R SIG Fedora - Dec 2011 - error installing geepack on 64bit fedora 16

Hi

Does anyone know how to install geepack on fedora 16 - 64bit - R

google only yields a couple of hits with unanswered Q

Installation just throws an error with an undefined symbol. Previous
version won't load due to lack of NAMESPACE.  Sadly, its a show
stopper w.r.t. upgrading my work PCs

Any hints/suggestions most welcome

Thanks

Cheers
Peter

===============================================================
> version
               _
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          14.0
year           2011
month          10
day            31
svn rev        57496
language       R
version.string R version 2.14.0 (2011-10-31)
>
> install.packages("geepack", dep=T)
Installing package(s) into ?/usr/lib64/R/library?
(as ?lib? is unspecified)
trying URL 'http://cran.csiro.au/src/contrib/geepack_1.1-3.tar.gz'
Content type 'application/x-gzip' length 206062 bytes (201 Kb)
opened URL
=================================================downloaded 201 Kb

* installing *source* package ?geepack? ...
** package ?geepack? successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -I../inst/include -DNDEBUG
-I/usr/local/include    -fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4  -m64 -mtune=generic -c famstr.cc -o
famstr.o


+++++++++++++++++  stuff deleted - all OK +++++++++++++++++++++

** building package indices ...
*** tangling vignette sources ...
   ?geepack-manual.Rnw? using ?latin1?
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/usr/lib64/R/library/geepack/libs/geepack.so':
  /usr/lib64/R/library/geepack/libs/geepack.so: undefined symbol:
_Z5ValidIiEN3TNT6VectorIT_EERS3_RNS1_IiEE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ?/usr/lib64/R/library/geepack?
* restoring previous ?/usr/lib64/R/library/geepack?
> library(geepack)
++++  startup stuff deleted  +++++

Error in library(geepack) :?? package ?geepack? does not have a
NAMESPACE and should be re-installed>
a bit of a catch 22

thanks

-- 
Dr Peter Baker | Senior Lecturer/Statistician | Epidemiology & Biostatistics

Room 416 | School of Population Health |The University of Queensland | Public
Health Building | Herston Rd | Herston Qld 4006 | Australia

Ph: +61 7 3346 4747 | Fax: +61 7 3365 5442 | http://www.sph.uq.edu.au/? |
Email: p.baker1 at uq.edu.au or baker.peter2009 at gmail.com

On Wed, 2011-12-14 at 18:08 +1000, Peter Baker wrote:
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object
> '/usr/lib64/R/library/geepack/libs/geepack.so':
>   /usr/lib64/R/library/geepack/libs/geepack.so: undefined symbol:
> _Z5ValidIiEN3TNT6VectorIT_EERS3_RNS1_IiEE 
Same issue if I try to compile it using R2rpm.

Pierre

On Dec 14, 2011, at 2:08 AM, Peter Baker wrote:
> Hi
> 
> Does anyone know how to install geepack on fedora 16 - 64bit - R
> 
> google only yields a couple of hits with unanswered Q
> 
> Installation just throws an error with an undefined symbol. Previous
> version won't load due to lack of NAMESPACE.  Sadly, its a show
> stopper w.r.t. upgrading my work PCs
> 
> Any hints/suggestions most welcome
> 
> Thanks
> 
> Cheers
> Peter
> 
> ===============================================================> 
>> version
>               _
> platform       x86_64-redhat-linux-gnu
> arch           x86_64
> os             linux-gnu
> system         x86_64, linux-gnu
> status
> major          2
> minor          14.0
> year           2011
> month          10
> day            31
> svn rev        57496
> language       R
> version.string R version 2.14.0 (2011-10-31)
>> 
> 
> 
>> install.packages("geepack", dep=T)
> Installing package(s) into ?/usr/lib64/R/library?
> (as ?lib? is unspecified)
> trying URL 'http://cran.csiro.au/src/contrib/geepack_1.1-3.tar.gz'
> Content type 'application/x-gzip' length 206062 bytes (201 Kb)
> opened URL
> =================================================> downloaded 201 Kb
> 
> * installing *source* package ?geepack? ...
> ** package ?geepack? successfully unpacked and MD5 sums checked
> ** libs
> g++ -m64 -I/usr/include/R -I../inst/include -DNDEBUG
> -I/usr/local/include    -fpic  -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4  -m64 -mtune=generic -c famstr.cc -o
> famstr.o
> 
> 
> +++++++++++++++++  stuff deleted - all OK +++++++++++++++++++++
> 
> ** building package indices ...
> *** tangling vignette sources ...
>   ?geepack-manual.Rnw? using ?latin1?
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object
'/usr/lib64/R/library/geepack/libs/geepack.so':
>  /usr/lib64/R/library/geepack/libs/geepack.so: undefined symbol:
> _Z5ValidIiEN3TNT6VectorIT_EERS3_RNS1_IiEE
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ?/usr/lib64/R/library/geepack?
> * restoring previous ?/usr/lib64/R/library/geepack?
> 
>> library(geepack)
> 
> ++++  startup stuff deleted  +++++
> 
> Error in library(geepack) :   package ?geepack? does not have a
> NAMESPACE and should be re-installed>
> a bit of a catch 22
> 
> thanks

Given the errors that you are seeing and other recent posts here and elsewhere
regarding errors with this package, your best bet is to contact the package
maintainer (Jun Yan).  There are also notes in the CRAN check log for the
package point out some coding issues as well as some comments in the package
changelog on CRAN regarding this error specifically (See entries for
2011-11-14).

Marc Schwartz