On 04/13/2011 11:34 AM, Dirk Eddelbuettel wrote:

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?

Maybe R CMD ldd /path/to/your/survival.so to pick up whatever environment R configures.

Martin


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@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@max:~$

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



--
Computational Biology
Fred Hutchinson Cancer Research Center
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