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

Wed, Dec 14, 2011 12:08 AM #

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

================================================================

_
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)

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?

++++  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

Pierre-Yves Chibon

Wed, Dec 14, 2011 12:29 AM #

On Wed, 2011-12-14 at 18:08 +1000, Peter Baker wrote:

Same issue if I try to compile it using R2rpm.

Pierre

Marc Schwartz

Wed, Dec 14, 2011 6:02 AM #

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