rjags installation trouble

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rjags installation trouble

bbolker
  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@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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Re: rjags installation trouble

Martyn Plummer-3
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@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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Re: rjags installation trouble

bbolker
On 12-01-11 11:45 AM, Martyn Plummer wrote:
> 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

  Thanks.  I managed to sort it out by assiduously cleaning out all
older versions of JAGS ...

  Ben Bolker

>
> 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@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
>
>
> -----------------------------------------------------------------------
> This message and its attachments are strictly confiden...{{dropped:8}}

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.