From edd at debian.org  Wed Apr 13 20:34:36 2011
From: edd at debian.org (Dirk Eddelbuettel)
Date: Wed, 13 Apr 2011 13:34:36 -0500
Subject: [Rd] Problem with dyn.load in R 2.13.0
In-Reply-To: <1302717605.12894.28.camel@nemo>
References: <1302717605.12894.28.camel@nemo>
Message-ID: <19877.60604.384710.321827@max.nulle.part>


On 13 April 2011 at 13:00, Terry Therneau wrote:
| I have a test directory for the survival suite, and dyn.load has ceased
| to work in it.  Below shows the log:
| 
| tmt1075% R --vanilla
| 
| R version 2.12.2 (2011-02-25)
| Copyright (C) 2011 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
| Platform: x86_64-unknown-linux-gnu (64-bit)
[...]
| > dyn.load('survival.so')
| > q()
[...]
| 
| tmt1076% R13 --vanilla
| 
| R version 2.13.0 RC (2011-04-11 r55409)
| Copyright (C) 2011 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
| Platform: x86_64-unknown-linux-gnu (64-bit)
[...]
| > dyn.load('survival.so')
| Error in dyn.load("survival.so") : 
|   unable to load shared object
| '/people/biostat2/therneau/research/surv/Rtest/survival.so':
|   libR.so: cannot open shared object file: No such file or directory
| > q()
| 
| --------------------------
| 
|  Is the issue that the .so file must have been created with the R2.13
| script?  That's not what the error message says, however.  It almost
| looks like it is ignoring my first argument and looking instead for
| "libR".

What does 'ldd /path/to/your/survial.so' say?  Does the system find libR.so?

I have no issues whatsoever on my Ubuntu box with the packages distributed
via CRAN (and now also a PPA if you want alpha/beta/rc builds) based on the
underlying Debian package I maintain.

I have a (pretty visible) hourly cronjob that drives our littler /usr/bin/r
frontend to do the CRANberries summaries---and even while /usr/bin/r was last
built under R 2.11.1, it continued to work merrily under R 2.12.0, 2.12.1,
2.12.2, and 2.13.0 prereleases:

edd at max:~$ r --version | head -4
r ('littler') version 0.1.3
        svn revision 178 as of 2010-01-05 20:57:41
        built at 20:08:17 on Oct 11 2010
        using GNU R Version 2.11.1 (2010-05-31)
edd at max:~$ 

edd at max:~$ R --version | head -1
R version 2.13.0 RC (2011-04-07 r55373)
edd at max:~$ 

Both use the same shared library version libR.so from whichever current
r-base-core is installed.

So I see no particular breakage.   Recompiling your project may also be a start.

Hth, Dirk

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com



[Rd] Problem with dyn.load in R 2.13.0
Dirk Eddelbuettel