Re: [R] unable to install rjags on 64-bit Debian Linux (etch)

From: <plummer_at_iarc.fr>
Date: Sun, 09 Nov 2008 12:12:34 +0100

Quoting Prof Brian Ripley <ripley_at_stats.ox.ac.uk>:

> On Sat, 8 Nov 2008, Roger Levy wrote:
>
> > While I have been able to install rjags on my Windows computer, oddly I
> have
> > been unable to install rjags successfully on my 64-bit Linux compute server
> > (etch, Linux kernel 2.6.18). I am required to specify the JAGS module
> > directory upon installation; when doing this within R, I get:

> >
> >
>
install.packages("rjags",configure.args="--with-jags-modules=/usr/local/lib/JAGS/modules/")

> >
> > which works fine, but then trying to load rjags gives an error:
> >
> >> library(rjags)
> > \Error in dyn.load(file, DLLpath = DLLpath, ...) :
> > unable to load shared library
> > '/usr/local/lib64/R/library/rjags/libs/rjags.so':
> > libjags.so.1: cannot open shared object file: No such file or directory
> > Error : .onLoad failed in 'loadNamespace' for 'rjags'

> > Error: package/namespace load failed for 'rjags'
> >
> > I'm not sure how to read this error. Does anyone have any suggestions?
>

> It means that ld.so (the runtime linker) cannot find libjags.so.1.
>
> Where is your libjags.so.1? My guess is that you installed it into
> /usr/local/lib, since that is what you have for your module path. On a
> 64-bit Linux system it should be in /usr/local/lib64. (I had to tell the
> JAGS installation that via libdir=/usr/local/lib64 on the configure line.)

Debian conforms to the filesystem hierarchy standard (FHS) which states that libraries go in <prefix>/lib and alternative format binaries go in <prefix>/lib<qual>. I would prefer it if everyone agreed on where 64-bit libraries should go. But they don't.

In the mean time, we have to rely on binary packaging to do "the right thing" on each platform. On Fedora, the rpmbuild system passes all the right arguments to the configure script so that JAGS is installed into /usr/lib64.

> R CMD ldd /usr/local/lib64/R/library/rjags/libs/rjags.so
> will probably confirm that libjags.so.1 is not found.
>
> If that is not the error, please note what the R posting guide says about
> asking the maintainer.
>
> --
> Brian D. Ripley, ripley_at_stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
>
> ______________________________________________
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>



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