source packages are in
> 	‘/tmp/RtmpIF6S0R/downloaded_packages’> sessionInfo()R version 3.0.1
> (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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=en_US.UTF-8
> LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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_3.0.1
>
>
>>
>
>
> I've changed the permissions, and updated the umask to 022.
>
> Any help would be much appreciated.
>
> Sincerely,
> Erin
>
>
>
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>


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595