From mtmorgan at fhcrc.org  Wed Apr 13 22:38:07 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Wed, 13 Apr 2011 13:38:07 -0700
Subject: [Rd] Problem with dyn.load in R 2.13.0
In-Reply-To: <19877.60604.384710.321827@max.nulle.part>
References: <1302717605.12894.28.camel@nemo>
	<19877.60604.384710.321827@max.nulle.part>
Message-ID: <4DA609AF.4000108@fhcrc.org>

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
>


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[Rd] Problem with dyn.load in R 2.13.0
Martin Morgan