Re: [Rd] Problem with dyn.load in R 2.13.0

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Wed, 13 Apr 2011 13:38:07 -0700

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_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
>

-- 
Computational Biology
Fred Hutchinson Cancer Research Center
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Telephone: 206 667-2793

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