R devel - Apr 2013 - Lubuntu 13.04 raring ringtail: Problems installing pnmath_0.0-4

Hola!

This is 64bit Lubuntu 13.04, with R-3.0.0 installed from
deb http://ppa.launchpad.net/marutter/rrutter/ubuntu raring  main
via synaptic.  gcc --version
gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-pc-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

other attached packages:
[1] MASS_7.3-26

loaded via a namespace (and not attached):
[1] compiler_3.0.0 fortunes_1.5-0 tools_3.0.0
>
I am trying to install pnmath from the commandline (outside R), this is
what happens:
kjetil@kjetil-HP-Pavilion-dv4-Notebook-PC:~/R/src$ sudo  R CMD INSTALL
pnmath_0.0-4.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘pnmath’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -O2
-pipe -g  -c bd0.c -o bd0.o
...
...
...
installing to /usr/local/lib/R/site-library/pnmath/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/usr/local/lib/R/site-library/pnmath/libs/pnmath.so':
  /usr/local/lib/R/site-library/pnmath/libs/pnmath.so: undefined symbol:
PRIMFUN
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/pnmath’

I have installed sufficient libraries as to compile R itself from source
without problems!

Kjetil

	[[alternative HTML version deleted]]

AFAIK pnmath is not a package on a public repository, and it seems it is 
using R internals not part of the API and not exposed in R 3.0.0.

I presume you got this from ~luke/R/experimental ... the clue is in the 
directory name.  My understanding was that this would eventually be 
merged into R rather than released as a package.

If you really want to use it you will need to modify the R sources to 
unhide PRIMFUN and SET_PRIMFUN and re-compile.


On 26/04/2013 19:39, Kjetil Halvorsen wrote:
> Hola!
>
> This is 64bit Lubuntu 13.04, with R-3.0.0 installed from
> deb http://ppa.launchpad.net/marutter/rrutter/ubuntu raring  main
> via synaptic.  gcc --version
> gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
>
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-pc-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
>
> other attached packages:
> [1] MASS_7.3-26
>
> loaded via a namespace (and not attached):
> [1] compiler_3.0.0 fortunes_1.5-0 tools_3.0.0
>>
> I am trying to install pnmath from the commandline (outside R), this is
> what happens:
> kjetil at kjetil-HP-Pavilion-dv4-Notebook-PC:~/R/src$ sudo  R CMD INSTALL
> pnmath_0.0-4.tar.gz
> * installing to library ???/usr/local/lib/R/site-library???
> * installing *source* package ???pnmath??? ...
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -O2
> -pipe -g  -c bd0.c -o bd0.o
> ...
> ...
> ...
> installing to /usr/local/lib/R/site-library/pnmath/libs
> ** R
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    unable to load shared object
> '/usr/local/lib/R/site-library/pnmath/libs/pnmath.so':
>    /usr/local/lib/R/site-library/pnmath/libs/pnmath.so: undefined symbol:
> PRIMFUN
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ???/usr/local/lib/R/site-library/pnmath???
>
> I have installed sufficient libraries as to compile R itself from source
> without problems!
>
> Kjetil
>
> 	[[alternative HTML version deleted]]
>
>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
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