[R-sig-Fedora] error installing geepack on 64bit fedora 16

[Marc Schwartz]

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