[R] rjags installation trouble

[Martyn Plummer]

It looks like you are cross-linking to an earlier version of the JAGS
library at run time. Check

/sbin/ldconfig -p | grep jags -

When compiling rjags, you can hard-code the location of the jags library
using the [GNU-specific] configure option --enable-rpath.

Martyn

On Tue, 2012-01-10 at 10:40 -0500, Ben Bolker wrote:
> Trying to install latest rjags (3-5) from CRAN with JAGS 3.2.0
> installed on Ubuntu 10.04, with r-devel ... the bottom line is that it
> fails while loading with
> 
>  /libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb
> 
>   Has anyone else seen this or is it a glitch somewhere in my system?
> 
>   thanks
>     Ben Bolker
> 
> ==================
> bolker at ubuntu-10-new:~/R/pkgs/rjags$ jags
> Welcome to JAGS 3.2.0 on Tue Jan 10 10:38:31 2012
> JAGS is free software and comes with ABSOLUTELY NO WARRANTY
> Loading module: basemod: ok
> Loading module: bugs: ok
> .
> 
> =======================
> 
> install.packages("rjags") starts out fine:
> 
> Installing package(s) into
> ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library’
> (as ‘lib’ is unspecified)
> trying URL 'http://probability.ca/cran/src/contrib/rjags_3-5.tar.gz'
> Content type 'application/x-gzip' length 66429 bytes (64 Kb)
> opened URL
> ==================================================
> downloaded 64 Kb
> 
> * installing *source* package ‘rjags’ ...
> ** package ‘rjags’ successfully unpacked and MD5 sums checked
> checking for prefix by checking for jags... /usr/bin/jags
> 
>   [snip snip]
> 
> ** libs
> g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS
> -I/usr/local/include    -fpic  -g -O2  -c jags.cc -o jags.o
> g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS
> -I/usr/local/include    -fpic  -g -O2  -c parallel.cc -o parallel.o
> g++ -shared -L/usr/local/lib -o rjags.so jags.o parallel.o -L/usr/lib -ljags
> installing to /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs
> ** R
> 
>   [snip snip]
> 
>   but fails at:
> 
> ** building package indices
> Error : .onLoad failed in loadNamespace() for 'rjags', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object
> '/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so':
> 
> /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so:
> undefined symbol: _ZN7Console15checkAdaptationERb
> ERROR: installing package indices failed
> * removing ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’
> * restoring previous
> ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’
> 
> The downloaded source packages are in
> 	‘/tmp/RtmpSKHIz5/downloaded_packages’
> Warning message:
> In install.packages("rjags") :
>   installation of package ‘rjags’ had non-zero exit status
> > sessionInfo()
> R Under development (unstable) (2012-01-01 r58032)
> Platform: i686-pc-linux-gnu (32-bit)
> 
> locale:
>  [1] LC_CTYPE=en_CA.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_CA.utf8        LC_COLLATE=en_CA.utf8
>  [5] LC_MONETARY=en_CA.utf8    LC_MESSAGES=en_CA.utf8
>  [7] LC_PAPER=C                LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] tools_2.15.0


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