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rjags install on Ubuntu 10.04

6 messages · Dirk Eddelbuettel, Michael Rutter, John C Nash +1 more

Original
John C Nash
# 
I have been having trouble with rjags on Ubuntu 10.04
Loading required package: coda
Loading required package: lattice
linking to JAGS 3.2.0
module basemod loaded
Error : .onLoad failed in loadNamespace() for 'rjags', details:
  call: dyn.load(file)
  error: unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
  /usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec
Error: package/namespace load failed for ?rjags?
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
Also I have tried
Error in dyn.load("/usr/lib/JAGS/modules-3/bugs.so") :
  unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
  /usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec

After several uninstalls and reinstalls of jags and rjags, I did (as superuser)

apt-get remove --purge r-base-core
apt-get autoremove

then reinstalled R, then rjags (the Michael Rutter PPA is in my sources list), i.e.,

apt-get install r-base-dev
apt-get install rjags

(I used the dev to make sure I got some of the tools etc.)

No joy.

On crunchbang stattler linux (under VirtualBox), things loaded fine. I haven't tried
actual computations though. (This is a debian squeeze variant.)

Suggestions welcome, especially about the fprec symbol above. I am planning to upgrade the
10.04 to something else soon, probably Mint Mate, but wanted to wait a few more weeks to
avoid doing this when having to travel.

Cheers, JN
Dirk Eddelbuettel
#
On 19 September 2012 at 20:38, John C Nash wrote:
| I have been having trouble with rjags on Ubuntu 10.04
                                           ^^^^^^^^^^^^

You may be on your own here. I would suggest updating to something current,
and remaining current -- at least that works for me. On Ubuntu 12.04 it
just works:

  R> library(rjags)
  Loading required package: coda
  Loading required package: lattice
  linking to JAGS 3.2.0
  module basemod loaded
  module bugs loaded
  R> 

Using 
  edd at max:~$ COLUMNS=76 dpkg -l | grep jags
  ii  jags           3.2.0-1precise Just Another Gibbs Sampler for Bayesian MCMC
  ii  r-cran-rjags   3.3-1          R interface to the JAGS Bayesian statistics 
  edd at max:~$ 
 
| > library(rjags)
| Loading required package: coda
| Loading required package: lattice
| linking to JAGS 3.2.0
| module basemod loaded
| Error : .onLoad failed in loadNamespace() for 'rjags', details:
|   call: dyn.load(file)
|   error: unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
|   /usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec
| Error: package/namespace load failed for ?rjags?
| 
| 
| > sessionInfo()
| R version 2.15.1 (2012-06-22)
| Platform: x86_64-pc-linux-gnu (64-bit)
| 
| locale:
|  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
|  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
|  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
|  [7] LC_PAPER=C                 LC_NAME=C
|  [9] LC_ADDRESS=C               LC_TELEPHONE=C
| [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
| 
| attached base packages:
| [1] stats     graphics  grDevices utils     datasets  methods   base
| >
| 
| Also I have tried
| 
| > dyn.load("/usr/lib/JAGS/modules-3/bugs.so")
| Error in dyn.load("/usr/lib/JAGS/modules-3/bugs.so") :
|   unable to load shared object '/usr/lib/JAGS/modules-3/bugs.so':
|   /usr/lib/JAGS/modules-3/bugs.so: undefined symbol: fprec
| 
| After several uninstalls and reinstalls of jags and rjags, I did (as superuser)
| 
| apt-get remove --purge r-base-core

Please.  R has not bearing here. 

You have a package out of sorts. Worst, remove the package (here: jags, as
'dpkg -S /usr/lib/JAGS/modules-3/bugs.so' clearly tells you) and install
locally.

Dirk

| apt-get autoremove
| 
| then reinstalled R, then rjags (the Michael Rutter PPA is in my sources list), i.e.,
| 
| apt-get install r-base-dev
| apt-get install rjags
| 
| (I used the dev to make sure I got some of the tools etc.)
| 
| No joy.
| 
| On crunchbang stattler linux (under VirtualBox), things loaded fine. I haven't tried
| actual computations though. (This is a debian squeeze variant.)
| 
| Suggestions welcome, especially about the fprec symbol above. I am planning to upgrade the
| 10.04 to something else soon, probably Mint Mate, but wanted to wait a few more weeks to
| avoid doing this when having to travel.
| 
| Cheers, JN
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Michael Rutter
#
On 09/19/2012 09:16 PM, Dirk Eddelbuettel wrote:
There is also a numbering issue at work here.  Version 3.3-1 is supplied 
by Ubuntu, while my PPA has 3-5, a newer version from Martyn, but not 
for Ubuntu.  For apt, 3.3 is > 3-5, so one solution is to use synaptic 
to force the install of the more recent version and see if that fixes 
the issue, although I would recommend upgrading Ubuntu as the first step.

Conveniently, Martyn release version 3-7 of the package Wednesday 
(9/18), so new versions will be hitting the PPA shortly, as soon as I 
resolve the numbering issue.

Michael

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      John C Nash
    

    

      
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OK. I figured it may be getting late in the LTS cycle. However, I'll be making two trips
in next 18 days, so don't want to rebuild my laptop just now. It has way too many
different tools on it that I'm using and have forgotten that they take time and bandwidth
to install. The folk who want jags runs are just going to have to wait.

Given I have tried Unity twice and Ubuntu's alternative Gnome once, I think I'll go to
Mint Mate (Ubuntu based) or else CrunchBang (debian squeeze).

JN

        
On 09/19/2012 09:24 PM, Michael Rutter wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Kjetil Halvorsen
    

    

      
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see inline below.

        
On Wed, Sep 19, 2012 at 10:34 PM, John C Nash <nashjc at uottawa.ca> wrote:

            

      
      
      
    

        
If you don like unity but otherwise like ubuntu, another alternative
is lubuntu. I have just installed this and it works very well!
lubuntu is ubuntu, but with LXDE desktop     http://lxde.org/
LXDE seems also to be based on gtk, so software working with gnome
should work there.

Kjetil

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      John C Nash
    

    

      
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To return to the original topic.

I installed Ubuntu Lucid on a VirtualBox platform (not, unfortunatly my laptop -- too
little disk left) and went through the huge initial updates and setting up R and Michaels
PPA. Installed rjags and things load fine.

So, it seems there's something in my laptop that is getting in the way. Possibly a 32/64
issue, since the laptop is amd64, but VBox guests seem to only like 32 bit mode.

This is annoying, but not devastating. I'll upgrade the laptop in a couple of weeks.

Best, JN